Research, teaching and outreach in Physics at UW–Madison
X-ray imaging and spectroscopy
Zain Abhari selected for SACLA graduate internship
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Zain Abhari on a tour at Himeji Castle, which is one of the last few fully intact castles in Japan and is located near the SACLA facility | Photo provided by Zain Abhari
Congrats to Physics PhD student Zain Abhari for being selected to the SACLA Research Support Program for Graduate Students. The one-year internship run by SACLA (the SPring-8 Angstrom Compact free electron LAser) accepts graduate students with a demonstrated interest in using X-ray free electron lasers (XFELs) for their research and provides them with training and beam time at the facility in Japan.
Prior to her acceptance in the program, Abhari had already spent time at SACLA as part of her research in Uwe Bergmann’s group. While there, her collaborator told her about the program and recommended she apply.
“My goal after the PhD is to work at one of these large-scale facilities, specifically the X-ray free electron lasers and there’s only six of them right now in the world,” Abhari says. “If I can get my foot in the door in Japan, or get the experience to then help me with any of the other ones, that would be pretty awesome.”
Abhari was also interested in the program because SACLA’s laser aligns well with the goals of her thesis research, which is to obtain intense, stable XFEL pulses to apply to different spectroscopy techniques. For about the past decade, XFEL has allowed researchers to make ultrafast movies of molecular changes, essentially helping them to see chemical reactions take place. But x-ray lasers are “dirty,” and they contain multiple wavelengths of light of varying intensity. Last year, Bergmann and his colleagues somewhat accidentally discovered a way to make the pulses cleaner through two intense, femtosecond-spaced pulses.
Even though the researchers think they know how the useful pulses work, producing and controlling them are a completely different story — and one that Abhari hopes to unravel in her research.
“Right now, they’re just random,” Abhari says. “So the goal is to understand them. And then if we understand them, can we control them? If we can control them, can we apply them?”
Abhari will travel to Japan for three months beginning in September, where the program provides on-campus housing and time on the laser. Without the access she is now granted by this internship, her research would have been much more focused on short rounds of data collection followed by off-site data analysis.
“Now, I can get my hands on the laser and collect data to try to understand parameters that allow us to get the specific output we’re looking for,” Abhari says. “I have data that allude me to what those parameters will be, but now in real time, I can be like, ‘If I do this, I see this; if I do that, I see that.’”
In addition to her thesis research, Abhari will be working with her SACLA collaborators on a machine learning project to optimize beam focusing, and helping learn about and improve a portable beam nanofocusing apparatus.
Physics researchers named part of $18M NSF materials research center
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The Department of Physics is part of a six-year, $18 million grant awarded to the University of Wisconsin–Madison’s Materials Research Science and Engineering Center (MRSEC) by the National Science Foundation. The award creates a National User Facility for X-FAST (XUV Femtosecond Absorption Spectroscopy Tabletop), a powerful XUV laser developed in the department.
Uwe Bergmann
MRSEC brings together 30 affiliated faculty from across nine departments to answer fundamental questions in materials science. The two interdisciplinary research groups (IRGs) funded by the award include one on stability in supercooled glasses and a second on magnetics in strained membranes. Physics professor Uwe Bergmann is a co-lead on IRG-2 along with materials science and engineering professor and physics affiliate faculty member Jason Kawasaki.
“The idea of our IRG is to make thin membranes of materials and then by straining them in various ways, changing their properties,” Bergmann says. “And our specific role is that we are in charge of x-ray and ultrafast characterization.”
The membranes being studied are 20-50 nanometer thin, crystalline materials. Kawasaki developed a way to produce very strong strains, up to 10%, which disrupt the perfect crystal lattice when applied. Once the atoms are pulled out of equilibrium by the strain, the energy levels change a little, the bonding changes, and exotic new phases are introduced. Bergmann is part of the IRG-2 team whose role is to perform ultrafast characterization of these changes. His team then informs the simulations group, whose theoretical calculations inform Kawasaki’s sample synthesis group.
“This is the typical circle between making the sample, finding out its properties, and understanding the properties — and then feeding it back to make new samples,” Bergmann says. “We’re trying to characterize these properties so that we can tailor them, so we can control them with light.”
The X-FAST XUV laser developed in the Bergmann group | courtesy of the Bergmann group
Being able to control the materials’ properties with fast, electromagnetic light pulses could be a boon to faster, more efficient computing and telecommunications, an important potential application of this work.
Bergmann’s role in MRSEC stems from his expertise in ultrafast x-ray spectroscopy. Since joining the department of physics in 2020, his group has developed and built the XUV transient absorption high harmonic generation instrument that will be used to characterize the changes in properties as a result of intense strain on the materials following ultrafast excitations. As part of the new funding, the X-FAST instrument is now a National User Facility, which provides access to researchers across the country. In addition, the new award is funding an upgrade that includes the terahertz (microwave to infrared) range for sample excitation, a range that team member and physics affiliate professor Jun Xiao has developed.
In addition to the two research thrusts, MRSEC also runs a robust outreach and education program as part of the funding.
MRSEC is one of 21 NSF-funded centers that conduct fundamental materials research, education and outreach at the nation’s leading research institutions. Paul Voyles, professor of materials science and engineering professor at UW–Madison, is MRSEC’s director.
Researchers capture elusive missing step in the final act of photosynthesis
Photosynthesis plays a crucial role in shaping and sustaining life on Earth, yet many aspects of the process remain a mystery. One such mystery is how Photosystem II, a protein complex in plants, algae and cyanobacteria, harvests energy from sunlight and uses it to split water, producing the oxygen we breathe. Now researchers from the Department of Energy’s Lawrence Berkeley National Laboratory and SLAC National Accelerator Laboratory, together with collaborators from the University of Wisconsin–Madison and other institutions have succeeded in cracking a key secret of Photosystem II.
Uwe Bergmann
Using SLAC’s Linac Coherent Light Source (LCLS) and the SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan, they captured for the first time in atomic detail what happens in the final moments leading up to the release of breathable oxygen. The data reveal an intermediate reaction step that had not been observed before.
The results, published today in Nature, shed light on how nature has optimized photosynthesis and are helping scientists develop artificial photosynthetic systems that mimic photosynthesis to harvest natural sunlight to convert carbon dioxide into hydrogen and carbon-based fuels.
“The splitting of water to molecular oxygen by photosynthesis has dramatically reshaped our early planet, eventually leading to complex life forms that rely on oxygen for respiration, including ourselves,” says Uwe Bergmann, a physics professor at UW–Madison. “Capturing the final steps of this process in real time with x-ray laser pulses, and bringing to light the individual atoms involved, is thrilling and adds an important piece to solving this over 3-billion-year-old puzzle.”
In 15th century Germany, Johannes Gutenberg developed a printing press, a machine that allowed for mass production of texts. It is considered by many to be one of the most significant technological advancements of the last millennium.
Though Gutenberg often receives credit as the inventor of the printing press, sometime earlier, roughly 5,000 miles away, Koreans had already developed a movable-type printing press.
There is no question that East Asians were first. There is also no question that Gutenberg’s invention in Europe had a far greater impact.
“What is not known is whether Gutenberg knew about the Korean printing or not. And if we could shed light on that question, that would be earth shattering,” says Uwe Bergmann, a professor of physics at the University of Wisconsin–Madison who, with UW–Madison physics graduate student Minhal Gardezi, is part of a large, interdisciplinary team that is analyzing historical texts.
He adds: “But even if we don’t, we can learn a lot about early printing methods, and that will already be a big insight.”
These texts include pages from a Gutenberg bible and Confucian texts, and they’re helping investigate these questions. The team includes 15th century Korean texts experts, Gutenberg experts, paper experts, ink experts and many more.
One of the leaves scanned was printed by a Korean movable type printing press in 1442. One of the team members from UNESCO, Angelica Noh, traveled with the preserved documents from Korea to SLAC. IMAGE PROVIDED BY MINHAL GARDEZI
How did two physicists end up participating in a seemingly very non-physics cultural heritage project? Bergmann had previously worked on other historical text analyses, where he pioneered the application of a technique known as X-ray fluorescence (XRF) imaging.
In XRF imaging, a powerful machine called a synchrotron sends an intense and very small X-ray beam — about the diameter of a human hair — at a page of text at a 45-degree angle. The beam excites electrons in the atoms that make up the text, requiring another electron to fill in the space left by the first (all matter is made up of atoms, which contain even smaller components called electrons).
The second electron loses energy in the process, and that energy is released as a small flash of light. A detector placed strategically nearby picks up that light, or its X-ray fluorescence, and measures both its intensity and the part of the light spectrum to which it belongs.
“Every single element on the periodic table emits an X-ray fluorescence spectrum that is unique to that atom when hit with a high-energy X-ray. Based on its ‘color,’ we know exactly which element is present,” says Gardezi. “It’s a very high-precision instrument that tells you all the elements that are at every location in a sample.”
With this information, researchers can effectively create an elemental map of the document. By rapidly scanning a page across the X-ray beam, they can create a record of the XRF spectrum at each pixel. One page can produce several million XRF spectra.
This summer, Bergmann and Gardezi were part of a team that used XRF scanning at the SLAC National Accelerator Laboratory in California to produce elemental maps of several large areas from original pages of a first-edition, 42-line Gutenberg Bible (dating back to 1450 to 1455 A.D.) and from Korean texts dating back to the early part of that. century.
They scanned the texts at a rate of around one pixel every 10 milliseconds, then filtered the data by elemental signature, providing high-resolution maps of which elements are present and in what relative quantities.
A photograph of a scanned Korean text. The white dotted box indicates the areas shown in the middle and bottom panels. Each element produces a unique X-ray fluorescence. After scanning the text, the researchers applied filters for the known XRF patterns of different elements and created a color-coded heat-map of their abundance, from lowest (blue) to highest (red). An element found in only small quantities is in the red circles in the bottom part of the image. IMAGE PROVIDED BY MINHAL GARDEZI
In a way, the work is like digging for treasure from an old map — Gardezi says the researchers do not know exactly what they are looking for, but they are most interested in the unexpected.
For example, she recently presented early results of scans to the team, to demonstrate the approach had worked and that the researchers could separate out different elements. It turns out this isn’t what the team found most interesting.
“Instead, these scholars spent 15-to-20 minutes talking about, ‘Why is (this element) present?’ and coming up with hypotheses,” Gardezi says. “As physicists, we wouldn’t even recognize if something is surprising or not. It’s really this interdisciplinary aspect that tells us what to look for, what the smoking gun is.”
As more questions arise based on the elemental analyses, Bergmann and Gardezi will help guide the team to address those questions quantitatively. They are already planning to recreate some early printings in the lab — with known types, papers and inks — then compare these XRF scans with the originals.
The research may never definitively determine if Gutenberg knew about the Korean presses or if he developed his press independently. But without access to the original presses themselves, these texts hold the only clues to understanding the nature of these transformative machines.
“The more you read about it, the more you learn that there is less certainty about several things related to early printing presses,” Bergmann says. “Maybe this technique will allow us to view these prints as a time capsule and gain invaluable insight into this watershed moment in human history.”
For tens of thousands of years, Aboriginal Australians have created some of the world’s most striking artworks. Today their work continues long lines of ancestral traditions, stories of the past and connections to current cultural landscapes, which is why researchers are keen on better understanding and preserving the cultural heritage within.
Secretions called exudate cover parts of the spike of a Xanthorrhoea plant — colloquially called “grass tree” or “yakka” — used in aboriginal art. PHOTO COURTESY FLINDERS UNIVERSITY, SOUTH AUSTRALIA
In particular, knowing the chemical composition of pigments and binders that Aboriginal Australian artists employ could allow archaeological scientists and art conservators to identify these materials in important cultural heritage objects. Now, researchers are turning to X-ray science to help reveal the composition of the materials used in Aboriginal Australian cultural heritage – starting with the analysis of century-old samples of plant secretions, or exudates.
Aboriginal Australians continue to use plant exudates, such as resins and gums, to create rock and bark paintings and for practical applications, such as hafting stone points to handles. But just what these plant materials are made of is not well known.
Therefore, scientists from six universities and laboratories around the world turned to high-energy X-rays at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory and the synchrotron SOLEIL in France. The team aimed X-rays at ten well-preserved plant exudate samples from the native Australian genera Eucalyptus, Callitris, Xanthorrhoea and Acacia. The samples had been collected more than a century ago and held in various institutions in South Australia.
The results of their study were clearer and more profound than expected.
“We got the breakthrough data we had hoped for,” says Uwe Bergmann, physicist at the University of Wisconsin–Madison and former SLAC scientist who develops new X-ray methods. “For the first time, we were able to see the molecular structure of a well-preserved collection of native Australian plant samples, which might allow us to discover their existence in other important cultural heritage objects.”
Researchers today published their results in the Proceedings of the National Academy of Sciences.
Uwe Bergmann
Looking below the surface
Over time, the surface of plant exudates can change as the materials age. Even if these changes are just nanometers thick, they can still block the view underneath it.
“We had to see into the bulk of the material beneath this top layer or we’d have no new information about the plant exudates,” SSRL Lead Scientist Dimosthenis Sokaras says.
Conventionally, molecules with carbon and oxygen are studied with lower-energy, so-called “soft” X-rays, that would not be able to penetrate through the debris layer. For this study, researchers sent high-energy X-ray photons, called “hard” X-rays, into the sample. The photons squeezed past foggy top layers and into the sample’s elemental arrangements beneath. Hard X-rays don’t get stuck in the surface, whereas soft X-rays do, Sokaras says.
Once inside, the high-energy photons scattered off of the plant exudate’s elements and were captured by a large array of perfectly aligned, silicon crystals at SSRL. The crystals filtered out only the scattered X-rays of one specific wavelength and funneled them into a small detector, kind of like how a kitchen sink funnels water drops down its drain.
Next, the team matched the wavelength difference between the incident and scattered photons to the energy levels of a plant exudate’s carbon and oxygen, providing the detailed molecular information about the unique Australian samples.
Century-old plant exudate samples in amber jars. Researchers mapped the chemistries of these samples using high-energy photons, knowledge that will help study and preserve the work of aboriginal artists who used plant material. PHOTO COURTESY FLINDERS UNIVERSITY, SOUTH AUSTRALIA
A path for the future
Understanding the chemistries of each plant exudate will allow for a better understanding of identification and conservation approaches of Aboriginal Australian art and tools, Rafaella Georgiou, a physicist at Synchrotron SOLEIL, said.
“Now we can go ahead and study other organic materials of cultural importance using this powerful X-ray technique,” she says.
Researchers hope that people who work in cultural heritage analysis will see this powerful synchrotron radiation technique as a valuable method for determining the chemistries of their samples.
“We want to reach out to that scientific community and say, ‘Look, if you want to learn something about your cultural heritage samples, you can come to synchrotrons like SSRL,’” Bergmann says.
SSRL is a DOE Office of Science user facility. In addition to SSRL, parts of this research were carried out at SOLEIL in France and three CNRS laboratories (PPSM, IPANEMA, IMPMC). The University of Pisa, the Université Paris-Saclay, the University of Melbourne, Flinders University, the Australian Synchrotron International Synchrotron Access Program, and other organizations also supported this research.
Fringe benefits: new technique makes x-rays more laser-like
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Detecting a chemical change is often easy: colors may change, heat may be released, or something may smell different. Seeing reactions at the molecular level is not quite so easy, but knowing exactly when and how chemical bonds form or atoms move around is crucial to understanding chemical processes.
X-ray pulses allow researchers to create real-time movies of chemical reactions at the molecular scale (click on image to see animation)
In a new study published March 15 in Proceedings of the National Academy of Sciences, University of Wisconsin–Madison physics professor Uwe Bergmann and his collaborators have turned ultrafast x-ray pulses into something more akin to an optical laser, with cleaner, directional pulses. Their work may lead to visualizing chemical reactions faster than ever at the atomic scale.
“This work is the first step to do with x-rays the same kind of [techniques] which you do with regular lasers,” says Bergmann, the study’s senior author. “We have opened a time window for looking at chemical processes with attosecond [one billionth of one billionth of a second] precision. It’s a new frontier.”
Uwe Bergmann
Around a decade ago, researchers began using powerful x-ray free-electron lasers, which allow them to make ultrafast movies of molecular changes in real time on the femtosecond scale (one thousand times slower than an attosecond). Compared to visible lasers, which provide clean, single-wavelength beams of light, x-ray lasers are somewhat dirty: they contain multiple wavelengths of light of randomly varying intensity.
“What all scientists have done, and are still doing, is that you just adapt to what you get and then you design your experiments around them,” Bergmann says. “That also means that certain experiments, which in the optical laser regime are now standard, have not been possible.”
Bergmann and his colleagues somewhat accidentally discovered a way to make x-rays more like an optical laser. In their experimental setup, they shine intense but dirty x-ray pulses at a manganese sample. When these pulses hit a manganese atom, a lower-level electron is ejected and the hole it leaves is rapidly filled by a higher-level electron. The energy difference is emitted as a photon of a characteristic color. Very intense pulses can create enough of these holes. An emitted photon can effectively stimulate the emission of another one, leading to an avalanche of stimulated X-ray emission, mostly in the forward direction towards their detector.
Every so often, the detector that captures these stimulated emissions showed something they were not expecting: strong fringes, the characteristic pattern that results from constructively and destructively interfering signals. The fringes suggested that they had observed two x-ray emission pulses, separated by only a few femtoseconds.
“We were confused,” Bergmann says. “How did such a pair of x-ray pulses come about?”
After many discussions, calculations, and simulations, the team ruled out many possible explanations, until they finally realized what had happened: occasionally, two of the many spikes in the dirty pulses were much stronger than the rest of them. When these strong spikes occurred a few femtoseconds apart, and each had enough intensity, a clean pair of stimulated x-ray emission pulses emerged.
Two strong x-ray pulses hit the manganese sample, are stretched through the monochromator, and overlap, leading to the characteristic fringes.
Before these two pulses reach the detector, they first travel through a monochromator — essentially a prism that stretches light, much like how white light passing through a clear prism is stretched into a rainbow. These stretched pulses then overlap timewise, and those frequencies that are in phase with each other can add up to become more intense or cancel each other out into dark troughs. Hence, the fringes.
“At times, each signal is rather clean and of similar strength, and one obtains very strong interference fringes,” Bergmann says. “We know that the fringe spacings are directly related to the time difference of the two pulses, and because we can measure them very precisely, we can obtain their time difference with extreme, attosecond precision.”
Currently, these pulse pairs are generated very rarely, Bergmann and his collaborators will work with the accelerator scientists to find ways to manipulate the ‘dirty’ pulses and enhance the chance of producing the pairs. They are optimistic that their work opens the door to new applications of such x-ray pulse pairs — the types of techniques that are used commonly with visible laser light.
“We’re trying to move nonlinear laser optics into the x-ray regime,” Bergmann says. “In the x-ray regime, you can probe certain phenomena that you just cannot optically access. X-ray wavelengths are comparable to the distances between atoms, and we can knock out lower-level electrons to get element specificity with them.”
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Bergmann’s contribution to this research was funded in part by the U.S. Department of Energy, Laboratory Directed Research and Development program at SLAC National Accelerator Laboratory (DE-AC02-76SF00515). Other authors were supported by various funding as described in the study.
Bucket brigades and proton gates: Researchers shed new light on water’s role in photosynthesis
Photosystem II is a protein in plants, algae and cyanobacteria that uses sunlight to break water down into its atomic components, unlocking hydrogen and oxygen. A longstanding question about this process is how water molecules are funneled into the center of Photosystem II, where water is split to produce the oxygen we breathe. A better understanding of this process could inform the next generation of artificial photosynthetic systemsthat produce clean and renewable energy from sunlight and water.
In a paper published last week in Nature Communications, an international collaboration between scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (LBNL), SLAC National Accelerator Laboratory and several other institutions uncovers how the protein takes in water and how hydrogen is removed in order to release the oxygen molecules.
Uwe Bergmann
“Plants use the energy from sunlight to split two water molecules and produce the oxygen we breath. The study shows for the first time atomic-resolution snapshots of the likely channel and gate, where the water molecules arrive to the catalytic center to be split apart, and the channel where the protons are shuttled out during the splitting,” says Uwe Bergmann, the Martin L. Perl professor in ultrafast x-ray science at UW–Madison. “This information will help our understanding of one of the most fundamental reactions on earth, and how we might use sunlight in the future to create fuels.”
At SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, the team illuminated samples from cyanobacteria with ultrafast pulses of X-rays to collect both X-ray crystallography and spectroscopy data to simultaneously map the protein structure and how electrons flow in the protein. Through this technique, they are able to test competing theories of how Photosystem II splits water into oxygen. Over the past few years, the team has used this method to observe various steps of this water-splitting cycle at the temperature at which it occurs in nature.
Scientists at UW–Madison have been instrumental to developing these and related x-ray imaging methods over the last decade.
The center of the protein acts as a catalyst, which drives certain chemical reactions to happen in a highly efficient manner. This research seeks to unlock how nature has optimized this catalytic process over millions of years of evolution. A cluster of four manganese atoms and one calcium atom are connected by oxygen atoms, and surrounded by water and the outer layers of the protein. In the step the scientists looked at, water flows through a pathway into the center of the protein, where one water molecule ultimately forms a bridge between a manganese atom and a calcium atom. The researchers showed that this water molecule likely provides one of the oxygen atoms in the oxygen molecule produced at the end of the cycle.
The proposed proton gate around D1-E65, D2-E312, and D1-R334 in the open and closed state. | In Nature Communications, https://doi.org/10.1038/s41467-021-26781-z
Last year, the researchers discovered that Photosystem II ferries water into the center as if through a bucket brigade: Water molecules move in many small steps from one end of the pathway to the other. They also showed that the calcium atom within the center could be involved in shuttling the water in. In this most recent study, the researchers pinpoint, for the first time, the exact pathway where this process unfolds.
“This might prevent water from interacting with the center prematurely, resulting in unwanted intermediates such as peroxide that can cause damage to the enzyme,” said Jan Kern, staff scientist at LBNL and one of the corresponding authors.
The researchers also showed that there is another pathway dedicated to removing hydrogen protons generated during the water-splitting reaction. In the proton pathway, they discovered the existence of a “proton gate,” which blocks the proton from coming back to the center.
“These results show where and how the water molecules enter the catalytic site, and where the protons are released, advancing our understanding of how two waters may come together to form the oxygen we breathe,” said Junko Yano, senior scientist at LBNL and one of the corresponding authors. “It demonstrates that it is just not enough to determine the structure of the main catalytic center, but it is also important to understand how the entire protein carries out the reaction.”
In addition to SLAC and LBNL, the collaboration includes researchers from Uppsala University in Sweden; Humboldt University of Berlin; and the University of Wisconsin-Madison.
LCLS is a DOE Office of Science user facility. This research was supported by the Office of Science.
