Category: Stanford Synchrotron Radiation Lightsource (SSRL)

Giving solid-state batteries a squeeze keeps them from short-circuiting

Giving solid-state batteries a squeeze keeps them from short-circuiting

SLAC and Stanford researchers found that compressing solid-state battery material reduced the formation of lithium-filled intrusions called dendrites, leading to faster charging and longer battery life.

Key takeways:

  • A SLAC/Stanford University research team found they could prevent short-circuiting of solid-state batteries by deflecting the dendrite propagation direction using mechanical compression.
  • They provided direct evidence that dendrites start in the interior rather than merely at the surface of the electrolyte, settling a long-standing debate within the field.
  • The results could have implications for future battery design, by incorporating built-in mechanical compression or electrolytes with more defect-free interiors that suppress dendrite initiation.

Lithium-ion batteries power transportation and grid storage and enable our digital lives, but these ubiquitous batteries require frequent recharging and can fail over time.    

To make batteries more reliable and longer lasting, researchers are exploring how to replace liquids inside batteries with a solid ceramic substance that could improve their performance. 

But researchers must first overcome a big problem: cracks filled with lithium that form within the solid material during charging, causing the batteries to quickly short-circuit. When that happens, devices powered by these batteries become useless.

Researchers have long debated whether these cracks and the lithium metal inside them, called dendrites, form at the surface or inside the solid material – a key insight needed to figure out how to stop them from forming.

Now, in a study published in the journal Nature, researchers have discovered a way to track these dendrites and suppress them enough to keep the battery from short-circuiting.

Read more on the SLAC website

Researchers find an inexpensive way to make batteries last longer

Researchers find an inexpensive way to make batteries last longer

By adjusting the heating process when making lithium-ion cathodes, the team created batteries that retained nearly 93% of their energy after 500 cycles.

Editor’s note: The following news brief was originally published by the U.S. Department of Energy’s (DOE) SLAC National Accelerator Laboratory. The research team used transmission X-ray microscopy at the Full Field X-ray Imaging (FXI) beamline at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science user facility at DOE’s Brookhaven National Laboratory, to visualize 3D changes in nickel oxidation states within individual particles of nickel-rich layered cathodes as they were heated. Understanding this process could help pave the way for longer-lasting battery structures.

To make batteries that last longer, scientists are creating internal battery structures that don’t degrade as quickly as current designs do. In fact, the reason many lithium-ion batteries ultimately fail is that their cathodes, or negative electrodes, crack after repeated charging and discharging.

Researchers at the SLAC-Stanford Battery Center, a partnership between Stanford University’s Precourt Institute for Energy and the Department of Energy’s SLAC National Accelerator Laboratory, have found a simple way to solve this problem in nickel-rich layered-oxide cathodes, the type of cathode used in powerful, long-lasting lithium-ion batteries for data centers and grid-scale energy storage.

By adjusting the heating process when making these cathodes – starting slowly, then ramping up the heat quickly – they found they could create more uniform cathode structures at the nanoscale level. These structures don’t crack and degrade as quickly as current batteries.

The resulting material was more resistant to strain and cracking, retaining nearly 93% of the battery’s energy after 500 cycles. 

Read more on the BNL website

50th Anniversary of the SSRL synchrotron radiation & protein crystallography initiative

50th Anniversary of the SSRL synchrotron radiation & protein crystallography initiative

Synchrotron-based protein crystallography continues to accelerate, driven by new and upgraded high-brightness sources, improved optics, faster large-area detectors, robust automation and streamlined data handling. These advances are making increasingly challenging structural biology projects feasible and are reshaping how synchrotron experiments integrate with today’s wider structural biology methods. While AI models are now routinely used in  molecular replacement software for macromolecular crystal structure determination, synchrotron experimental methods remain vital for detailed model refinement, and even validating AI models. Also extracting key chemical information, with anomalous dispersion at tuneable beamlines still playing an important role especially in identifying metals and other such atoms in proteins.

This special issue in Journal of Synchrotron Radiation, edited by John R. Helliwell and Marian Szebenyi, and their Overview with Colin Nave, with a Perspective from Keith Hodgson, as well as articles from a majority of the facilities worldwide, explores the evolving landscape in depth. It also highlights the expanding impact of fragment screening and binding studies (from cryogenic up to body temperatures) and the rapidly developing frontiers of time-resolved and serial crystallography. In particular, the issue charts the synergy between XFEL-based serial femtosecond crystallography and serial synchrotron crystallography, culminating in recent demonstrations of microsecond time resolution at upgraded synchrotrons such as ESRF–EBS, pointing to a future where synchrotrons and X-ray lasers together enable ever more powerful studies of biological structure, dynamics and function.

Access the special issue here

Image Credit:

Phillips, J.C., Wlodawer, A., Yevitz, M.M. and Hodgson, K.O., 1976. Applications of synchrotron radiation to protein crystallography: preliminary results. Proceedings of the National Academy of Sciences, 73(1), pp.128-132. 

Rosenbaum, G., Holmes, K.C. and Witz, J., 1971. Synchrotron radiation as a source for X-ray diffraction. Nature, 230(5294), pp.434-437.

Researchers find a potential treatment for mitochondrial damage that causes disease

Researchers find a potential treatment for mitochondrial damage that causes disease

Oxidizing chemicals break this cellular power plant into useless bits, leading to Parkinson’s disease, ALS, heart disease, diabetes, cancer and more. A small molecule could block the process.

Mitochondria are the cell’s power plants: They turn the food we eat into the energy our cells can use. But when stress hijacks the process they use to maintain their quality, they get snipped into useless fragments and go into a tailspin that spreads from cell to cell and triggers a wide range of human diseases. As researchers learn more about the health impacts of rogue mitochondria, they’ve been searching for ways to prevent or treat them. 

Now researchers at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University say they’ve found a way to protect mitochondria from stress induced by exposure to a highly reactive molecule called hydrogen peroxide. This particular type of damage is linked to neurogenerative diseases like Parkinson’s and Amyotrophic Lateral Sclerosis (ALS), heart disease, diabetes, inflammatory bowel disease and cancer, among others.

In experiments with human kidney cells, the research team reported, adding a small molecule called SP11 to the fragmented mitochondria made them hale and whole again. 

The team described their work in a May 6 report in Nature Communications, and Stanford has patented SP11 as a potential candidate for drug development.

“If we can keep mitochondria in pristine shape, we may really help address many chronic human diseases. That’s why we embarked on this project,” said Stanford Professor Daria Mochly-Rosen, a senior author of the report whose research into the chemistry of proteins has yielded both potential and successfully deployed drugs.

When bad mitochondria do this to a healthy cell, they can kill it. When healthy mitochondria do it to a sick cell, they can help it heal.Daria Mochly-RosenStanford University Professor of Chemical and Systems Biology

Not just a power plant 

Although mitochondria are best known for producing energy, that’s not their only role. “They’re so busy! This organelle is so critical,” Mochly-Rosen said. For instance, they’re responsible for constructing some of the cell’s molecular building blocks and for deliberately killing cells whose DNA is damaged. 

For a long time, scientists assumed that mitochondria were confined to their host cells, but they recently discovered this isn’t true. “Now we know they can exit one cell and enter another one,” Mochly-Rosen said. “When bad mitochondria do this to a healthy cell, they can kill it. When healthy mitochondria do it to a sick cell, they can help it heal.”

Seventeen years ago, Mochly-Rosen and her colleagues trained a microscope on cells from a rat with high blood pressure and discovered that the mitochondria were fragmented into small pieces. This set off a quest to find out what was happening and how to prevent or fix it.

Hijacking fission

Mitochondria are often depicted as little jellybeans whose shape never changes, said Suman Pokhrel, who was a PhD student at SLAC and Stanford at the time he led the study. But in real life they form an ever-changing, fibril-like network. Thousands of them surround the nucleus of each cell, and they’re constantly dividing and fusing with each other. Mitochondria need to maintain a balance between division and fusion to stay healthy, increase their numbers and make enough energy.

In healthy mitochondria, a protein called Drp1 attaches to the mitochondrial membrane and initiates division via a go-between protein called Mff. But when mitochondria send out distress signals – for instance, if they’ve been attacked by a reactive oxygen molecule like hydrogen peroxide and can’t repair the damage fast enough – Drp1 attaches to a protein called Fis1 and uses it as a go-between instead. 

Fis1 directs mitochondrial fission in yeast, but in humans it only brings grief. It hijacks the normal process mitochondria use to divide neatly in half and instead squeezes them into uneven pieces that fragment into even smaller ones that don’t produce enough energy. 

Read more on SLAC website

Image: An image shows thousands of mitochondria (purple dots) surrounding nuclei of about 50 human kidney cells. 

Credit: Gwangbeom Heo/Stanford University

Monitoring Avian Flu Evolution Using SLAC’s Synchrotron

Monitoring Avian Flu Evolution Using SLAC’s Synchrotron

In the game of evolution, viruses are among the most adaptable players, constantly changing in response to their environments. Researchers in immunology and structural biology regularly monitor these changes, especially those that could pose a threat to public health. Scientists use X-ray facilities like the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory to examine the underlying structures of individual proteins, which influence a virus’ behavior and ability to spread between species. 

Since the first recorded case of highly pathogenic avian influenza H5N1 – commonly known as avian flu or bird flu – in 1996, Ian Wilson, professor of structural biology at Scripps Research, and his colleagues have been closely tracking the evolution of several key proteins using SSRL. 

Recently, Wilson’s team investigated the evolution of a protein that plays a crucial role in H5N1’s ability to transmit between species. Their analysis found that the protein is susceptible to a mutation that could help the virus attach to human cells, potentially increasing the risk of human transmission. The findings – published in Proceedings of the National Academy of Sciences – underscore the need for ongoing monitoring of H5N1’s evolution. 

“Facilities like SSRL enable research on infectious diseases and pandemic threats, accelerating our ability to respond to global health emergencies,” said Aina Cohen, division director of Structural Molecular Biology at SSRL. “Discoveries made in areas like drug development, vaccine design and diagnostics can lead to more effective treatments, earlier disease detection and stronger preventive measures.” 

Studying proteins with SSRL 

Though H5N1 viruses are prevalent in birds and some mammals around the world, transmission to and between humans is rare. However, this could change as the virus continues to mutate. Wilson’s team focuses on H5N1’s hemagglutinin (HA) protein, which enables the virus to attach to receptors on the surfaces of host cells. If this protein mutates from its current receptor specificity – which favors avian-type receptors – to one that effectively binds to human-type receptors, the potential for transmission to humans could rise significantly. 

“Monitoring changes in receptor specificity – the way a virus recognizes host cells – is crucial because receptor binding is a key step toward transmissibility,” Wilson said. “That being said, receptor mutations alone don’t guarantee that the virus will transmit between humans.” 

To build a timeline of the HA protein’s evolution, Wilson’s team analyzes proteins from samples collected in various years. These studies do not use live virus samples; instead, the research team generates proteins using data from the Global Initiative on Sharing All Influenza Data. The team then crystallizes these proteins and sends the crystallized samples to SSRL. 

At SSRL’s Beam Line 12-1, the Scripps team collects data remotely with assistance from on-site scientists at SLAC. By analyzing how X-rays diffract when passing through the protein crystals, researchers can reconstruct the protein’s 3D structure, gaining insights into the behavior of various HA proteins.

“The bright X-ray microbeams produced by SSRL, combined with a high level of experimental automation and user-friendly experimental control interface, make Beam Line 12-1 a premiere resource for these types of experiments,” Cohen said. “With decades of experience, SSRL staff support our users, helping them achieve the highest quality data.” 

Read more on SLAC website

Unique Novel Drug Shows Promise Against SARS-CoV-2

Unique Novel Drug Shows Promise Against SARS-CoV-2

SARS-CoV-2 is an RNA virus that caused a three-year long pandemic with millions of reported deaths worldwide.1,2  Despite the unprecedented speed of development and approval of SARS-CoV-2 vaccines and oral antivirals especially Paxlovid (co-administered Nirmatrelvir with ritonavir), there remain risks for emerging variants of concern (VOCs) with increased virulence and infectivity, and clinical challenges especially for population at risk who cannot benefit from existing drugs due to potential drug-drug interactions (DDIs). Continued development of oral antiviral drugs with improved antiviral potency and safety are needed to address current challenges in clinical practice for treatment of COVID-19.

Olgotrelvir (STI-1558) is designed as a potent standalone antiviral drug with excellent oral bioavailability, limited drug-drug interactions, and antiviral efficacy at doses with low safety concerns.  Olgotrelvir and its parent drug AC1115 potently inhibit activities of SARS-CoV-2 main protease (Mpro) including Mpro mutants found in SARS-CoV-2 VOCs, as well as Mpro mutants such as E166 found to be resistant to Paxlovid. In addition, olgotrelvir inhibits activity of human cathepsin L (CTSL), the major host cysteine protease aiding in virus entry through the endosomal pathway.3-5 The dual inhibition of both virus entry and virus replication pathways may enhance the robustness of the antiviral effect and reduce potential drug resistance. Indeed, olgotrelvir and AC1115 displayed potent antiviral activities against SARS-CoV-2 variants in cell-based models and in humanized transgenic mouse models. In phase 1 clinical trials, orally administered olgotrelvir demonstrated effective plasma exposure, limited mild adverse events, and a positive trend of reducing the SARS-CoV-2 viral RNA copy loads. Considering the favorable efficacy and pharmacokinetic profile along with data supporting the positive safety profile of the compound, olgotrelvir is a promising anti-SARS-CoV-2 drug candidate, which warrants further development as a next-generation therapeutic intervention for COVID-19 and potentially other coronaviruses.

Read more on SLAC website

Image: High resolution of co-crystal structure of SARS-CoV-2 Mpro or human cathepsin L complexed with AC1115. (A) SARS-CoV-2 Mpro (gray surface) bound with AC1115 (pink sticks). Electron density corresponding to AC1115 is shown in pink mesh. Hydrophobic residues of the Mpro catalytic active site binding pocket are labeled; with the active site cysteine shown in yellow. (B) Hydrogen bond interactions between AC1115 and Mpro are denoted with black lines. AC1115 forms 7 direct hydrogen bonds with Mpro residues, with additional polar interactions mediated by water molecules (red spheres). (C) CTSL protein (surface and cartoon) with covalently bound AC1115 (green sticks). Amino acid residues contacting AC1115 are labeled; the catalytic cysteine (Cys25) is additionally indicated by the yellow protein surface. (D) AC1115 hydrogen bonds with CTSL amino acids are shown (red dashed lines), along with the covalent bond to the Cys25 side chain sulfur atom (black line).   The two structures were deposited to PDB with IDs of 8UAB and 8UAC.

Stanford study shows how modifying enzymes’ electric fields boosts their speed

Stanford study shows how modifying enzymes’ electric fields boosts their speed

A seemingly subtle swap of metals—substituting a zinc ion with a cobalt ion—and a mutation ramps up the overall electric field strength at the active site of an enzyme, Stanford scientists find. The result is a predictably modified enzyme that works an astonishing 50 times faster than its unmodified analog.

Stanford researchers have demonstrated a way to dramatically speed up the reaction rate of an enzyme, a finding that could pave the way to designing ultra-fast synthetic enzymes for a range of industrial and medical uses.

Honed over billions of years of evolution, biological enzymes are marvels of chemistry. These specialized proteins serve as catalysts for accelerating chemical reactions essential to life as well as processes used in the food, pharmaceutical, and cosmetic industries.    

Ever since enzymes’ discovery nearly two centuries ago, scientists have sought ways to make them even faster. Most fabricated enzymes, though, have failed to match the lofty efficiency standards of nature-made varieties. And even where some successes have been realized through directed evolution, a protein engineering method that mirrors nature’s trial-and-error approach, these successes so far have been by chance, not because of a deeper understanding of how enzymes work or could be modified to work more swiftly.

Now, in a new study, researchers at Stanford’s School of Humanities and Sciences and SLAC National Accelerator Laboratory have debuted a modified enzyme that works an astonishing 50 times faster than its unmodified analog. The findings derive from pioneering research at the university regarding electric fields generated at “active sites,” the pocketlike places where revved up chemical reactions occur. Based on this concept, the researchers tweaked the chemistry of the active site, boosting its electric field strength and specificity to deliver the zippy results.  

Read more on Stanford University website

Image: X-ray crystallography was used to investigate and compare the 3D crystal structures of the unmodified enzyme containing an ion of zinc (Zn) (pictured left) and the modified enzyme with a cobalt (Co) ion in place of zinc (pictured right).

New catalyst could cut pollution from millions of engines

New catalyst could cut pollution from millions of engines

Researchers demonstrate a way to remove the potent greenhouse gas from the exhaust of engines that burn natural gas.

Individual palladium atoms attached to the surface of a catalyst can remove 90% of unburned methane from natural-gas engine exhaust at low temperatures, scientists reported today in the journal Nature Catalysis. 

While more research needs to be done, they said, the advance in single atom catalysis has the potential to lower exhaust emissions of methane, one of the worst greenhouse gases, which traps heat at about 25 times the rate of carbon dioxide. 

Researchers from the Department of Energy’s SLAC National Accelerator Laboratory and Washington State University showed that the catalyst removed methane from engine exhaust at both the lower temperatures where engines start up ­­­and the higher temperatures where they operate most efficiently, but where catalysts often break down. 

“It’s almost a self-modulating process which miraculously overcomes the challenges that people have been fighting – low temperature inactivity and high temperature instability,” said Yong Wang, Regents Professor in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering and one of four lead authors on the paper. 

A growing source of methane pollution 

Engines that run on natural gas power 30 million to 40 million vehicles worldwide and are popular in Europe and Asia. The natural gas industry also uses them to run compressors that pump gas to people’s homes. They are generally considered cleaner than gasoline or diesel engines, creating less carbon and particulate pollution.

However, when natural-gas engines start up, they emit unburnt, heat-trapping methane because their catalytic converters don’t work well at low temperatures. Today’s catalysts for methane removal are either inefficient at lower exhaust temperatures or they severely degrade at higher temperatures. 

“There’s a big drive towards using natural gas, but when you use it for combustion engines, there will always be unburnt natural gas from the exhaust, and you have to find a way to remove that. If not, you cause more severe global warming,” said co-author Frank Abild-Pedersen, a SLAC staff scientist and co-director of the lab’s SUNCAT Center for Interface Science and Catalysis, which is run jointly with Stanford University. “If you can remove 90% of the methane from the exhaust and keep the reaction stable, that’s tremendous.”

A catalyst with single atoms of the chemically active metal dispersed on a support also uses every atom of the expensive and precious metal, Wang added. 

“If you can make them more reactive,” he said, “that’s the icing on the cake.”

Unexpected help from a fellow pollutant 

In their work, the researchers showed that their catalyst made from single palladium atoms on a cerium oxide support efficiently removed methane from engine exhaust, even when the engine was just starting. 

They also found that trace amounts of carbon monoxide that are always present in engine exhaust played a key role in dynamically forming active sites for the reaction at room temperature. The carbon monoxide helped the single atoms of palladium migrate to form two- or three-atom clusters that efficiently break apart the methane molecules at low temperatures. 

Then, as the exhaust temperatures rose, the clusters broke up into single atoms and redispersed, so that the catalyst was thermally stable. This reversible process enabled the catalyst to work effectively and used every palladium atom the entire time the engine was running – including when it started cold.

Read more on SLAC website

New SLAC-Stanford Battery Center targets roadblocks to a sustainable energy transition

New SLAC-Stanford Battery Center targets roadblocks to a sustainable energy transition

The center at SLAC aims to bridge the gaps between discovering, manufacturing and deploying innovative energy storage solutions. 

The Department of Energy’s SLAC National Accelerator Laboratory and Stanford University today announced the launch of a new joint battery center at SLAC. It will bring together the resources and expertise of the national lab, the university and Silicon Valley to accelerate the deployment of batteries and other energy storage solutions as part of the energy transition that’s essential for addressing climate change.

A key part of this transition will be to decarbonize the world’s transportation systems and electric grids ­– to power them without fossil fuels. To do so, society will need to develop the capacity to store several hundred terawatt-hours of sustainably generated energy. Only about 1% of that capacity is in place today.

Filling the enormous gap between what we have and what we need is one of the biggest challenges in energy research and development. It will require that experts in chemistry, materials science, engineering and a host of other fields join forces to make batteries safer, more efficient and less costly and manufacture them more sustainably from earth-abundant materials, all on a global scale. 

The SLAC-Stanford Battery Center will address that challenge. It will serve as the nexus for battery research at the lab and the university, bringing together large numbers of faculty, staff scientists, students and postdoctoral researchers from SLAC and Stanford for research, education and workforce training. 

 “We’re excited to launch this center and to work with our partners on tackling one of today’s most pressing global issues,” said interim SLAC Director Stephen Streiffer. “The center will leverage the combined strengths of Stanford and SLAC, including experts and industry partners from a wide variety of disciplines, and provide access to the lab’s world-class scientific facilities. All of these are important to move novel energy storage technologies out of the lab and into widespread use.”

Expert research with unique tools

Research and development at the center will span a vast range of systems – from understanding chemical reactions that store energy in electrodes to designing battery materials at the nanoscale, making and testing devices, improving manufacturing processes and finding ways to scale up those processes so they can become part of everyday life. 

“It’s not enough to make a game-changing battery material in small amounts,” said Jagjit Nanda, a SLAC distinguished scientist, Stanford adjunct professor and executive director of the new center, whose background includes decades of battery research at DOE’s Oak Ridge National Laboratory. “We have to understand the manufacturing science needed to make it in larger quantities on a massive scale without compromising on performance.”

Longstanding collaborations between SLAC and Stanford researchers have already produced many important insights into how batteries work and how to make them smaller, lighter, safer and more powerful. These studies have used machine learning to quickly identify the most promising battery materials from hundreds made in the lab, and measured the properties of those materials and the nanoscale details of battery operation at the lab’s synchrotron X-ray facility. SLAC’s X-ray free-electron laser is available, as well, for fundamental studies of energy-related materials and processes. 

SLAC and Stanford also pioneered the use of cryogenic electron microscopy (cryo-EM), a technique developed to image biology in atomic detail, to get the first clear look at finger-like growths that can degrade lithium-ion batteries and set them on fire. This technique has also been used to probe squishy layers that build up on electrodes and must be carefully managed, in research performed at the Stanford Institute for Materials and Energy Sciences (SIMES).

Nanda said the center will also focus on making energy storage more sustainable, for instance by choosing materials that are abundant, easy to recycle and can be extracted in a way that’s less costly and produces fewer emissions.

Read more on the SLAC website

Structural evidence that rodents facilitated the evolution of the SARS-CoV-2 Omicron variant

Structural evidence that rodents facilitated the evolution of the SARS-CoV-2 Omicron variant

The omicron variant of COVID-19 was identified in the fall of 2021. It stood out from all of the other variants because of the many mutations that simultaneously occurred in its spike protein1. So far, surveillance and bioinformatics have been the main scientific tools in tracking COVID-19 evolution. Eventually, however, understanding COVID-19 evolution comes down to understanding the functions of key viral mutations. This is where structural biology kicks in and plays a critical role in tracking COVID-19 evolution.

In a study recently published in the journal Proceedings of National Academy of Sciences USA, Dr. Fang Li and colleagues at the University of Minnesota determined the high-resolution crystal structure of the omicron strain’s spike protein and its mouse receptor (Fig. 1A)2, using macromolecular cystallography x-ray data measured at Beam Line 12-1 of SSRL. Through detailed analysis, the researchers identified three mutations (Q493R, Q498R, and Y505H) in the omicron spike protein that are specifically adapted to two residues (Asn31 and His353) in the mouse receptor (Fig. 1B, 1C). After searching all of the available receptor sequences in the database, the researchers found that only the receptor from mice contains Asn31 and His353, while the receptors from several other rodent species contain one but not both Asn31 and His353. Thus, the researchers hypothesized that rodents, particularly mice, played a role in the omicron evolution. In contrast, these three mutations in omicron are structurally incompatible with the corresponding two residues (Lys31 and Lys353) in the human receptor (Fig.1D, 1E)2, further suggesting that non-human animal reservoirs facilitated the omicron evolution.

Read more on the SSRL website

Image: Figure 1 (C) Structural details of the omicron RBD/mouse ACE2 interface showing Arg498 and His353 in omicron RBD are both structurally adapted to His353 in mouse ACE2.

SARS-CoV-2 protein caught severing critical immunity pathway

SARS-CoV-2 protein caught severing critical immunity pathway

Powerful X-rays from SLAC’s synchrotron reveal that our immune system’s primary wiring seems to be no match for a brutal SARS-CoV-2 protein.

BY DAVID KRAUSE

Over the past two years, scientists have studied the SARS-CoV-2 virus in great detail, laying the foundation for developing COVID-19 vaccines and antiviral treatments. Now, for the first time, scientists at the Department of Energy’s SLAC National Accelerator Laboratory have seen one of the virus’s most critical interactions, which could help researchers develop more precise treatments.

The team caught the moment when a virus protein, called Mpro, cuts a protective protein, known as NEMO, in an infected person. Without NEMO, an immune system is slower to respond to increasing viral loads or new infections. Seeing how Mpro attacks NEMO at the molecular level could inspire new therapeutic approaches.

To see how Mpro cuts NEMO, researchers funneled powerful X-rays from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) onto crystallized samples of the protein complex. The X-rays struck the protein samples, revealing what Mpro looks like when it dismantles NEMO’s primary function of helping our immune system communicate.

“We saw that the virus protein cuts through NEMO as easily as sharp scissors through thin paper,” said co-senior author Soichi Wakatsuki, professor at SLAC and Stanford. “Imagine the bad things that happen when good proteins in our bodies start getting cut into pieces.”

The images from SSRL show the exact location of NEMO’s cut and provide the first structure of SARS-CoV-2 Mpro bound to a human protein.

“If you can block the sites where Mpro binds to NEMO, you can stop this cut from happening over and over,” SSRL lead scientist and co-author Irimpan Mathews said. “Stopping Mpro could slow down how fast the virus takes over a body. Solving the crystal structure revealed Mpro’s binding sites and was one of the first steps to stopping the protein.”

The research team from SLAC, DOE’s Oak Ridge National Laboratory, and other institutions published their results today in Nature Communications.

Read more on the SLAC website

A new leap in understanding nickel oxide superconductors

A new leap in understanding nickel oxide superconductors

Researchers discover they contain a phase of quantum matter, known as charge density waves, that’s common in other unconventional superconductors. In other ways, though, they’re surprisingly unique.

BY GLENNDA CHUI

A new study shows that nickel oxide superconductors, which conduct electricity with no loss at higher temperatures than conventional superconductors do, contain a type of quantum matter called charge density waves, or CDWs, that can accompany superconductivity.

The presence of CDWs shows that these recently discovered materials, also known as nickelates, are capable of forming correlated states – “electron soups” that can host a variety of quantum phases, including superconductivity, researchers from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University reported in Nature Physics today.

“Unlike in any other superconductor we know about, CDWs appear even before we dope the material by replacing some atoms with others to change the number of electrons that are free to move around,” said Wei-Sheng Lee, a SLAC lead scientist and  investigator with the Stanford Institute for Materials and Energy Science (SIMES) who led the study.

“This makes the nickelates a very interesting new system – a new playground for studying unconventional superconductors.”

Nickelates and cuprates

In the 35 years since the first unconventional “high-temperature” superconductors were discovered, researchers have been racing to find one that could carry electricity with no loss at close to room temperature. This would be a revolutionary development, allowing things like perfectly efficient power lines, maglev trains and a host of other futuristic, energy-saving technologies.

But while a vigorous global research effort has pinned down many aspects of their nature and behavior, people still don’t know exactly how these materials become superconducting.

So the discovery of nickelate’s superconducting powers by SIMES investigators three years ago was exciting because it gave scientists a fresh perspective on the problem. 

Since then, SIMES researchers have explored the nickelates’ electronic structure – basically the way their electrons behave – and magnetic behavior. These studies turned up important similarities and subtle differences between nickelates and the copper oxides or cuprates – the first high-temperature superconductors ever discovered and still the world record holders for high-temperature operation at everyday pressures.

Since nickel and copper sit right next to each other on the periodic table of the elements, scientists were not surprised to see a kinship there, and in fact had suspected that nickelates might make good superconductors. But it turned out to be extraordinarily difficult to construct materials with just the right characteristics.

“This is still very new,” Lee said. “People are still struggling to synthesize thin films of these materials and understand how different conditions can affect the underlying microscopic mechanisms related to superconductivity.”

Read more on the SLAC website

Image: An illustration shows a type of quantum matter called charge density waves, or CDWs, superimposed on the atomic structure of a nickel oxide superconductor. (Bottom) The nickel oxide material, with nickel atoms in orange and oxygen atoms in red. (Top left) CDWs appear as a pattern of frozen electron ripples, with a higher density of electrons in the peaks of the ripples and a lower density of electrons in the troughs. (Top right) This area depicts another quantum state, superconductivity, which can also emerge in the nickel oxide. The presence of CDWs shows that nickel oxides are capable of forming correlated states – “electron soups” that can host a variety of quantum phases, including superconductivity.

Credit: Greg Stewart/SLAC National Accelerator Laboratory

Introducing Stephen Streiffer

Introducing Stephen Streiffer

After decades of experience in the DOE lab system and as director of a leading synchrotron light source, he’s back to where he earned his PhD – with a much bigger mission.

Thirty years after earning his PhD at Stanford University, materials scientist Stephen Streiffer will be back on campus next week – this time with an outsized role to play. As Stanford’s new vice president for the Department of Energy’s SLAC National Accelerator Laboratory, he’ll play a key part in advising and supporting the lab as it carries out its scientific mission.

Streiffer comes to Stanford and SLAC after 24 years at Argonne National Laboratory, where he did research at the lab’s Advanced Photon Source, directed APS for eight years and most recently served as chief research officer and deputy lab director for science and technology.

So he’s more than familiar with both the national lab system and the importance of DOE Office of Science user facilities, like APS and SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Linac Coherent Light Source (LCLS), for both fundamental research and experiments with more immediate practical value.

Read Glennda Chui’s Q & A interview with Stephen on the SLAC website

Image: Stephen Streiffer, the new Stanford vice president for SLAC National Accelerator Laboratory

Credit: Mark Lopez, Argonne National Laboratory

Piero Pianetta’s #My1stLight

Piero Pianetta’s #My1stLight

First light from the SPEAR Ring at SLAC July 6, 1973
Ingolf Lindau & Piero Pianetta

#My1stLight memory submitted by Piero Piantetta, Deputy Director of SSRC at SLAC


Pilot project to extract synchrotron radiation from the SPEAR ring at SLAC. In-alcove video camera imaging light emitted from a fluorescent screen just downstream of the Be exit window. No beam steering beyond global steering for colliding beam operation. Our group, including Gerry Fisher, waiting to see if beam would even make it through all the apertures. SUCCESS on first opening of line!!!!!

How a soil microbe could rev up artificial photosynthesis

How a soil microbe could rev up artificial photosynthesis

Researchers discover that a spot of molecular glue and a timely twist help a bacterial enzyme convert carbon dioxide into carbon compounds 20 times faster than plant enzymes do during photosynthesis. The results stand to accelerate progress toward converting carbon dioxide into a variety of products.

Plants rely on a process called carbon fixation – turning carbon dioxide from the air into carbon-rich biomolecules ­– for their very existence. That’s the whole point of photosynthesis, and a cornerstone of the vast interlocking system that cycles carbon through plants, animals, microbes and the atmosphere to sustain life on Earth. 

But the carbon fixing champs are not plants, but soil bacteria. Some bacterial enzymes carry out a key step in carbon fixation 20 times faster than plant enzymes do, and figuring out how they do this could help scientists develop forms of artificial photosynthesis to convert the greenhouse gas into fuels, fertilizers, antibiotics and other products.

Now a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory, Stanford University, Max Planck Institute for Terrestrial Microbiology in Germany, DOE’s Joint Genome Institute (JGI) and the University of Concepción in Chile has discovered how a bacterial enzyme – a molecular machine that facilitates chemical reactions – revs up to perform this feat.

Rather than grabbing carbon dioxide molecules and attaching them to biomolecules one at a time, they found, this enzyme consists of pairs of molecules that work in sync, like the hands of a juggler who simultaneously tosses and catches balls, to get the job done faster. One member of each enzyme pair opens wide to catch a set of reaction ingredients while the other closes over its captured ingredients and carries out the carbon-fixing reaction; then, they switch roles in a continual cycle.  

Read more on the SLAC website

What drives rechargeable battery decay?

What drives rechargeable battery decay?

How quickly a battery electrode decays depends on properties of individual particles in the battery – at first. Later on, the network of particles matters more.

Rechargeable lithium-ion batteries don’t last forever – after enough cycles of charging and recharging, they’ll eventually go kaput, so researchers are constantly looking for ways to squeeze a little more life out of their battery designs.

Now, researchers at the Department of Energy’s SLAC National Accelerator Laboratory and colleagues from Purdue University, Virginia Tech, and the European Synchrotron Radiation Facility have discovered that the factors behind battery decay actually change over time. Early on, decay seems to be driven by the properties of individual electrode particles, but after several dozen charging cycles, it’s how those particles are put together that matters more.

“The fundamental building blocks are these particles that make up the battery electrode, but when you zoom out, these particles interact with each other,” said SLAC scientist Yijin Liu, a researcher at the lab’s Stanford Synchrotron Radiation Lightsource and a senior author on the new paper. Therefore, “if you want to build a better battery, you need to look at how to put the particles together.”

Read more on the SLAC website

Image: A piece of battery cathode after 10 charging cycles. A machine-learning feature detection and quantification algorithm allowed researchers to automatically single out the most severely damaged particles of interest, which are highlighted in the image.

Credit: Courtesy Yijin Liu/SLAC National Accelerator Laboratory