Advanced Light Source (ALS) – Page 2

The Secret to Drought Tolerance Lies in a Lilac Crypt

2025/03/312025/04/02

Growing in the wild and in gardens, from Humboldt forests all the way to San Diego chaparral, the California lilac is a plant genus divided into two groups, Ceanothus and Cerastes. Ceanothus are associated with moister climates, whereas Cerastes have adaptations for surviving drier conditions. While both categories have stomata, pores that open and close to regulate CO₂ intake, Cerastes pores have a special configuration—they’re housed in leaf indentations called stomatal crypts.

“Stomatal crypts are very rare among plants,” said Joseph Zailaa, Yale doctoral student and the corresponding author on a study of the California lilac. “This anatomical structure is thought to help provide drought tolerance.”

Using Beamline 8.3.2 at the Advanced Light Source (ALS), his research team has now uncovered secrets from the Cerastes crypts. “Classic microscopy techniques only give us a 2D picture of the leaf’s internal structure,” said Zailaa, “but microtomography at the ALS allowed us to image and view these crypts in three dimensions for the first time.” They also obtained 3D models of hydrated and dehydrated samples, allowing the researchers to observe the plants’ responses to drought.

Many arid-climate plants are drought tolerant. “They maintain functions such as water transport and photosynthesis despite the onset of drought, which uses up the plant’s water reserves,” Zailaa explained. California lilacs have developed an additional adaptation: drought avoidance. “Their stomata close and they shut down most of their function at the onset of drought to conserve water reserves,” Zailaa described. “This delays the plant from experiencing damage caused by excessive dehydration,” he added. His team’s work showed how stomatal crypts provide even further benefits to Cerastes. The researchers found that Cerastes had greater water storage capacity and water use efficiency than Ceanothus.

Image: Ceanothus megacarpus is a member of the Cerastes subgroup of California lilacs. This species has a characteristic associated only with Cerastes, the stomatal crypts. In this 3D visualization obtained at ALS Beamline 8.3.2, white arrows indicate stomata, which are found exclusively within the crypts, or indentations in the leaf. The stomatal crypts help Cerastes species survive drought. Scale bar is 200 µm.

Credit: Craig Brodersen and Joseph Zailaa/Yale School of the Environment; Leila Fletcher/Southern Oregon University Biology Department

A New Way to Engineer Composite Materials

2025/03/062025/03/13

Researchers have developed a way to engineer pseudo-bonds in a polymer material.
Their work represents a new way of solidifying materials without relying on permanent chemical bonds.
Like an epoxy, the material serves as a strong and stable filler—but can also be dissolved and reused, as though untangling a ball of yarn.

Composite adhesives like epoxy resins are excellent tools for joining and filling materials including wood, metal, and concrete. But there’s one problem: once a composite sets, it’s there forever. Now there’s a better way. Researchers have developed a simple polymer that serves as a strong and stable filler that can later be dissolved. It works like a tangled ball of yarn that, when pulled, unravels into separate fibers.

A new study led by researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) outlines a way to engineer pseudo-bonds in materials. Instead of forming chemical bonds, which is what makes epoxies and other composites so tough, the chains of molecules entangle in a way that is fully reversible. The research is published in the journal Advanced Materials.

“This is a brand new way of solidifying materials. We open a new path to composites that doesn’t go with the traditional ways,” said Ting Xu, a faculty senior scientist at Berkeley Lab and one of the lead authors for the study.

Image: Silica nanoparticles affixed with a distribution of polystyrene chains (purple) self-assemble into hexagonal lattices. Depending on how the chains are organized on the particle surface, they tangle together (purple) or unravel (blue) when compressed.

Credit: Tiffany Chen; Ting Xu

Berkeley Lab Helps Explore Mysteries of Asteroid Bennu

2025/01/292025/02/06

The Advanced Light Source and Molecular Foundry provided powerful tools to study asteroid samples returned by NASA’s OSIRIS-REx mission. Researchers found a telltale set of salts formed by evaporation that illuminate Bennu’s watery past.

During the past year, there’s been an unusual set of samples at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab): material gathered from the 4.5-billion-year-old asteroid Bennu when it was roughly 200 million miles from Earth.

Berkeley Lab is one of more than 40 institutions investigating Bennu’s chemical makeup to better understand how our solar system and planets evolved. In a new study published today in the journal Nature, researchers found evidence that Bennu comes from an ancient wet world, with some material from the coldest regions of the solar system, likely beyond the orbit of Saturn.

The asteroid contained a set of salty mineral deposits that formed in an exact sequence when a brine evaporated, leaving clues about the type of water that flowed billions of years ago. Brines could be a productive broth for cooking up some of the key ingredients of life, and the same type of minerals are found in dried-up lake beds on Earth (such as Searles Lake in California) and have been observed on Jupiter’s moon Europa and Saturn’s moon Enceladus.

“It’s an amazing privilege to be able to study asteroid material, direct from space,” said Matthew Marcus, a Berkeley Lab scientist who runs the Advanced Light Source (ALS) beamline where some of the samples were studied and who wrote one of the programs used to analyze their chemical composition. “We have highly specialized instruments that can tell us what Bennu is made of and help reveal its history.”

The samples from Bennu were gathered by NASA’s OSIRIS-REx mission, the first U.S. mission to return samples from an asteroid. The mission returned nearly 122 grams of material from Bennu – the largest sample ever captured in space and returned to Earth from an extraterrestrial body beyond the Moon.

Marcus teamed up with Scott Sandford from NASA Ames Research Center and Zack Gainsforth from the UC Berkeley Space Sciences Laboratory to study the Bennu sample using scanning transmission X-ray microscopy (STXM) at the ALS. By varying the energy of the X-rays, they were able to determine the presence (or absence) of specific chemical bonds at the nanometer scale and map out the different chemicals found in the asteroid. The science team discovered that some of the last salts to evaporate from the brine were mixed into the rock at the finest levels.

“This sort of information provides us with important clues about the processes, environments, and timing that formed the samples,” Sandford said. “Understanding these samples is important, since they represent the types of materials that were likely seeded on the surface of the early Earth and may have played a role in the origins and early evolution of life.”

At Berkeley Lab’s Molecular Foundry, researchers used a beam of electrons to image the same Bennu samples with transmission electron microscopy (TEM). The Foundry also helped prepare the samples for the experiments run at the ALS. Experts used an ion beam to carve out microscopic sections of the material that are about a thousand times thinner than a sheet of paper.

“Being able to examine the same exact atoms using both STXM and TEM removed many of the uncertainties in interpreting our data,” Gainsforth said. “We were able to confirm that we really were seeing a ubiquitous phase formed by evaporation. It took a lot of work to get Bennu to give up its secrets, but we are delighted with the final result.”

This is not the first time the ALS and Molecular Foundry have studied material from space. Researchers also used the two facilities to investigate samples from the asteroid Ryugu, building up our understanding of our early solar system. And there’s still more to come, with additional studies of Bennu at both the STXM and infrared beamlines at the ALS planned for the coming year.

Understanding the Role of Manganese in Fuel Production Catalysts

2025/01/222025/01/27

SCIENTIFIC ACHIEVEMENT

Using specialized equipment at the Advanced Light Source (ALS), including a custom-built reaction cell, researchers uncovered the role of manganese in cobalt manganese oxide catalysts used for fuel production.

SIGNIFICANCE AND IMPACT

This work opens the door to improved catalyst designs that could decrease the production of harmful methane byproducts in a common petrochemical process.

Sustainable fuel production

First developed in the 1920s, the Fischer-Tropsch synthesis remains a common chemical process used to convert carbon monoxide and hydrogen from coal into liquid hydrocarbons, or fuel. Cobalt is an efficient catalyst for this reaction, and its combination with manganese has been known for decades to further improve the process by promoting the preferential production of long-chain hydrocarbons over methane, a contributor to climate change. However, the molecular scale origin for why manganese improves the efficiency of this reaction remains unclear.

In this work, researchers uncovered the role of manganese in cobalt-manganese-oxide systems by combining well-defined model catalysts with advanced x-ray spectroscopy techniques. These results provide a platform for how customized equipment can answer challenging scientific questions and set the stage for new catalyst designs that may further decrease the production of methane during Fischer-Tropsch synthesis.

Custom-built instrumentation

Numerous studies have investigated the mechanisms for catalytic performance in cobalt-manganese-oxide systems, proposing particular interfaces, mixed oxides, or nanostructures as reasons for the improved efficiency. However, due to the heterogeneity of widely used powder catalysts, resulting in separated domains of cobalt and manganese, the molecular-scale mechanism of these catalysts remains under debate. To circumvent this, the researchers created model catalysts of well-defined cobalt-manganese-oxide nanocrystals and films where the components were intermixed at the sub-nanometer scale.

The model catalysts were investigated using ambient-pressure x-ray photoelectron spectroscopy (APXPS) at Beamline 9.3.2, which is equipped with commercial instrumentation uniquely designed for ambient-condition experiments that mimic real reaction conditions (this instrumentation was previously developed by the researchers, is now available at Beamline 9.0.2 and Beamline 11.0.2, and induced the application of APXPS at other synchrotron facilities). Similarly, to achieve realistic reaction conditions for x-ray absorption spectroscopy (XAS), a custom-built reaction cell was designed for Beamline 8.0.1, allowing experiments that typically occur under high vacuum to be performed under ambient pressure. The challenging and iterative process of perfecting this reaction cell was key to the success of this study, and the reaction cell is now available to other ALS users.

The magic of manganese

Using the custom-built reaction cell for XAS, the researchers were able to observe the real-time breakdown of carbon monoxide during the introduction of hydrogen to the cobalt-manganese-oxide catalyst at ambient conditions. Next, APXPS showed a significant increase in CH_x hydrocarbon species after the addition of carbon monoxide and hydrogen on the cobalt-manganese-oxide catalyst surface–which was in stark contrast to the systems without manganese, where the production of cobalt carbide was more dominant instead. In other words, these results demonstrated that the addition of manganese creates more CH_x, which ultimately allows for the production of more long-chain hydrocarbons.

The ALS data was complemented by computational density functional theory (DFT) calculations. DFT demonstrated that manganese helps with the production of long-chain hydrocarbons because manganese oxide binds with hydrogen, making it unavailable for reacting with CH_x to stop propagation, resulting in less methane and more long-chain hydrocarbons. Moving forward, this work paves the way for improved catalyst designs that can make these reactions even more efficient.

$Inprentus Awarded Contract to Provide 6 Diffraction Gratings for X-ray Optics at The ALS$

Inprentus Awarded Contract to Provide 6 Diffraction Gratings for X-ray Optics at The ALS

2024/12/312025/01/07

Inprentus manufactures the world’s most advanced diffraction gratings for x-ray applications, offering unparalleled efficiency and high resolving power

Inprentus has been awarded a $427,300 contract to provide Lawrence Berkeley National Lab’s Advance Light Source (ALS) with 6 diffraction gratings for its facility upgrade, 2 for the COSMIC beamline, and 4 for the MAESTRO beamline.

The upgraded ALS will occupy the same facility as the current ALS, replacing the existing electron storage ring and leveraging $500 million in existing ALS infrastructure and experimental systems. Recent accelerator physics breakthroughs now enable the production of highly focused beams of soft x-ray light that are at least 100 times brighter than those of the existing ALS. The upgraded facility will produce bright, steady beams of high-energy light to probe matter with unprecedented detail. Applying this technology at the ALS will help enable a better understanding of and development of new materials and chemical systems needed to advance our energy, economic, and national security needs in the 21st century, securing the United States’ world scientific leadership for decades to come.

To allow users to take full advantage of the source’s state of the art upgraded capabilities, the ALS requires advanced cutting-edge optics. The cutting-edge variable line spacing (VLS) blazed gratings, provided by Inprentus, will be part of beamline optical instrumentation. Inprentus’ differentiating capability to produce a blaze angle of less than 2 degrees across the grating, as well as providing the highest efficiency and resolving power and an ultra-low blaze angle to accommodate grazing optics with a large beam footprint, were important factors in the choice to award Inprentus with this contract.

“The Inprentus team has dedicated many years of planning and scientific excellence into qualifying for this mammoth project. We are excited to take on this challenge and have already started delivering the gratings way ahead of schedule. That is why Inprentus is sought-after in the gratings industry – we have lowered the barrier for radiation hard, scientifically complex, master diffraction gratings with high-performance deliverables, in addition to our industry-leading fast turn-around time. We will continue to expand on this excellence,” explained Jeff MacDonald, Inprentus CEO.

Not All Gaps Are Created Equal

2024/12/022024/12/09

In a charge density wave (CDW), conduction electrons in a metal (typically a low-dimensional material) arrange themselves in a regular pattern, sometimes accompanied by lattice distortions. One material that undergoes a CDW transition is a compound of tantalum, selenium, and iodine [(TaSe₄)₂I]. Its quasi-one-dimensional structure consists of TaSe₄ molecular chains interspersed with I^– ionic chains.

The CDW transition in (TaSe₄)₂I is of particular interest because it’s potentially a mechanism that could lead to a spontaneous transformation into an “axion” state of matter. Axions are hypothetical particles that were proposed as a way to solve a well-known problem in particle physics. But the concept has crossed over to condensed matter physics, as a way to describe emergent properties in topological materials.

Prevailing theories predict that the CDW transition in (TaSe₄)₂I—a type of topological material known as a Weyl semimetal—should lead to a dispersion gap at points where linear Weyl bands intersect, but this has never been confirmed experimentally through angle-resolved photoemission spectroscopy (ARPES), because of difficulties arising from a very weak ARPES intensity near the Fermi level.

To address this, a team led by Meng-Kai Lin (National Central University, Taiwan) and Tai-Chang Chiang (University of Illinois at Urbana-Champaign) re-examined the electronic structure of (TaSe₄)₂I at Advanced Light Source Beamline 10.0.1 and other facilities, using high-statistics ARPES to bring out subtle features in the data.

Image: Left: ARPES map for (TaSe₄)₂I in the normal phase at room temperature. Right: Corresponding ARPES map in the CDW phase at a low temperature.

Studying Interfacial Effects in Solid-Electrolyte Batteries

2024/10/212024/11/15

At the Advanced Light Source (ALS), an ambient-pressure probe of a solid electrolyte revealed how surface electrochemical mechanisms lead to poor electrolyte performance and battery failure.

The results can help scientists engineer better coatings and interfaces, which are essential for building safer and better-performing batteries, particularly for use in vehicles.

A solid prospect for better batteries

Global efforts to electrify transportation and provide grid-level energy storage have driven demand for new battery technologies with improved safety, power density, and energy density. Ceramic solid electrolytes potentially offer significant advantages compared to the traditional liquid electrolytes used in lithium-ion batteries, including lower flammability and greater compatibility with high-energy electrode materials such as lithium metal. Among solid-electrolyte contenders, tantalum-doped lithium lanthanum zirconium oxide (LLZO) has garnered significant attention as a separator material because of its high bulk ionic conductivity and minimal chemical reactivity with lithium metal.

However, LLZO performance is limited by reactions that produce surface contaminants. Understanding the mechanisms behind these reactions is crucial for improving material processing. In this work, researchers used ambient-pressure x-ray photoelectron spectroscopy (APXPS) as part of a systematic investigation of the impacts of electrochemical reactions and contamination. The results will inform the design of safer and more-efficient batteries for electric vehicles or renewable energy storage.

Facing the interfacial challenges

It is well known that, in the presence of water vapor in air, LLZO undergoes Li⁺/H⁺ exchange, where protons (H⁺) can take up lithium-ion (Li⁺) sites without modifying the cubic crystal structure. This results in the formation of surface contaminants such as LiOH and Li₂CO₃ that contribute to poor interfacial contact and the constriction of current.

Numerous studies have explored different aspects of the surface contamination mechanisms on LLZO along with various processing techniques aimed at improving surface properties. However, most studies have focused on critical current density (CCD) tests, which provide limited mechanistic insight, or impedance analyses, with limited rationale behind their interpretation.

In this study, the researchers utilized a variety of surface-treatment processes on LLZO pellets to selectively induce proton exchange and contamination reactions in LLZO. The resulting bulk and surface chemistry was systematically characterized and correlated to changes in electrochemical properties.

ALS studies at ambient pressure

To observe the evolution of chemical species near the LLZO surface, ambient-pressure x-ray photoelectron spectroscopy (APXPS) was performed at ALS Beamline 9.3.2. The ability to tune the gas environment and temperature during measurement was crucial, as it allowed the researchers to optimize conditions (pressure, temperature, time) for removing surface contaminants. Also, the ability to vary the probe depth via beam energy was also essential for chemical speciation.

Image: Illustrations of some of the surface treatments applied to a solid-state battery-electrolyte material (LLZO) as part of this study: glovebox polishing (Gb:Pol), heat treatment (HT), acid treatment (AT), water treatment (WT), and water treatment + heat treatment (WT:HT). Proton concentration (the result of H⁺ displacing Li⁺) is indicated by the color gradient, from low (orange) to high (blue). Pink and purple indicate surface contaminants.

The Spatial Dynamics of Bone Remodeling During Lactation

2024/10/162024/11/21

Lactation places large metabolic demands on a mother’s skeleton. To mobilize the minerals needed for milk production, osteocytes—the cells responsible for maintaining bone quality—facilitate the release of calcium and other minerals from the bone. In this study, researchers investigated how this process occurs throughout the bone during lactation and how osteocytes balance the rapid release of calcium while maintaining bone integrity.

“We know that lactation leads to significant changes in bone, but understanding how these changes occur at both the osteocyte cellular and bone structural levels was crucial,” said Claire Acevedo, an assistant professor at the University of California San Diego. Researchers from UC San Diego and UC San Francisco compared virgin and lactating mice, with and without the osteocyte-specific deletion of an enzyme (MMP13) responsible for the resorption of bone matrix surrounding the osteocytes. To visualize and quantify local changes in mouse tibias, they employed microcomputed tomography at Advanced Light Source (ALS) Beamline 8.3.2.

The team discovered that lactation-induced bone remodeling is highly spatially controlled. Osteocytes located near the bone’s vascular structures experienced significant local bone matrix resorption and calcium release, leading to a substantial increase in the volume of lacunae (i.e., cavities where osteocytes reside). In contrast, osteocytes near the bone’s outer surface showed little activity. The findings suggest that osteocytes located near vasculature, facilitating calcium transport, play a more active role in calcium mobilization during lactation.

Additionally, the researchers discovered that lactation led to the formation of hypomineralized regions 14–20 µm away from the osteocyte lacunae, particularly in larger lacunae undergoing active resorption. These hypomineralized regions, indicative of calcium removal, demonstrate that osteocytes can resorb minerals not only around the lacunae via MMP13 but also further away, at the tips of their branches (called “dendritic processes”), independent of peri-lacunar resorption and MMP13.

Image: Representative 3D renderings of the lacunae and vasculature in mouse bones, generated using synchrotron microcomputed tomography. Vasculature is colored white, and lacunae are colored according to volume.

A New Way to “Squeeze” Infrared Light Down to Size

2024/10/072024/10/07

SCIENTIFIC ACHIEVEMENT

Using the Advanced Light Source (ALS), researchers demonstrated a new way to confine, or “squeeze,” infrared light by coupling photons with phonons (lattice vibrations) within a certain type of thin film.

SIGNIFICANCE AND IMPACT

The work heralds a new class of optical materials for controlling infrared light, with potential applications in photonics, sensors, and microelectronic heat management.

A light squeeze

Researchers have demonstrated that thin films of strontium titanate (SrTiO₃, or STO) can confine, or “squeeze,” infrared light 10 times more than its bulk form can—a finding that holds promise for next-generation microelectronic and photonic devices. While this unusual behavior had been theoretically predicted for STO membranes, it had not yet been experimentally observed.

The researchers took advantage of advances in the synthesis of freestanding, large-scale crystalline oxide membranes, then used a combination of infrared micro- and nanospectroscopy to observe how infrared light couples to lattice vibrations in the membranes. They found that the coupling produced hybrid vibrational and electromagnetic waves (phonon polaritons) in the material, with different modes characterized by highly compressed wavelengths or greatly enhanced fields inside the sample.

Transferable membranes

Theoretical studies have suggested that ultrathin STO and other perovskite membranes can host highly confined surface phonon polaritons (SPhPs) with good propagation quality. Other compounds may have higher figures of merit, but because they are typically manually exfoliated, their lateral size is constrained to the micrometer range, which limits their potential for large-scale device fabrication.

Image: In this experiment, an atomic force microscope tip focuses broadband synchrotron infrared light onto the surface of a strontium titanate (SrTiO₃) membrane, just 100 nm thick. The infrared light excites phonon polaritons—quasiparticles that arise when light strongly interacts with dipole oscillations in the material’s lattice. Spectroscopic analysis of the scattered light enabled researchers to determine the properties of phonon polaritons on the material surface.

Manganese Cathodes Could Boost Lithium-ion Batteries

2024/09/252024/10/01

Rechargeable lithium-ion batteries are growing in adoption, used in devices like smartphones and laptops, electric vehicles, and energy storage systems. But supplies of nickel and cobalt commonly used in the cathodes of these batteries are limited. New research led by the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) opens up a potential low-cost, safe alternative in manganese, the fifth most abundant metal in the Earth’s crust.

Researchers showed that manganese can be effectively used in emerging cathode materials called disordered rock salts, or DRX. Previous research suggested that to perform well, DRX materials had to be ground down to nanosized particles in an energy-intensive process. But the new study found that manganese-based cathodes can actually excel with particles that are about 1000 times larger than expected. The work was published Sept. 19 in the journal Nature Nanotechnology.

“There are many ways to generate power with renewable energy, but the importance lies in how you store it,” said Han-Ming Hau, who researches battery technology as part of Berkeley Lab’s Ceder Group and is a PhD student at UC Berkeley. “By applying our new approach, we can use a material that is both earth-abundant and low-cost, and that takes less energy and time to produce than some commercialized Li-ion battery cathode materials. And it can store as much energy and work just as well.”

The researchers used a novel two-day process that first removes lithium ions from the cathode material and then heats it at low temperatures (about 200 degrees Celsius). This contrasts with the existing process for manganese-based DRX materials, which takes more than three weeks of treatment.

Researchers used state-of-the-art electron microscopes to capture atomic-scale pictures of the manganese-based material in action. They found that after applying their process, the material formed a nanoscale semi-ordered structure that actually enhanced the battery performance, allowing it to densely store and deliver energy.

The team also used different techniques with X-rays to study how battery cycling causes chemical changes to manganese and oxygen at the macroscopic level. By studying how the manganese material behaves at different scales, the team opens up different methods for making manganese-based cathodes and insights into nano-engineering future battery materials.

Image: A new process for manganese-based battery materials lets researchers use larger particles, imaged here by a scanning electron microscope.

Credit: Han-Ming Hau/Berkeley Lab and UC Berkeley

A promising compound for reversible male contraception

2024/09/032024/09/10

Researchers found that a small-molecule protein inhibitor—screened from billions of compounds and analyzed using structural insights from protein crystallography performed at the Advanced Light Source (ALS)—reversibly suppresses male fertility in mice.

The work addresses the pressing need for more contraceptive options that enable all individuals to control their own fertility.

Eight billion and counting

The United Nations designated November 15, 2022, as the Day of Eight Billion, the day the population of our planet passed eight billion people. This number is projected to reach ten billion by 2050. A sobering statistic is that nearly half of all pregnancies worldwide are unintended, which results in emotional, physical, and financial burdens on individuals as well as health care systems.

Contraception enables individuals to choose when and whether to conceive. But more options are needed—for nonhormonal contraceptives (which target specific proteins related to reproduction) and for non-barrier, reversible methods for men.

Here, researchers identified a molecule that blocks an enzyme key to male fertility. Using protein crystallography, they gained valuable structure–activity insight and, in tests on mice, showed that an optimized version of the compound is both effective and reversible.

Shining light on a “dark kinase”

The protein target in this work is an enzyme called serine/threonine kinase 33 (STK33). Kinases activate cellular processes and are therefore prime targets for drug therapies. However, there are over 500 human kinases, and many—sometimes called “dark kinases”—are under-researched and poorly understood. STK33 fell into this category, until a study of men with STK33 mutations and experiments in which the STK33 gene was nullified in mice established that deactivating STK33 in males suppresses fertility.

To identify small-molecule drug candidates for blocking STK33, the researchers used a high-throughput screening process whereby each candidate molecule was tagged with a unique DNA sequence. This enabled the screening of billions of molecules together with STK33 in a single test tube. Compounds that ended up tightly bound to the protein (“hits”) could then be identified by sequencing the DNA tags.

Structure-guided design

To understand the molecular basis for high-affinity STK33 inhibitors, the researchers used protein crystallography at ALS Beamline 5.0.2 to determine the structure of STK33, co-crystallized with a hit from the screening process (CDD-2211) that proved amenable to crystallization.

Because the structure of STK33 had never been previously determined, the researchers were surprised to discover that it formed a dimer. The data also settled the question of how molecules are oriented in the binding pocket, after predictive models had given two different possibilities. Specific interactions between the molecule and the protein’s amino acids showed why CD-2211 has such high affinity for STK33. This information will prove very useful in tailoring compounds for greater STK33 specificity.

Image: Surface view of a protein (STK33) that, when inhibited, produces contraceptive effects. A small-molecule inhibitor is shown as a stick model (yellow=carbon, red=oxygen, and blue=nitrogen) in the protein’s binding pocket.

Three additional projects named finalists in race for the “Oscars of Innovation”

2024/08/122024/08/19

Six projects by researchers at the U.S. Department of Energy’s (DOE) Argonne National Laboratory were recognized with 2024 R&D 100 Awards. The awards, frequently referred to as the “Oscars of Innovation,” recognize exciting new products or processes that have been developed in the past two years. An additional three projects were named finalists.

“I would like to send my heartfelt congratulations to the Argonne researchers and their partners who were named winners or finalists in this year’s program,” said Argonne Director Paul Kearns. “Their impactful research is an inspiration for our laboratory and the entire science community.”

Argonne has a decades-long history of winning R&D 100 awards, including 151 winners since the competition began in 1963. Past winners also include Fortune 500 companies, other DOE national laboratories, academic institutions and smaller companies.

Image: Argonne National Laboratory.

Credit: Agonne National Laboratory.

Mechanistic Insight into a Viral-Factory Component

2024/06/232024/07/02

“Viral factories” are areas in virus-infected host cells where the tools and materials necessary for viral replication are concentrated. In this study, researchers sought to learn more about an important component of some viral factories, a protein called σNS. This protein takes part in the replication of reoviruses, which are generally nonpathogenic and can be used as an oncolytic agent to target cancer cells. Despite its importance, the underlying mechanics of σNS have remained unclear.

A collaborative team led by B.V.V. Prasad at Baylor College of Medicine and Terence Dermody at the University of Pittsburgh conducted protein crystallography studies at Beamline 5.0.1 of the Advanced Light Source. They looked at a mutant version of σNS, σNS-R6A, which forms dimers rather than the longer chains (oligomers) of the unmutated protein, which resists crystallization.

The team discovered that σNS-R6A dimers interact by inserting protruding arms into a pocket of its neighbor, forming a helical assembly. The interior of the helical assembly is positively charged, making it suitable for binding RNA.

Image: Interacting dimers are shown in pink and blue, with the two monomeric subunits in the pink dimer labeled A and A’. The N-terminal arms (in red frames) project in opposite directions (red arrows) to chain-link the dimers to form a helical assembly.

ALS Machine Learning Models at Beamtimes around the World

2024/06/212024/07/16

From the types of samples to the techniques used to study them, user experiences at beamlines around the world can vary, but one commonality connects them: beamtime is precious. At different facilities, users encounter different beamline controls, and varying availability of compute infrastructure to process their data. Beyond needing to familiarize themselves with different equipment and software setups, they also need to ensure that they’re collecting meaningful, consistent data no matter where they are. For the past several months, the ALS Computing group has been traveling around the world for beamtime. Their firsthand experience is informing the development of a suite of tools aimed at lowering the barriers of access to advanced data processing for all users.

Today’s beamtime experience

As a beamline scientist at the ALS, Dula Parkinson has helped numerous users with microtomography, a technique that can yield ten gigabytes of data in two seconds. “In many cases, users won’t have done this kind of experiment or analysis before, and they won’t have the computing infrastructure or software needed to analyze the huge amounts of complex data being produced,” he said.

Computational tools and machine-learning models can help the users, from adjusting their experimental setup in real time to processing the data after the experiment has concluded. Eliminating these bottlenecks can make the limited beamtime more efficient and help users glean scientific insights more quickly.

As a former beamline scientist himself, Computing Program Lead Alex Hexemer has first-hand knowledge of the user experience. He was instrumental in the creation of a dedicated computing group at the ALS in 2018, which continues to grow in both staff numbers and diversity of expertise. A current focus for the group is to advance the user experience with intuitive interfaces.

Computing approach to beamtime

Recently, Hexemer and two of his group members, Wiebke Koepp and Dylan McReynolds, traveled to Diamond Light Source, where they worked with Beamline Scientist Sharif Ahmed to test some of their tools during a beamline experiment. “It is always useful to see other facilities from the user’s perspective,” McReynolds said. “We want our software to be usable at many facilities, so getting to test in other environments was very valuable.”

The computational infrastructure is an essential complement to the beamline instrumentation. To standardize their experiments across different microtomography beamlines, the team performed measurements on a reference material—sand with standardized size distributions. Each scan captures a “slice” from the sample; the slices then need to be reconstructed into three-dimensional images that contain 50 to 200 gigabytes of data.

Image: The ALS Computing group performed experiments and tested their machine learning models at Beamline 8.3.2. Clockwise from back left: Tanny Chavez, Dylan McReynolds, Raja Vyshnavi Sriramoju, Seij De Leon, Dula Parkinson, Wiebke Koepp.

Superhard Materials at the Nanoscale: Smaller is Better

2024/06/182024/07/19

Scientific Achievement

Using high-pressure radial x-ray diffraction at the Advanced Light Source (ALS), researchers found that in the superhard material, rhenium diboride, smaller grain size leads to greater yield strength (i.e., the amount of stress tolerated before permanent deformation).

The cutting edge

As we get better at making robust, durable materials that resist wear, corrosion, and extreme temperatures—think aerospace, automotive, and industrial machining applications—we also need to step up the quality of the tools we use to cut, form, and polish these hardened materials. Researchers have found that transition-metal borides are promising in this regard because of their low costs and advantageous mechanical properties. Metal borides combine highly incompressible transition metals (e.g., tungsten, rhenium, and osmium) with boron, which readily forms strong covalent bonds—a key characteristic of the prototypical superhard material, diamond. In this work, researchers used radial x-ray diffraction at high pressures to gain insight into how grain size affects the nanoscale deformation mechanics of the superhard material, rhenium diboride (ReB₂).

Inspired by diamonds

Diamond is a well-known superhard material. But diamond production requires both high temperatures and high pressures, both of which naturally occur deep underground. To replicate the hardness of diamond under ambient conditions, researchers have looked for materials that incorporate two diamond-like characteristics: densely packed electrons and a highly covalent bonding network.

Electron-dense, incompressible elements can be found toward the bottom of the periodic table, but those elements are also metals, characterized by malleability and ductility. A promising strategy is to combine the metals with boron, which readily forms strong covalent bonds. The first example of a superhard metal boride following this design principle was ReB₂, consisting of alternating layers of rhenium and boron. While size-induced hardening has been previously studied in softer inorganic materials, size effects in hard materials have been relatively unexplored.

High-pressure radial x-ray diffraction

In this work, the researchers synthesized ReB₂ powder samples with grain sizes of 20, 50, and 60 nm. They then used high-pressure radial x-ray diffraction at ALS Beamline 12.2.2—a dedicated high-pressure beamline—to explore the effect of grain size on yield strength, which is directly related to hardness.

Image: Schematic of radial x-ray diffraction under high pressure. A rhenium diboride (ReB₂) powder sample is compressed uniaxially, creating differential compressive stresses that provide insight into the strength, deformation mechanisms, and elasticity of the material.

A Novel Staircase Pattern in Spin-Stripe Periodicity

2024/05/282024/06/06

SCIENTIFIC ACHIEVEMENT

At the Advanced Light Source (ALS), striped patterns of spins in a magnetic thin film were found to evolve under an applied magnetic field in steps reminiscent of a structure known as the “Devil’s Staircase.”

SIGNIFICANCE AND IMPACT

Such studies are valuable for understanding competing interactions at the atomic level for applications such as magnetic sensors and spintronic devices.

Devilishly complex systems

The “Devil’s Staircase” is a peculiar mathematical function that rises continuously but has no slope (i.e., its derivative is zero almost everywhere). This is because it consists of “runs” (flat sections) connected by “rises” that are fractal: each contains successively smaller copies of the main step, to the infinitesimal limit. Similar structures have emerged in phenomena ranging from earthquakes to charge density waves—systems characterized by competing pressures that result in periods of stability punctuated by short bursts of activity.

Here, researchers report the observation of novel staircase patterns in the evolution of spin-stripe domains in an iron/gadolinium (Fe/Gd) multilayer system. Theoretical modeling that builds on the measurements revealed which of the competing atomic-level interactions in this system is the dominant cause of the staircase structure. The findings help unravel the complex interplay of forces affecting spins in systems relevant to applications in magnetic sensing, information storage, and spintronics.

Image: A scattering image of one of the sample’s magnetic phases