Advanced Light Source (ALS) – Lightsources.org

Thin-Film Coating Boosts X-Ray Instrument Performance

2026/01/272026/02/12

Researchers developed optimized coatings for diffraction gratings at the Advanced Light Source (ALS) that use thin-film interference to double the light reaching the sample, capturing power otherwise lost to absorption.

Every soft x-ray beamline monochromator uses gratings and can benefit from increased diffraction efficiency.

How to win back lost x-rays

Soft x-rays allow us glimpses into the most fundamental properties of many materials by revealing what electrons are doing in a solid. But, the gratings that separate and bend x-rays in these studies struggle to deliver more than a small fraction of an incoming beam’s energy to its target. This has led researchers on a quest to improve the efficiency of gratings, without compromising the resolution of the output data.

Gratings are the key technology for soft x-ray experiments and most spectroscopy tools. Their periodic structures parse light into separate wavelengths, which are then either selected individually or dispersed across a detector. To achieve high resolution, these metal-coated gratings need an extremely high number of closely packed grooves. The grooves, however, are a double-edged sword: they deflect incoming x-rays toward the sample, but some x-rays are absorbed by the coating and cannot usefully contribute.

In this study, researchers sought to win back some of the x-rays that are lost. They examined how very thin metal coatings impacted a grating’s performance. The team, led by ALS Staff Scientist Dmitriy Voronov, tested gratings coated with atoms-thick layers of chromium (Cr) and gold (Au) and showed that an optimized configuration doubled the efficiency compared with standard designs.

Image: A silicon grating with half a million grooves and coated with atoms-thick layers of chromium and gold will provide higher energy resolution at Advanced Light Source Beamline 6.0.2 QERLIN. QERLIN is a double-dispersion resonant inelastic x-ray scattering (RIXS) beamline.

Engineering Division pilots equipment protection interlock system for Berkeley Lab user endstations

2026/01/232026/01/28

A new user-configurable equipment protection interlock system that helps protect scientific equipment and users will provide more flexibility and reliability while improving safety at the Lab.

Equipment protection interlock systems are a vital component of the infrastructure for many types of scientific equipment and facilities, especially at Berkeley Lab facilities like the Advanced Light Source (ALS), BELLA, and the Joint Genome Institute. These specialized interlock systems control the mechanisms that prevent unsafe conditions when using equipment. Actions like protecting beamline slits and components from overheating fall to interlock systems that have been custom-configured to meet the specific requirements of equipment and experiments. The Engineering Division is currently piloting a system for Berkeley Lab that will make setting up and using equipment protection system interlocks safer, faster, and more consistent—with minimal training and no need for coding on the user side.

This new tool has been developed at the ALS in collaboration with the European Synchrotron Radiation Facility (ESRF). The underlying idea for the interlock system comes from ESRF, where more than 400 of the devices are already in use. When Ernesto Paiser, ALS Instrument Software Support Group Lead, formerly of ESRF, arrived at Berkeley Lab, he saw an opportunity to implement a similar system that would provide increased reliability and flexibility while improving safety and efficiency.

“When I started at the Lab,” says Paiser, “I was immediately confronted with numerous challenges related to the equipment protection system (EPS). One of the most significant issues was how complex and inaccessible the system was for end users when they needed to define or modify interlock requirements at the end stations. Even a minor request often required changes to the main front-end interlock program. Each modification triggered a full system retest, regardless of the scope of the change. In many cases, by the time the work was completed, the original request was no longer needed, yet the changes remained permanently embedded in the system.”

Image: Ernesto Paiser, ALS Instrument Software Support Group Lead, pictured with the new no-code interlock system.

Credit: Engineering Division

Ancient Asteroid Provides Evidence of Amino Acid Precursors

2025/12/102025/12/19

SCIENTIFIC ACHIEVEMENT

Using the Advanced Light Source (ALS), researchers identified nitrogen-rich polymers in samples from the asteroid Bennu, revealing early chemical alterations in rocky bodies.

SIGNIFICANCE AND IMPACT

The results support the idea that asteroids, such as Bennu, may have carried water and the other chemical building blocks of life to Earth in the distant past.

Asteroid holds hidden secrets

In 2023, NASA returned material gathered from the 4.5-billion-year-old asteroid Bennu, which formed from minerals and ice in a primordial nebula. The rocks were gathered as part of NASA’s OSIRIS-REx mission, the first US mission to return samples from an asteroid. Lawrence Berkeley National Laboratory (Berkeley Lab) continues to participate in a series of multi-institutional research studies investigating Bennu’s chemical makeup to better understand how our solar system and planets evolved.

Past research on Bennu samples at Berkeley Lab’s ALS revealed that many minerals formed in watery environments. In the current study, the researchers rolled back the clock to examine a narrow period shortly after the asteroid formed but before it was exposed to the water that altered the chemical nature of the rock.

The researchers identified long chains of organic molecules, richer in nitrogen and oxygen than the previous samples. With this information, the team reconstructed the conditions during the earliest periods of the asteroid’s existence.

X-Rays Shed Light on Possible New Treatments for TB

2025/10/282025/10/30

SCIENTIFIC ACHIEVEMENT

X-ray diffraction data, collected at the Advanced Light Source (ALS) and other Department of Energy light sources, revealed the crystal structure of CMX410, a new compound that targets a key enzyme (Pks13) in the cell membrane of the bacterium responsible for tuberculosis (TB).

SIGNIFICANCE AND IMPACT

CMX410 is a promising new candidate to treat TB, including multidrug-resistant strains.

New treatments needed to tackle an old foe

TB is a deadly infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb). According to the World Health Organization, an estimated 10.8 million people contracted TB globally in 2023, and 1.25 million died from the disease. While antibiotics are effective for drug-sensitive TB cases, multidrug-resistant Mtb strains can evade common drug therapies.

Drug-resistant cases require a regimen that is often more expensive, toxic, and time-intensive. Patients are required to take six or more medications daily for up to 20 months. New approaches are urgently needed to shorten the course of drug interventions and address widespread multidrug-resistant strains.

A multi-institutional study led by researchers at Texas A&M University and the Calibr-Skaggs Institute for Innovative Medicine sought to find new treatments to address multidrug-resistant TB. The team screened a library of 406 compounds that belong to an active class of molecules [i.e., sulfur fluoride exchange (SuFEx)] to evaluate their efficacy against Mtb. The team developed one promising compound into CMX410, which targets Pks13, an enzyme essential for microbial cell wall biosynthesis.

Image: A cross-section of the crystal structure for the enzyme Pks13 (the surface colored pink and blue by hydrophobicity) as it interacts with CMX410 (shown as stick-like structure), a new drug candidate for TB

Credit: ALS

Sharks Shed Light on Origins of Adaptive Immune System

2025/08/262025/09/11

The Advanced Light Source (ALS) characterized a protein from a modern shark gene that explains the evolution of the adaptive immune system shared by all vertebrates.

Understanding the emergence of the adaptive immune system may aid researchers in advancing immunology, genetics, and biotechnology.

Left: The crystallographic model of the N-terminus of the UrIg2 protein from a nurse shark. Right: An example of one modern human antibody (IgG) whose variable region gene undergoes rearrangement.

The rise of adaptive immunity

Humans defend against infections through both the innate and adaptive immune systems. The innate response provides the first line of rapid defense, but it lacks both a way to address specific pathogens and a memory response to launch against attack by a returning invader. The adaptive immune system acts as a second line of defense. It lags behind the innate system because it must construct the antibodies to fight specific pathogens. The strength of this dual approach lies in the memory retained in the cells that produce antibodies that can be recalled to neutralize a returning threat.

The adaptive immune system is shared by all vertebrates and is believed to have developed soon after a genome-wide duplication event that occurred approximately 500 million years ago. The scientific community theorizes that the adaptive immune system developed when a mobile genetic element from a microbe—a recombination-activating gene (RAG) transposon—inserted itself into and split a gene in a eukaryotic cell, likely a white blood cell.

This random event led to a monumental and life-altering outcome. The process brought the repetitive elements from the transposon into this fractured gene with the RAG enzymes, which sparked the generation of an incalculable number of new proteins. To repair the fracture, the cell called in specialized machinery—double strand break repair enzymes—to fix the broken strands of genetic material. Proteins encoded by such “rearranged” genes eventually became antibodies—the front line of defense in the adaptive immune response.

A New Twist for Superconductivity in Bilayer Graphene

2025/06/202025/06/24

Using the Advanced Light Source (ALS) to study twisted bilayer graphene (TBG) systems, researchers found intriguing spectroscopic features in a superconducting “magic-angle” TBG—features that are absent in non-superconducting TBG.

The results provide crucial information on superconductivity in magic-angle TBG for next-gen electronics and advanced energy technologies.

Searching for the science behind the magic

Two-dimensional materials like graphene give scientists great flexibility in engineering electronic properties because they can be stacked like sheets of paper. Besides choosing what materials to stack and in what order, researchers can manipulate the electrical and optical properties of these stacks by controlling the twist angle between layers. Because of this versatility, two-dimensional materials provide an ideal platform for investigating the complex interplay between phenomena such as band topology, strong electron correlation, magnetism, and superconductivity, all of which are relevant to next-gen electronics and advanced energy technologies.

So-called “magic-angle” twisted bilayer graphene (MATBG) attracts broad research interest primarily because of its surprising and unusual superconducting properties, which resemble those of high-temperature superconductors. The superconductivity in MATBG devices is thought to arise from flat bands that form in a material’s electronic band structure when two layers of graphene are twisted at a “magic” angle of about 1.08 degrees. Flat bands indicate a high density of states, which significantly enhances electron interactions and the resulting potential for exotic phenomena. Despite intensive experimental efforts, the origin of MATBG superconductivity remains elusive.

Advanced micro-ARPES at the ALS

Angle-resolved photoemission spectroscopy (ARPES) is a powerful tool for probing the fine electronic structure of materials and has played a pivotal role in unraveling the mechanisms of high-temperature superconductivity and discovering novel topological quantum materials. However, due to the microscale dimensions of MATBG devices, traditional ARPES techniques, typically limited to a spatial resolution of hundreds of microns, cannot be directly applied. Persistent efforts have led to the development of advanced micro- and nano-ARPES techniques, extending ARPES research to sub-micrometer quantum materials and devices.

Here, researchers systematically characterized the electronic structure of several twisted bilayer graphene (TBG) devices using micro-ARPES at ALS Beamline 7.0.2 (MAESTRO), where a world-leading nano-ARPES system has also been developed. The high-quality moiré superlattice and superconductivity of these devices were characterized by a group at Princeton University.

Image: Artistic depiction of a twisted bilayer graphene system. A very slight twist in the alignment of the two graphene layers creates a moiré pattern—a periodic modulation of the electronic environment that can give rise to exotic behaviors such as superconductivity. Advanced nanoscale probes provide important clues as to the connections between electronic structure and material properties.

Efficient Upcycling of Plastic Waste into Useful Liquid Fuels

2025/06/202025/06/24

Plastic waste is a serious problem, especially with items meant to be used once and then thrown away. Such plastics are tough to break down, and current recycling methods either use a lot of energy or expensive materials. In this study, researchers aimed to develop a more sustainable, efficient, and selective approach for converting polyolefins (i.e., polyethylene and polypropylene, used in plastic bags and packaging) into valuable liquid chemicals.

“What we discovered is a simple way to turn this kind of plastic into useful liquid fuels, like components of gasoline or diesel, without needing high heat, rare metals, or added chemicals,” said Zhenzhen Yang, a Research and Development Associate in the Chemical Sciences Division at Oak Ridge National Laboratory. “This could be a big step toward turning plastic waste into something valuable instead of letting it pile up in landfills or oceans.”

The researchers studied a reaction mixture containing low-density polyethylene (LDPE) and AlCl₃/NaCl, a special type of molten salt that can act like a super-reactive soup, breaking down the plastic efficiently. Using soft x-ray absorption spectroscopy (XAS) at Advanced Light Source (ALS) Beamline 7.3.1 combined with nuclear magnetic resonance measurements, the researchers probed the chemical bonding of aluminum species both at the surface (10 nm deep) and in the bulk (beyond 100 nm). The mixture was quenched (the reaction was halted) at different intervals without any post-treatment, to allow observation of the mixture’s evolution over time.

ALS Captures Structure of Engineered Protein, Opening New Options to Treat IBD

2025/06/172025/06/18

According to the Centers for Disease Control and Prevention, Inflammatory Bowel Disease (IBD) affects more than three million people across the United States, costing the nation’s healthcare system about $8.5 billion in 2018. IBD occurs when the body’s immune system mistakenly attacks healthy bowel tissue, leading to inflammation and damage.

The exact cause of IBD is unknown but is characterized by long-term inflammation. While many factors can influence inflammation, Interleukin-10 (IL-10), a specialized protein, plays a role in regulating the immune response in the human body and has potential to treat inflammation-related conditions. Unfortunately, wild-type IL-10 is complicated. It possesses a dual nature and can initiate both pro- and anti-inflammatory pathways. It is also ephemeral, only lasting three hours in the human body.

“Natural proteins can be problematic as biotherapeutics, because these compounds often have a limited half-life and toxicity,” said Glen Spraggon, executive director of Structure Bioinformatics and Data Science at the Novartis Biologics Research Center and senior author on the study. “We decided to try to combine the positive properties of antibodies—half-life and good manufacturability—with the functional properties of IL-10.”

Spraggon and his colleagues grafted a modified IL-10 protein into the complementary determining regions (CDR) of an antibody. Through this process, they engineered six graft variants. One graft (GFT-IL10M) had the desired properties, but the actual molecule structure of the design remained unclear. The joints in the graft connecting the antibody and IL-10 are incredibly flexible. The team crystallized the engineered sample and analyzed it at the Advanced Light Source Beamline 5.0.3. They used the diffraction data to define the three-dimensional structure of the IL-10 fusion protein at the atomic level.

“We love to have a visual to understand the molecular structure of what we have actually created in the lab,” said Spraggon. “This structure confirmed how, with this fusion approach, we largely change the signaling profile of the molecule, biasing it away from its pro-inflammatory nature towards anti-inflammatory.”

Image: Molecular rendering of the engineered graft of IL-10 (red) with an antibody (blue/yellow). Structural analysis of GFT-IL10M using X-ray Crystallography at the ALS provided insight into its improved anti-inflammatory properties. The designed biotherapeutic enhanced monocyte activation whilst minimizing pro-inflammatory signaling observed in wild-type IL-10which also stimulates B, T, and NK white-blood cells.

Credit: Michael DiDonato/Novartis Biomedical Research

Catching “Hydrogen Spillover” onto a Catalytic Surface

2025/05/272025/06/06

Researchers uncovered the precise mechanism of hydrogen spillover (H₂ splitting and migration) onto a catalytic surface by watching it happen under various conditions at the Advanced Light Source (ALS).

The research lays the foundation for designing more efficient catalysts and storage materials essential for next-generation hydrogen energy technologies.

Hydrogen on the move

The splitting and migration of molecular hydrogen (H₂) over a catalytic surface (a process known as “hydrogen spillover”) is a fundamental yet elusive phenomenon in catalysis that affects a wide range of uses, from hydrogenation (which can be used to upgrade or purify crude oil components) to energy storage (when bonded to a metal, hydrogen can be stored in the solid state). Despite its importance, direct experimental evidence capturing the real-time mechanistic steps of hydrogen spillover remains scarce.

In particular, tungsten oxide (WO₃), a widely used catalytic material, exhibits dynamic interactions with hydrogen, yet the precise nature of these interactions has been a subject of long-standing debate, especially for distinguishing the chemical dynamics occurring on the surface from those in the bulk.

This research was driven by the need to resolve these ambiguities using ambient-pressure x-ray photoelectron spectroscopy (APXPS), which provides direct spectroscopic evidence of the spillover process as it unfolds. By integrating experimental observations with theoretical models, the researchers unlocked a comprehensive understanding of how hydrogen interacts with reducible oxide surfaces and influences their catalytic properties.

Operando APXPS at the ALS

This study focused on WO₃ thin films “decorated” with Pt metal clusters that facilitate hydrogen activation and dissociation. To directly visualize the stepwise evolution of hydrogen spillover on WO₃, the researchers employed APXPS at ALS Beamline 9.3.2, a technique pioneered at the ALS and uniquely suited for studying solid–gas interfaces in real time under realistic (“operando”) reaction conditions.

APXPS detected the oxidation states of tungsten and the presence of surface hydrogen species as the samples were exposed over time to hydrogen gas at various temperatures. The tunable incident photon energy allowed selective analysis of different elements (including differentiating between various hydrogen species—molecular, protonic, or hydride-like) at variable depths, enabling the researchers to track hydrogen-induced changes with high precision. The ability to collect real-time spectra while exposing the sample to hydrogen enabled the detection of intermediates that would be difficult to observe with other methods.

Furthermore, by combining the APXPS experimental observations with first-principles-based microkinetic modeling and simulations, the researchers gained a comprehensive understanding of the reaction mechanisms underlying hydrogen spillover.

Image: Artistic depiction of a tungsten trioxide (WO₃) surface (purple/red) “decorated” with a platinum nanocluster (metallic gray). Green arrows trace the evolution of hydrogen (white) from gas form (H₂) to dissociation into H⁺ on the platinum, to spillover (migration) onto the WO₃ surface, and, at elevated temperatures, desorption as water vapor (H₂O) and diffusion into the bulk.

Self-Generated Magnetic Handles in Modified Mammalian Cells

2025/05/212025/05/22

CIENTIFIC ACHIEVEMENT

Researchers genetically engineered mammalian cells to produce their own magnetic “handles” and revealed their magnetic, physical, and chemical properties, measured in part at the Advanced Light Source (ALS).

SIGNIFICANCE AND IMPACT

The work provides a foundation for future bioengineering efforts aimed at enabling genetically controlled magnetic manipulation of molecular processes in living mammalian cells.

An internal compass for cells

Some bacteria have evolved the remarkable ability to align themselves with Earth’s magnetic field, owing to self-synthesized chains of magnetic nanocrystals that provide them with an internal compass needle. It’s thought that following magnetic field lines helps these single-celled organisms propel themselves toward optimal (for them) environments.

Multicellular organisms—including humans—can also benefit from cellular compasses, or magnetic “handles,” to maneuver cells as needed. Possible future applications include cell sorting, cell tracking (and imaging), and targeted drug delivery. However, the genetic programming that allows bacteria to natively produce magnetic organelles is lacking in mammals, and attempts to introduce magnetic agents into mammalian cells are stymied by cellular defense mechanisms.

To get around this, a large multinational research collaboration based in Germany genetically modified mammalian cells to self-produce protein nanocompartments in which iron oxides can be created and stored. The group then characterized the magnetic, physical, and chemical properties of the nanocompartment cargo and demonstrated the ability to manipulate the resulting live engineered cells using magnetic fields.

Sample synthesis and analysis

The researchers introduced into mammalian cells a set of genetic constructs (engineered DNA) for the overexpression of encapsulin, the protein building block of nanocompartment shells produced by Quasibacillus thermotolerans bacteria. Also included were constructs for a red fluorescent protein for detection purposes and a ferroxidase, an enzyme that promotes the oxidation of reactive Fe²⁺ to more stable Fe³⁺ (to facilitate iron oxide accumulation). Cellular uptake of Fe²⁺ was enhanced by co-expression of a protein that transports iron into cells. Finally, to provide a source of iron, the cell medium was supplemented with ferrous ammonium sulfate.

After 72 hours, the modified cells were sorted using magnetic-activated cell sorting (MACS) columns. Within the cell fraction retained in the MACS columns, the researchers discovered encapsulin shells that contained ultrafine (1–3 nm) quasicrystalline ferric oxide/hydroxide cores that exhibited ferrimagnetism and paramagnetism. However, determining the precise identity of the magnetic particles required the ability to distinguish between different species of iron oxide at the scale of individual particles.

Image: Mammalian cells were genetically modified to synthesize protein nanocompartments in which iron oxide biomineralization takes place. The compartments, naturally produced by the bacterium Quasibacillus thermotolerans (Qt), are constructed of proteins called encapsulins. The shell size and symmetry are indicated by a triangulation number (T = 4 corresponds to a relatively large, ~43 nm shell). Co-expressed with the encapsulin was a ferroxidase (IMEF), which facilitates the accumulation of iron oxide by catalyzing oxidation of Fe²⁺ to Fe³⁺.

A Deeper Look into Emergent Magnetism at Interfaces

2025/05/162025/05/19

Recently, a research team led by Alexander Gray from Temple University shed new light on interfacial ferromagnetism in superlattices—i.e., multilayer structures composed of thin antiferromagnetic and paramagnetic layers. Their findings offer detailed insights into the electronic and structural factors influencing atomic-level interactions at magnetic interfaces.

“Nanoscale control of interfacial magnetic phenomena is central to spintronic device innovation,” said Gray. “Experiments using polarized x-rays get us closer to that goal by allowing us to extract depth-resolved magnetic profiles from stacks of alternating magnetic layers.”

At Advanced Light Source (ALS) Beamline 4.0.2, the team probed superlattices of antiferromagnetic CaMnO₃ and paramagnetic CaRuO₃ using x-ray resonant magnetic reflectivity (XRMR) together with x-ray magnetic circular dichroism (XMCD). When these techniques are combined, they can provide sensitivity to magnetization direction, elemental composition, and (by varying the x-ray incidence angle) sample depth.

Graduate student Jay Paudel, who led the measurements and data analysis and is now a postdoctoral scholar at the ALS, along with ALS Beamline Scientist Christoph Klewe, discovered that interfacial ferromagnetism exhibits an asymmetric distribution and may extend beyond the interfacial layer, suggesting more complex interfacial behavior than previously recognized.

“These results challenge previous assumptions by demonstrating that interfacial magnetism can span multiple unit cells and that the alternating interfaces are not magnetically symmetric, as confirmed independently by both depth-resolved and depth-averaged x-ray resonant magnetic measurements,” said Paudel.

Density functional calculations from Nicola Spaldin’s group at ETH Zurich identified the driving force behind this phenomenon as a double-exchange mechanism facilitated by charge transfer from Ru to Mn across the interface. Furthermore, the calculations revealed that oxygen vacancies significantly influence the magnitude of interfacial magnetic moments, offering a potential method to manipulate interfacial ferromagnetism.

“We are seeing more and more that defects such as oxygen vacancies, which we used to think of as a nuisance, can actually be used as a design tool to engineer functionalities such as magnetism at interfaces,” said Spaldin. Samples for these experiments were grown using pulsed laser deposition by Jak Chakhalian’s group at Rutgers University.

The study enhances our understanding of interfacial magnetism, presenting practical strategies for controlling magnetic interfaces and fostering future innovations in magnetic storage and spintronic technologies.

From Sequence to Structure: A Fast Track for RNA Modeling

2025/05/152025/05/15

In Biology 101, we learn that RNA is a single, ribbon-like strand of base pairs that is copied from our DNA then read like a recipe to build a protein. But there’s more to the story. Some RNA strands fold into complex shapes that allow them to drive cellular processes like gene regulation and protein synthesis, or catalyze biochemical reactions. We know that these active molecules, called non-coding RNAs, are present in all life forms, yet we’re just starting to understand their many roles – and how they can be harnessed for applications in environmental science, agriculture, and medicine.

To study – and potentially modify – the functions of non-coding RNAs, we need to determine their structure. Scientists from Lawrence Berkeley National Laboratory (Berkeley Lab) and the Hebrew University of Jerusalem have developed a streamlined process that predicts the structure of an RNA molecule down to the atomic level. Members of the research community can come to Berkeley Lab’s Advanced Light Source (ALS) user facility knowing nothing more than the molecule’s nucleotide sequence and get a structure, or they can do it themselves using the team’s open-source software.

“We were looking at the bigger picture with structure prediction, like how we can go from A to Z rather than working on A, B, and D. That’s what we try to do at Berkeley Lab, make it user friendly,” said Michal Hammel, a staff scientist in Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) division. Hammel co-developed the process, called SOlution Conformation PrEdictor for RNA (SCOPER), with MBIB colleague Scott Classen and Hebrew University collaborators Dina Schneidman-Duhovny and Edan Patt.

A paper describing SCOPER was recently published in Biophysical Journal.

Historically, it has ranged between difficult to impossible to accurately determine the three-dimensional atomic blueprint of a folded RNA because they rarely convert into a neat crystalline form to be imaged with X-ray crystallography. And because the twists and folds of the RNA strand move around as the molecule functions, there are actually multiple correct structures.

In recent years, artificial intelligence (AI) tools like AlphaFold have become very accurate at generating protein structure predictions based on amino acid sequence, making life a lot easier for scientists worldwide and greatly accelerating the pace of drug discovery. These algorithms have been expanded to RNA structures, but the accuracy remains middling. Getting a reliable model currently involves combining the outputs of multiple computational tools and imaging data. It’s a long process, and still fraught with uncertainty.

SCOPER has simplified it significantly. Say you want to study a new RNA: First, put the nucleotide sequence into one of the open-source, AI-based structure prediction tools available today. Then, take your sample to a small angle X-ray scattering (SAXS) facility for characterization. Better yet, let Hammel and his colleagues at the ALS’s SAXS beamline get that data for you.

Take the SAXS data and predicted structures, and put them through SCOPER’s pipeline. The first step uses an existing program to generate possible flexible arrangements of the RNA from the predicted static structures. Next, a new machine learning program, developed and trained on existing atomic structures by Patt, refines the structures by adding the placements of magnesium ions. Inside cells, positively charged magnesium ions interact with negatively charged RNAs to keep them folded stably. Their presence also helps elucidate structure when using SAXS.

Next, SCOPER generates simulated SAXS data representing the theoretical structures and compares them with the real-world SAXS data to determine which structure is correct.

Image: These renderings show RNA structures that were used to evaluate the accuracy of the new SCOPER process. The AI-generated initial structure predictions based on sequence (blue) is pictured with the refined predicted structure generated by SCOPER (red), which includes the placement of magnesium ions (violet).

Credit: Michal Hammel/Berkeley Lab

Building a Gated-Access Fast Lane for Ions

2025/04/252025/04/28

In organic conductors where charge is carried by both electrons and ions, scientists have discovered a way to make the ions move more than ten times faster than in comparable ion-tranport methods. The results could apply to a host of areas, including improved battery charging, biosensing, soft robotics, and neuromorphic computing.

Organic mixed ionic-electronic conductors (OMIECs) combine the advantages of the ion signaling used by many biological systems with the electron signaling used by computers. However, exactly how these conductors coordinate movement of both ions and electrons has not been well understood.

“Being able to control these signals that life uses all the time in a way that we’ve never been able to do is pretty powerful,” said Brian Collins, WSU physicist and senior author on the study. “This acceleration could also have benefits for energy storage, which could be a big impact.”

Collins and his colleagues observed that ions in OMIECs moved slowly relative to electrons. Because of their coordinated movement, the slow ion movement also slowed the electrical current. To solve this problem, the researchers created a straight, nanometer-sized channel just for the ions, which moved through the channel more than ten times faster than they would through water alone.

At the Advanced Light Source (ALS), resonant soft x-ray scattering (RSoXS) at Beamline 11.0.1.2 was used to explore the interplay between the superhighway effect and the internal nano-morphology of the channel.

Gated access to the channel was achieved by lining it with hydrophilic molecules, which attracted ions dissolved in water. Chemical reactions could turn this attraction off, opening and closing the channel, much the same way that biological systems control access through cell walls.

Image: Record ion speeds are achieved in organic conductors where local molecules can attract or repel ions from nanochannels that act as ion superhighways. Credit: Second Bay Studios

Mapping the Quantum Landscape of Electrons in Solids

2025/03/312025/04/02

SCIENTIFIC ACHIEVEMENT

Using data from the Advanced Light Source (ALS), researchers found a way to reconstruct quantum geometric tensors (QGTs)—mathematical entities that encode how an electron’s wave function is shaped by its quantum environment.

SIGNIFICANCE AND IMPACT

The mapping of QGTs enables the discovery and control of novel quantum phenomena such as superconductivity and unconventional electronic phases.

Toward a second quantum revolution

The development of quantum mechanics—featuring concepts such as quantized energy levels, wave-particle duality, and the uncertainty principle—revolutionized physics in the early 20th century. It led to the rise of the wave function as a way to describe, mathematically, the quantum state of a system (such as electrons in a crystal).

A more recent development, the quantum geometric tensor (QGT) is also a mathematical entity, this time describing how wave functions are affected by changes in a material’s quantum “landscape” (e.g., the material’s structure, its topological properties, electron-electron interactions, and spin-orbit coupling). The QGT is therefore a fundamental physical concept that helps explain a range of quantum phenomena in materials. However, despite its importance, a generic method for measuring the QGT in solids has been lacking.

In this work, researchers outline a way to measure the momentum-resolved QGT of solids using angle-resolved photoemission spectroscopy (ARPES). In addition to being fundamentally interesting, the QGT is also important for potential applications in next-generation microelectronics and advanced energy technologies. Studies involving the QGT will contribute immensely to what’s been dubbed the “second quantum revolution,” focusing on the control and harnessing of quantum nature at the device scale.

Introducing the quasi-QGT

Previously, the tools available for determining the QGT could only measure momentum-integrated phenomena, which are summed over all electron momenta. However, the QGT is, by definition, momentum resolved. To overcome this problem, a collaboration—primarily between theorists from Seoul National University and experimentalists from Massachusetts Institute of Technology (MIT)—introduced a quasi-QGT that is proportional to the QGT in two-band systems and an excellent approximation in multiband systems.

Like the QGT, the quasi-QGT is a complex quantity with real and imaginary parts. However, unlike the QGT, the real and imaginary parts of the quasi-QGT correspond to quantities measurable using ARPES: the momentum-resolved effective mass of electrons (i.e., the band Drude weight) for the real part, and the orbital angular momentum (OAM) of photoemitted electrons for the imaginary part.

Image: The curvature of the surface where it touches the sphere depicts one aspect of an electron’s quantum landscape: the momentum-resolved effective mass of electrons in a solid. In this work, researchers established that measurements of this quantity plus the orbital angular momentum of photoemitted electrons—both accessible using angle-resolved photoemission spectroscopy (ARPES)—enable the experimental reconstruction of the QGT. The sphere is shown as a local approximation to the curvature of the surface.

Credit: Comin lab/MIT

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