From BNL- “National Synchrotron Light Source II User Profile: Stephan Hruszkewycz”

Brookhaven Lab

June 19, 2017
Laura Mgrdichian
mgrdichian@gmail.com

Stephan Hruszkewycz. No image credit.

Stephan Hruskewycz is an assistant physicist in the Materials Science Division at the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

While he regularly conducts research at Argonne’s own synchrotron user facility, the Advanced Photon Source (APS), his work on the nanoscale structure and behavior of materials has led him to book beamtime at the DOE’s newest synchrotron, the National Synchrotron Light Source II (NSLS-II). Both NSLS-II and APS are DOE Office of Science User Facilities.

ANL APS

ANL APS

BNL NSLS-II

BNL NSLS II

What are you studying at NSLS-II?

The focus of our NSLS-II experiments has been to image defects and imperfections in the crystal lattice of nanoscale materials using a new imaging technique known as Bragg Projection Ptychography. Specifically, we have been studying stacking faults in nanowires made of III-V semiconductors, a class of semiconductor that results from the combination of elements from column III on the periodic table (mainly aluminum, gallium, and indium) and column V (nitrogen, phosphorous, arsenic, and antimony). These materials have properties that make them excellent for certain applications; for example, solar cells made of III-V cells are very efficient.

During our next run, we will be imaging strain fields in complex oxide thin-film nanostructures. These classes of materials have potential uses for energy conversion in solar and fuel cell applications, and their nanoscale structure plays a large role in performance. By studying these structures in detail, we may be able to figure out how to make these materials perform better.

Why is NSLS-II is particularly suited to your work?

The Hard X-ray Nanoprobe (HXN) beamline at NSLS-II delivers a coherent hard x-ray beam focused to a few tens of nanometers and the ability to rotate the sample and detector to enable Bragg diffraction with a nanofocused beam. We are capitalizing on the coherence and stability of the focused beam to convert a series of Bragg diffraction patterns measured from different overlapping positions of the sample into an image of the lattice structure inside a specific region of the crystal. The result provides an image with a resolution down to just a few nanometers, as well as picometer-level sensitivity to lattice distortions.

Tell us about your background and how you arrived at this field of research.

I have been interested for some time in developing new methods to exploit coherent hard x-rays to reveal of the structure and dynamics of materials. Recently, I have focused on applying these methods to materials with inhomogeneous internal lattice structures that dictate their overall properties, such as nanostructured oxide thin films and semiconductors. To me, this is an exciting area of research, one where cutting-edge materials science questions can be answered with new x-ray imaging methods at state-of-the-art synchrotron sources that deliver highly coherent beams.

Who else is involved in this work?

So far, I have been joined at NSLS-II by Megan Hill, a graduate student in Northwestern University’s Materials Science and Engineering Department; Martin Holt, a staff scientist in Argonne’s Center for Nanoscale Materials; and Brian Stephenson, a senior physicist in Argonne’s Materials Science Division.

See the full article here .

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One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

From LBNL: “Study Sheds Light on How Bacterial Organelles Assemble”

Berkeley Lab

June 22, 2017
Sarah Yang
scyang@lbl.gov
(510) 486-4575

Cheryl Kerfeld and Markus Sutter handle crystallized proteins at Berkeley Lab’s Advanced Light Source. (Credit: Marilyn Chung/Berkeley Lab)

Researchers at Berkeley Lab and MSU have obtained the first atomic-level view of an intact bacterial microcompartment, shown here. Credit: Markus Sutter/Berkeley Lab and MSU

Scientists with joint appointments at DOE’s Lawrence Berkeley National Laboratory and Michigan State University reveal the building blocks of bacteria. (Video Credit: Michigan State University)

Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing at atomic-level resolution the structure and assembly of the organelle’s protein shell.

The work, led by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Michigan State University (MSU), will appear in the June 23 issue of the journal Science. They studied the organelle shell of an ocean-dwelling slime bacteria called Haliangium ochraceum.

“It’s pretty photogenic,” said corresponding author Cheryl Kerfeld, a Berkeley Lab structural biologist with a joint appointment as a professor at the MSU-DOE Plant Research Laboratory. “But more importantly, it provides the very first picture of the shell of an intact bacterial organelle membrane. Having the full structural view of the bacterial organelle membrane can help provide important information in fighting pathogens or bioengineering bacterial organelles for beneficial purposes.”

These organelles, or bacterial microcompartments (BMCs), are used by some bacteria to fix carbon dioxide, Kerfeld noted. Understanding how the microcompartment membrane is assembled, as well as how it lets some compounds pass through while impeding others, could contribute to research in enhancing carbon fixation and, more broadly, bioenergy. This class of organelles also helps many types of pathogenic bacteria metabolize compounds that are not available to normal, non-pathogenic microbes, giving the pathogens a competitive advantage.

The contents within these organelles determine their specific function, but the overall architecture of the protein membranes of BMCs are fundamentally the same, the authors noted. The microcompartment shell provides a selectively permeable barrier which separates the reactions in its interior from the rest of the cell. This enables higher efficiency of multi-step reactions, prevents undesired interference, and confines toxic compounds that may be generated by the encapsulated reactions.

Unlike the lipid-based membranes of eukaryotic cells, bacterial microcompartments (BMCs) have polyhedral shells made of proteins.

“What allows things through a membrane is pores,” said study lead author Markus Sutter, MSU senior research associate and affiliate scientist at Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) division. “For lipid-based membranes, there are membrane proteins that get molecules across. For BMCs, the shell is already made of proteins, so the shell proteins of BMCs not only have a structural role, they are also responsible for selective substrate transfer across the protein membrane.”

Earlier studies revealed the individual components that make up the BMC shell, but imaging the entire organelle was challenging because of its large mass of about 6.5 megadaltons, roughly equivalent to the mass of 6.5 million hydrogen atoms. This size of protein compartment can contain up to 300 average-sized proteins.

The researchers were able to show how five different kinds of proteins formed three different kinds of shapes: hexagons, pentagons and a stacked pair of hexagons, which assembled together into a 20-sided icosahedral shell.

The intact shell and component proteins were crystallized at Berkeley Lab, and X-ray diffraction data were collected at Berkeley Lab’s Advanced Light Source and the Stanford Synchrotron Radiation Lightsource, both DOE Office of Science User Facilities.

LBNL/ALS

SLAC/SSRL

The study authors said that by using the structural data from this paper, researchers can design experiments to study the mechanisms for how the molecules get across this protein membrane, and to build custom organelles for carbon capture or to produce valuable compounds.

Other co-authors of the study are Basil Greber, an affiliate of Berkeley Lab’s MBIB division and a UC Berkeley postdoctoral fellow in the California Institute for Quantitative Biosciences, and Clement Aussignargues, a postdoctoral fellow at the MSU-DOE Plant Research Laboratory.

See the full article here .

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A U.S. Department of Energy National Laboratory Operated by the University of California

From SLAC: “How a Single Chemical Bond Balances Cells Between Life and Death”

SLAC Lab

June 22, 2017
Amanda Solliday

An optical laser (green) excites the iron-containing active site of the protein cytochrome c, and then an X-ray laser (white) probes the iron a few femtoseconds to picoseconds later. The critical iron-sulfur bond is broken as the optical laser heats the protein, and rebinds as the system cools. (Greg Stewart/SLAC National Accelerator Laboratory)

Slight changes in the machinery of a cell determine whether it lives or begins a natural process known as programmed cell death. In many forms of life—from bacteria to humans—a single chemical bond in a protein called cytochrome c can make this call. As long as the bond is intact, the protein transfers electrons needed to produce energy through respiration. When the bond breaks, the protein switches gear and triggers the breakdown of mitochondria, the structures that power the cell’s activities.

For the first time, scientists have measured exactly how much energy cytochrome c puts into maintaining that bond in a state where it’s strong enough to endure, but easy enough to break when the cell’s life span is ending.

They used intense X-rays from two facilities, the Linac Coherent Light Source (LCLS) X-ray free-electron laser and the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory.

SLAC/LCLS

SLAC/SSRL

The collaboration, led by Edward Solomon, professor of chemistry at Stanford University and of photon science at SLAC, published their results today in Science.

“This is a very general yet extremely important process in biochemistry, and with an X-ray laser we now have insight into how this regulation works,” says Roberto Alonso-Mori, LCLS staff scientist and a co-author of the study. “These are processes that are going on a million-fold in our bodies and everywhere there is life.”

The study marks the first time that anyone has been able to experimentally quantify how the rigid structure of the cytochrome c molecule supports this crucial bond between iron and sulfur atoms in what’s known as an entatic state, where the protein maintains a bond that is just strong enough to perform both of its jobs, says Michael Mara, lead author of the study and a former postdoctoral researcher at Stanford University, now at University of California, Berkeley.

“This was important because we had shown the bond is weak and shouldn’t be present at room temperature in the absence of the protein constraints,” says Solomon. “But the protein is able to contribute energy to keep this bond intact for electron transfer. In this LCLS experiment, we determined exactly how much energy the rest of the protein contributes to maintaining the bond: about 4 kcal/mol that is derived from an adjacent hydrogen bond network.”

“We were able to show how nature tunes this system to change the properties on a fundamental level and perform two very different functions,” Mara says. “The energy contribution by cytochrome c is really at a sweet spot. It makes me wonder what sort of similar effects you might see in other protein systems, and it makes us realize that there is exciting new science on the horizon.”

Ultrafast Changes

Cytochrome c is present in a wide range of life forms and contributes to both cellular respiration and programmed cell death, the pathway to the natural end of a cell’s life cycle. How exactly the state of the bond relates to these two functions had not yet been demonstrated or quantified.

Scientists knew from earlier studies that a particular iron-sulfur bond is key. When iron in the protein binds to sulfur contained in one of the protein’s amino-acid building blocks, cytochrome c participates in electron transfer. By transferring electrons, the protein helps generate energy needed for biological processes that maintain life.

But when cytochrome c encounters cardiolipin, a lipid present in the membrane of the cell’s mitochondria, the iron-sulfur bond breaks, and the protein becomes an enzyme that creates holes in the mitochondria’s outer membrane – the first step in programmed cell death.

These changes occur incredibly fast, in less than 20 picoseconds, so the experiment required ultrafast pulses of X-rays generated by LCLS to take snapshots of the process.

“We photoexcited the iron atoms in the protein’s active site—which contains an iron-rich compound known as heme—with an ultrafast laser before probing it with the LCLS X-ray pulses at different time delays,” says Alonso-Mori.

Each 50-femtosecond laser pulse heated the heme by a couple of hundred degrees. X-ray pulses from LCLS took images of what happened as the heat traveled from the iron to other parts of the protein. After 100 femtoseconds, the iron-sulfur bond would break, only to form again once the sample cooled. Watching this process allowed the scientists to measure energy fluctuations in real time and better understand how this critical bond forms and breaks.

“The entatic state concept is really interesting, but you have to come up with creative ways to demonstrate and quantify it,” says Ryan Hadt, a former Stanford University doctoral student on an Enrico Fermi Fellowship at Argonne National Laboratory who together with his advisor, Professor Solomon, came up with the idea for the experiment and co-wrote the initial proposal around the time LCLS first came online in 2009.

“Our research group was excited about this new instrument and wanted to use it to do a definitive experiment,” Hadt adds.

A Question Raised by Earlier Work

This experiment builds on an earlier study [JACS] conducted at SSRL that found that the iron-sulfur bond was quite weak, says Thomas Kroll, staff scientist at SSRL and lead author of this prior study.

In the latest study, spectroscopy at SSRL also built the framework for the LCLS pump-probe experiment. It allowed the scientists to compare what the molecule originally looked like to how it changed when the temperature rose.

“It’s important to understand how these proteins actually work,” Kroll says. “Because if you don’t understand how they work, how can we create better medicines in an informed and controlled way?”

Knowledge of cytochrome c’s function is also valuable to the fields of bioenergy and environmental science, since it is a critically important protein in bacteria and plants.

The DOE Office of Science and the National Institute of General Medical Sciences of the National Institutes of Health supported this research. The Structural Molecular Biology program at SSRL is funded by DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences. LCLS and SSRL are DOE Office of Science User Facilities.

See the full article here .

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SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From SLAC: “A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response”

SLAC Lab

June 22, 2017
Glennda Chui

Thymine – the molecule illustrated in the foreground – is one of the four basic building blocks that make up the double helix of DNA. It’s such a strong absorber of ultraviolet light that the UV in sunlight should deactivate it, yet this does not happen. Researchers used an X-ray laser at SLAC National Accelerator Laboratory to observe the infinitesimal leap of a single electron that sets off a protective response in thymine molecules, allowing them to shake off UV damage. (Greg Stewart/SLAC National Accelerator Laboratory)

In experiments at the Department of Energy’s SLAC National Accelerator Laboratory, scientists were able to see the first step of a process that protects a DNA building block called thymine from sun damage: When it’s hit with ultraviolet light, a single electron jumps into a slightly higher orbit around the nucleus of a single oxygen atom.

This infinitesimal leap sets off a response that stretches one of thymine’s chemical bonds and snaps it back into place, creating vibrations that harmlessly dissipate the energy of incoming ultraviolet light so it doesn’t cause mutations.

The technique used to observe this tiny switch-flip at SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser can be applied to almost any organic molecule that responds to light – whether that light is a good thing, as in photosynthesis or human vision, or a bad thing, as in skin cancer, the scientists said. They described the study in Nature Communications today.

SLAC/LCLS

“All of these light-sensitive organic molecules tend to absorb light in the ultraviolet. That’s not only why you get sunburn, but it’s also why your plastic eyeglass lenses offer some UV protection,” said Phil Bucksbaum, a professor at SLAC and Stanford University and director of the Stanford PULSE Institute at SLAC. “You can even see these effects in plastic lawn furniture – after a couple of seasons it can become brittle and discolored simply due to the fact that the plastic was absorbing ultraviolet light all the time, and the way it absorbs sun results in damage to its chemical bonds.”

Catching Electrons in Action

Thymine and the other three DNA building blocks also strongly absorb ultraviolet light, which can trigger mutations and skin cancer, yet these molecules seem to get by with minimal damage. In 2014, a team led by Markus Guehr ­– then a SLAC senior staff scientist and now on the faculty of the University of Potsdam in Germany – reported that they had found the answer: The stretch-snap of a single bond and resulting energy-dissipating vibrations, which took place within 200 femtoseconds, or millionths of a billionth of a second after UV light exposure.

But what made the bond stretch? The team knew the answer had to involve electrons, which are responsible for forming, changing and breaking bonds between atoms. So they devised an ingenious way to catch the specific electron movements that trigger the protective response.

It relied on the fact that electrons don’t orbit an atom’s nucleus in neat concentric circles, like planets orbiting a sun, but rather in fuzzy clouds that take a different shape depending on how far they are from the nucleus. Some of these orbitals are in fact like a fuzzy sphere; others look a little like barbells or the start of a balloon animal. You can see examples here.

No image caption or credit, but there is a comment,
“I see the distribution in different orbitals. So if for example I take the S orbitals, they are all just a sphere. So wont the 2S orbital overlap with the 1S overlap, making the electrons in each orbital “meet” at some point? Or have I misunderstood something?”

Strong Signal Could Solve Long-Standing Debate

For this new experiment, the scientists hit thymine molecules with a pulse of UV laser light and tuned the energy of the LCLS X-ray laser pulses so they would home in on the response of the oxygen atom that’s at one end of the stretching, snapping bond.

The energy from the UV light excited one of the atom’s electrons to jump into a higher orbital. This left the atom in a sort of tippy state where just a little more energy would boost a second electron into a higher orbital; and that second jump is what sets off the protective response, changing the shape of the molecule just enough to stretch the bond.

The first jump, which was previously known to happen, is difficult to detect because the electron winds up in a rather diffuse orbital cloud, Guehr said. But the second, which had never been observed before, was much easier to spot because that electron ended up in an orbital with a distinctive shape that gave off a big signal.

“Although this was a very tiny electron movement, the signal kind of jumped out at us in the experiment,” Guehr said. “I always had a feeling this would be a strong transition, just intuitively, but when we saw this come in it was a special moment, one of the best moments an experimentalist can have.”

Settling a Longstanding Debate

Study lead author Thomas Wolf, an associate staff scientist at SLAC, said the results should settle a longstanding debate about how long after UV exposure the protective response kicks in: It happens 60 femtoseconds after UV light hits. This time span is important, he said, because the longer the atom spends in the tippy state between the first jump and the second, the more likely it is to undergo some sort of reaction that could damage the molecule.

Henrik Koch, a theorist at NTNU in Norway who was a guest professor at Stanford at the time, led the study with Guehr. He led the effort to model, understand and interpret what happened in the experiment, and he participated in it to an unusual extent, Guehr said.

“He is extremely experienced in applying theory to methodology development, and he had this curiosity to bring this to our experiment,” Guehr said. “He was so fascinated by this research that he did something completely untypical of a theorist – he came to LCLS, into the control room, and he wanted to see the data coming in. I found that completely amazing and very motivating. It turned out that some of my previous thinking was completely right but other aspects were completely wrong, and Henrik did the right theory at the right level so we could learn from it.”

See the full article here .

Please help promote STEM in your local schools.

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SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From LBNL: “R&D Effort Produces Magnetic Devices to Enable More Powerful X-ray Lasers”

Berkeley Lab

June 20, 2017
Glenn Roberts Jr.
geroberts@lbl.gov
(510) 486-5582

Berkeley Lab demonstrates a record-setting magnetic field for a prototype superconducting undulator.

This Berkeley Lab-developed device, a niobium tin superconducting undulator prototype, set a record in magnetic field strength for a device of its kind. This type of undulator could be used to wiggle electron beams to emit light for a next generation of X-ray lasers.
(Credit: Marilyn Chung/Berkeley Lab)

Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL.

SLAC LCLS-II

This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

LBNL/ALS

ANL APS

SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

“This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.

The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

Researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Argonne National Laboratory have collaborated to design, build, and test two devices, called superconducting undulators, which could make X-ray free-electron lasers (FELs) more powerful, versatile, compact, and durable.

X-ray FELs are powerful tools for studying the microscopic structure and other properties of samples, such as proteins that are key to drug design, exotic materials relevant to electronics and energy applications, and chemistry that is central to industrial processes like fuel production.

The recent development effort was motivated by SLAC National Accelerator Laboratory’s upgrade of its Linac Coherent Light Source (LCLS), the nation’s only X-ray FEL. This upgrade, now underway, is known as LCLS-II. All existing X-ray FELS, including both LCLS and LCLS-II, use permanent magnet undulators to generate intense pulses of X-rays. These devices produce X-ray light by passing high-energy bunches of electrons through alternating magnetic fields produced by a series of permanent magnets.

Superconducting undulators (SCUs) offer another technical solution and are considered among the most promising technologies to improve the performance of the next generation FELs, and of other types of light sources, such as Berkeley Lab’s Advanced Light Source (ALS) and Argonne’s Advanced Photon Source (APS).

SCUs replace the permanent magnets in the undulator with superconducting coils. The prototype SCUs have successfully produced stronger magnetic fields than conventional undulators of the same size. Higher fields, in turn, can produce higher-energy free-electron laser light to open up a broader range of experiments.

Berkeley Lab’s 1.5-meter-long prototype undulator, which uses a superconducting material known as niobium-tin (Nb3Sn), set a record in magnetic field strength for a device of its design during testing at the Lab in September 2016.

“This is a much-anticipated innovation,” agreed Wim Leemans, Director, Accelerator Technology and Applied Physics (ATAP) . “Higher performance in a smaller footprint is something that benefits everyone – the laboratories that host the facilities, the funding agencies, and above all, the user community.”

Argonne’s test of another superconducting material, niobium-titanium, successfully reached its performance goal, and additionally passed a bevy of quality tests. Niobium-titanium has a lower maximum magnetic field strength than niobium-tin, but is further along in its development.
Photo – The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

The superconducting undulator R&D project at Berkeley Lab was a team effort. Among the contributors: (from left) Heng Pan, Jordan Taylor, Soren Prestemon, Ross Schlueter, Diego Arbelaez, Jim Swanson, Ahmet Pekedis, Scott Myers, Tom Lipton, and Xiaorong Wang. (Credit: Marilyn Chung/Berkeley Lab)

“The superconducting technology in general, and especially with the niobium tin, lived up to its promise of being the highest performer,” said Ross Schlueter, Head of the Magnetics Department in Berkeley Lab’s Engineering Division. “We’re very excited about this world record. This device allows you to get a much higher photon energy” from a given electron beam energy.

“We have expertise here both in free-electron laser undulators, as demonstrated in our role in leading the construction of LCLS-II’s undulators, and in synchrotron undulator development at the ALS,” noted Soren Prestemon, Director of the Berkeley Center for Magnet Technology (BCMT), which brings together the Accelerator Technology and Applied Physics Division (ATAP) and Engineering Division, to design and build a range of magnetic devices for scientific, medical, and other applications.

“The Engineering Division has a long history of forefront research on undulators, and this work continues that tradition,” states Henrik von der Lippe, Director, Engineering Division.

Diego Arbelaez, the lead engineer in the development of Berkeley Lab’s device, said earlier work at the Lab in building superconducting undulator prototypes for a different project were useful in informing the latest design, though there were still plenty of challenges.

Niobium-tin is a brittle material that cannot be drawn into a wire. For practical use, a pliable wire, which contains the components that will form niobium-tin when heat-treated, is used for winding the undulator coils. The full undulator coil is then heat-treated in a furnace at 1,200 degrees Fahrenheit.

The niobium-tin wire is wound around a steel frame to form tightly wrapped coils in an alternating arrangement. The precision of the winding is critical for the performance of the device. Arbelaez said, “One of the questions was whether you can maintain precision in its winding even though you are going through these large temperature variations.”

After the heat treatment, the coils are placed in a mold and impregnated with epoxy to hold the superconducting coils in place. To achieve a superconducting state and demonstrate its record-setting performance, the device was immersed in a bath of liquid helium to cool it down to about minus 450 degrees Fahrenheit.

Ahmet Pekedis, left, and Diego Arbelaez inspect the completed niobium tin undulator prototype. (Credit: Marilyn Chung/Berkeley Lab)

Another challenge was in developing a fast shutoff to prevent catastrophic failure during an event known as “quenching.” During a quench, there is a sudden loss of superconductivity that can be caused by a small amount of heat generation. Uncontrolled quenching could lead to rapid heating that might damage the niobium-tin and surrounding copper and ruin the device.

This is a critical issue for the niobium-tin undulators due to the extraordinary current densities they can support. Berkeley Lab’s Marcos Turqueti led the effort to engineer a quench-protection system that can detect the occurrence of quenching within a couple thousandths of a second and shut down its effects within 10 thousandths of a second.

Arbelaez also helped devise a system to correct for magnetic-field errors while the undulator is in its superconducting state.

SLAC’s Paul Emma, the accelerator physics lead for LCLS-II, coordinated the superconducting undulator development effort.

Emma said that the niobium-tin superconducting undulator developed at Berkeley Lab shows potential but may require more extensive continuing R&D than Argonne’s niobium-titanium prototype. Argonne earlier developed superconducting undulators that are in use at its APS, and Berkeley Lab also hopes to add superconducting undulators at its ALS.

“With superconducting undulators,” Emma said, “you don’t necessarily lower the cost but you get better performance for the same stretch of undulator.”

A close-up view of the superconducting undulator prototype developed at Berkeley Lab. To construct the undulator, researchers wound a pliable wire in alternating coils around a steel frame. The pliable wire was baked to form a niobium-tin compound that is very brittle but can achieve high magnetic fields when chilled to superconducting temperatures. (Credit: Marilyn Chung/Berkeley Lab)

A superconducting undulator of an equivalent length to a permanent magnetic undulator could produce light that is at least two to three times – perhaps up to 10 times – more powerful, and could also access a wider range in X-ray wavelengths, Emma said, producing a more efficient FEL.

Superconducting undulators also have no macroscopic moving parts, so they could conceivably be tuned more quickly with high precision. Superconductors also are far less prone to damage by high-intensity radiation than permanent-magnet materials, a significant issue in high-power accelerators such as those that will be installed for LCLS-II.

There appears to be a clear path forward to developing superconducting undulators for upgrades of existing and new X-ray free-electron lasers, Emma said, and for other types of light sources.

“Superconducting undulators will be the technology we go to eventually, whether it’s in the next 10 or 20 years,” he said. “They are powerful enough to produce the light we are going to need – I think it’s going to happen. People know it’s a big enough step, and we’ve got to get there.”

James Symons, Berkeley Lab’s Associate Director for Physical Sciences, said, “We look forward to building on this effort by furthering our R&D on superconducting undulator systems.

The Advanced Light Source, Advanced Photon Source, and Linac Coherent Light Source are DOE Office of Science User Facilities. The development of the superconducting undulator prototypes was supported by the DOE’s Office of Science.”

See the full article here .

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From SLAC: “SLAC Experiment is First to Decipher Atomic Structure of an Intact Virus with an X-ray Laser”

SLAC Lab

June 20, 2017

Surface structure of the bovine enterovirus 2. The three virus proteins are color-coded. (Jingshan Ren/University of Oxford)

A ground-breaking experimental method developed by an international research team will substantially speed up protein analysis.

An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team led by Alke Meents, a scientist at Germany’s DESY lab, reports in the journal Nature Methods.

The researchers tested their method with the Linac Coherent Light Source (LCLS) X-ray free-electron laser at the Department of Energy’s SLAC National Accelerator Laboratory. Now they are working to increase the capacity and speed of the technique in anticipation of future experiments at the European XFEL X-ray free-electron laser, which is just going into operation near Hamburg, Germany.

SLAC/LCLS

European XFEL

“This is a much-welcome and important technological development that will greatly optimize data collection at LCLS and other X-ray free-electron lasers for certain classes of challenging experiments,” says co-author Roberto Alonso Mori, a staff scientist in the LCLS hard X-ray group. “The same technology could be used not only for biological science but could also help data collection in other areas.”

Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. (Philip Roedig/DESY)

A Well-Rounded View of Life

In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of fundamental biological processes, such as the way substances are transported in and out of a cell, and can also inform drug development.

“Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, director of life sciences at the Diamond Light Source synchrotron facility in the United Kingdom and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defense for the cell to make the virus incapable of attacking it.”

X-ray crystallography is by far the most prolific tool used by structural biologists and has already been used to determine the structure of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

“X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” says co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through an X-ray laser beam that pulses in a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

This method is very successful and has already been used to determine the structure of more than 80 biomolecules, the researchers point out in their paper. However, most of the sample material is wasted. “The hit rate is typically less than 2 percent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beam time and significant amounts of sample material.

Protein Crystals on a Chip

In order to use the limited beam time and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

The research team tested its method on two virus samples using SLAC’s LCLS X-ray laser, which produces 120 pulses per second. They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that causes miscarriages, stillbirths and infertility in cattle, and which is very difficult to crystallise.

In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to 9 percent, five times the hit rate of the previous method. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from other experiments – down to a scale of 2.3 angstroms.

“To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents says. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanoliters, or billionths of a liter, we managed using crystals that were more than 10 times smaller, having a total volume of just 0.23 nanoliters.”

This experiment was conducted at room temperature; while rapidly cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen and in a second test, the researchers studied a viral protein called polyhedrin that makes up a viral occlusion body — a container used by certain virus species to protect up to several thousand virus particles at a time against environmental influences so they can remain intact much longer.

From Room Temperature to a Deep Chill

For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 percent. In just 10 minutes they recorded more than enough diffraction images to determine the protein structure to within 2.4 angstroms.

“For the structure of polyhedrin, we only had to scan a single chip that was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

“Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the European XFEL, which will be able to produce up to 27,000 X-ray laser pulses per second, as well as an upgraded LCLS that is scheduled to come on line in the early 2020s and produce up to a million pulses per second. Furthermore, the next generation of chips will expose only those micropores that are targeted for analysis, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being on Diamond’s I02 and I24 beamlines. Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, Lawrence Berkeley National Laboratory and SLAC were also involved in the research. LCLS is a DOE Office of Science User Facility.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From DESY: “First atomic structure of an intact virus deciphered with an X-ray laser”

DESY

2017/06/19

Groundbreaking experimental method will speed up protein analysis substantially.

Surface structure of the bovine enterovirus 2, the three virus proteins are colour coded. Credit: Jingshan Ren, University of Oxford

An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method used dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team lead by DESY scientist Alke Meents reports in the journal Nature Methods.

In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of the fundamental biological processes taking place inside organisms, such as the way in which substances are transported in and out of a cell, and can also be used to develop new drugs.

“Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, Director of Life Sciences at the synchrotron facility Diamond Light Source in the UK and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defence for the cell to make the virus incapable of attacking it.”

X-ray crystallography is by far the most prolific tool used by structural biologists and has already revealed the structures of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

“X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” adds co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through a pulsed X-ray laser, which releases a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

This method is very successful and has already been used to determine the structure of more than 80 biomolecules. However, most of the sample material is wasted. “The hit rate is typically less than two per cent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beamtime and significant amounts of sample material.

Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. Credit: Philip Roedig, DESY

n order to use the limited beamtime and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

The research team tested its method on two different virus samples using the LCLS X-ray laser at the SLAC National Accelerator Laboratory in the US, which produces 120 pulses per second.

SLAC/LCLS

They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that can cause miscarriages, stillbirths, and infertility in cattle, and which is very difficult to crystallise.

In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to nine per cent. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from experiments at other X-ray light sources – down to a scale of 0.23 nanometres (millionths of a millimetre).

“To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents points out. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanolitres, we managed using crystals that were more than ten times smaller, having a total volume of just 0.23 nanolitres.”

This experiment was conducted at room temperature. While cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen, and in a second test, the researchers studied the viral protein polyhedrin that makes up a viral occlusion body for up to several thousands of virus particles of certain species. The virus particles use these containers to protect themselves against environmental influences and are therefore able to remain intact for much longer times.

Schematic of the experimental set-up: The chip loaded with nanocrystals is scanned by the fine X-ray beam (green) pore by pore. Ideally, each crystal produces a distinctive diffraction pattern. Credit: Philip Roedig, DESY

For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 per cent. In just ten minutes they had recorded more than enough diffraction images to determine the protein structure to within 0.24 nanometres. “For the structure of polyhedrin, we only had to scan a single chip which was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

“Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the new X-ray free-electron laser European XFEL, which is just going into operation in the Hamburg region and which will be able to produce up to 27,000 pulses per second.

European XFEL

Furthermore, the next generation of chips will only expose those micropores that are currently being analysed, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, the Lawrence Berkeley National Laboratory in the US and SLAC were also involved in the research. Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being done on Diamond’s I02 and I24 beamlines.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.

From SLAC: “New Research Finds a Missing Piece to High-Temperature Superconductor Mystery”

SLAC Lab

June 14, 2017
Mike Ross

This sketch shows how resonant inelastic X-ray scattering (RIXS) helps scientists understand the electronic behavior of copper oxide materials. An X-ray photon aimed at the sample (blue arrow) is absorbed by a copper atom, which then emits a new, lower-energy photon (red arrow) as it relaxes. The amount of momentum transferred and energy lost in this process can induce changes in the charge density waves thought to be important in high-temperature superconductivity. (Wei-Sheng/SLAC National Accelerator Laboratory)

An international team led by scientists from the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University has detected new features in the electronic behavior of a copper oxide material that may help explain why it becomes a perfect electrical conductor – a superconductor – at relatively high temperatures.

Using an ultrahigh-resolution X-ray instrument in France, the researchers for the first time saw dynamic behaviors in the material’s charge density wave (CDW) – a pattern of electrons that resembles a standing wave – that lend support to the idea that these waves may play a role in high-temperature superconductivity.

Data taken at low (20 kelvins) and high (240 kelvins) temperatures showed that as the temperature increased, the CDW became more aligned with the material’s atomic structure. Remarkably, at the lower temperature, the CDW also induced an unusual increase in the intensity of the oxide’s atomic lattice vibrations, indicating that the dynamic CDW behaviors can propagate through the lattice.

“Previous research has shown that when the CDW is static, it competes with and diminishes superconductivity,” said co-author Wei-Sheng Lee, a SLAC staff scientist and investigator with the Stanford Institute for Materials and Energy Sciences (SIMES), which led the study published June 12 in Nature Physics. “If, on the other hand, the CDW is not static but fluctuating, theory tells us they may actually help form superconductivity.”

A Decades-long Search for an Explanation

The new result is the latest in a decades-long search by researchers worldwide for the factors that enable certain materials to become superconducting at relatively high temperatures.

Since the 1950s, scientists have known how certain metals and simple alloys become superconducting when chilled to within a few degrees of absolute zero: Their electrons pair up and ride waves of atomic vibrations that act like a virtual glue to hold the pairs together. Above a certain temperature, however, the glue fails as thermal vibrations increase, the electron pairs split up and superconductivity disappears.

In 1986, complex copper oxide materials were found to become superconducting at much higher – although still quite cold – temperatures. This discovery was so unexpected it caused a worldwide scientific sensation. By understanding and optimizing how these materials work, researchers hope to develop superconductors that work at room temperature and above.

At first, the most likely glue holding superconducting electron pairs together at higher temperatures seemed to be strong magnetic excitations created by interactions between electron spins. But in 2014, a theoretical simulation and experiments led by SIMES researchers concluded that these high-energy magnetic interactions are not the sole factor in copper oxide’s high-temperature superconductivity. An unanticipated CDW also appeared to be important.

The latest results continue the SIMES collaboration between experiment and theory. Building upon previous theories of how electron interactions with lattice vibrations can be probed with resonant inelastic X-ray scattering, or RIXS, the signature of CDW dynamics was finally identified, providing additional support for the CDW’s role in determining the electronic structure in superconducting copper oxides.

The Essential New Tool: RIXS

The new results are enabled by the development of more capable instruments employing RIXS. Now available at ultrahigh resolution at the European Synchrotron Radiation Facility (ESRF) in France, where the team performed this experiment, RIXS will also be an important feature of SLAC’s upgraded Linac Coherent Light Source X-ray free-electron laser, LCLS-II.

ESRF. Grenoble, France

SLAC LCLS-II

The combination of ultrahigh energy resolution and a high pulse repetition rate at LCLS-II will enable researchers to see more detailed CDW fluctuations and perform experiments aimed at revealing additional details of its behavior and links to high-temperature superconductivity. Most importantly, researchers at LCLS-II will be able to use ultrafast light-matter interactions to control CDW fluctuations and then take femtosecond-timescale snapshots of them.

RIXS involves illuminating a sample with X-rays that have just enough energy to excite some electrons deep inside the target atoms to jump up into a specific higher orbit. When the electrons relax back down into their previous positions, a tiny fraction of them emit X-rays that carry valuable atomic-scale information about the material’s electronic and magnetic configuration that is thought to be important in high-temperature superconductivity.

“To date, no other technique has seen evidence of propagating CDW dynamics,” Lee said.

RIXS was first demonstrated in the mid-1970s [Physical Review Letters], but it could not obtain useful information to address key problems until 2007, when Giacomo Ghiringhelli, Lucio Braicovich at Milan Polytechnic in Italy and colleagues at Swiss Light Source made a fundamental change that improved its energy resolution to a level where significant details became visible – technically speaking to about 120 milli-electronvolts (meV) at the relevant X-ray wavelength, which is called a copper L edge. The new RIXS instrument at ESRF is three times better, routinely attaining an energy resolution down to 40 meV. Since 2014, the Milan group has collaborated with SLAC and Stanford scientists in their RIXS research.

“The new ultrahigh resolution RIXS makes a huge difference,” Lee said. “It can show us previously invisible details.”

Other researchers involved in this result were from Milan Polytechnic, European Synchrotron Radiation Facility, Japan’s National Institute of Advanced Industrial Science and Technology and Italy’s National Research Council Institute for Superconductors, Oxides and Other Innovative Materials and Devices (CNR-SPIN). Funding for this research came from the DOE Office of Science.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From SLAC: “The World’s Most Powerful X-ray Laser Beam Creates ‘Molecular Black Hole’”

SLAC Lab

May 31, 2017
Andrew Gordon
agordon@slac.stanford.edu
(650) 926-2282

When the X-rays blast electrons out of one atom, stripping it from the inside out, it steals more from its neighbors – a new insight that could help advance high-res imaging of whole viruses, bacteria and complex materials.

In this illustration, an ultra-intense X-ray laser pulse from SLAC’s Linac Coherent Light Source knocks so many electrons out of a molecule’s iodine atom (right) that the iodine starts pulling in electrons from the rest of the molecule (lower left), like an electromagnetic version of a black hole. Many of the stolen electrons are also knocked out by the laser pulse; then the molecule explodes. (DESY/Science Communication Lab)

When scientists at the Department of Energy’s SLAC National Accelerator Laboratory focused the full intensity of the world’s most powerful X-ray laser on a small molecule, they got a surprise: A single laser pulse stripped all but a few electrons out of the molecule’s biggest atom from the inside out, leaving a void that started pulling in electrons from the rest of the molecule, like a black hole gobbling a spiraling disk of matter.

Within 30 femtoseconds – millionths of a billionth of a second – the molecule lost more than 50 electrons, far more than scientists anticipated based on earlier experiments using less intense beams or isolated atoms. Then it blew up.

The results, published today in Nature, give scientists fundamental insights they need to better plan and interpret experiments using the most intense and energetic X-ray pulses from SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser.

SLAC/LCLS

Experiments that require these ultrahigh intensities include attempts to image individual biological objects, such as viruses and bacteria, at high resolution. They are also used to study the behavior of matter under extreme conditions, and to better understand charge dynamics in complex molecules for advanced technological applications.

“For any type of experiment you do that focuses intense X-rays on a sample, you want to understand how it reacts to the X-rays,” said Daniel Rolles of Kansas State University. “This paper shows that we can understand and model the radiation damage in small molecules, so now we can predict what damage we will get in other systems.”

Like Focusing the Sun Onto a Thumbnail

The experiment, led by Rolles and Artem Rudenko of Kansas State, took place at LCLS’s Coherent X-ray Imaging instrument (CXI). It delivers X-rays with the highest possible energies achievable at LCLS, known as hard X-rays, and records data from samples in the instant before the laser pulse destroys them.

How intense are those X-ray pulses?

“They are about a hundred times more intense than what you would get if you focused all the sunlight that hits the Earth’s surface onto a thumbnail,” said LCLS staff scientist and co-author Sebastien Boutet.

For this study, researchers used special mirrors to focus the X-ray beam into a spot just over 100 nanometers in diameter – about a hundredth the size of the one used in most CXI experiments, and a thousand times smaller than the width of a human hair. They looked at three types of samples: individual xenon atoms, which have 54 electrons each, and two types of molecules that each contain a single iodine atom, which has 53 electrons.

Heavy atoms around this size are important in biochemical reactions, and researchers sometimes add them to biological samples to enhance contrast for imaging and crystallography applications. But until now, no one had investigated how the ultra-intense CXI beam affects molecules with atoms this heavy.

X-rays Trigger Electron Cascades

The team tuned the energy of the CXI pulses so they would selectively strip the innermost electrons from the xenon or iodine atoms, creating “hollow atoms.” Based on earlier studies with less energetic X-rays, they thought cascades of electrons from the outer parts of the atom would drop down to fill the vacancies, only to be kicked out themselves by subsequent X-rays. That would leave just a few of the most tightly bound electrons. And, in fact, that’s what happened in both the freestanding xenon atoms and the iodine atoms in the molecules.

But in the molecules, the process didn’t stop there. The iodine atom, which had a strong positive charge after losing most of its electrons, continued to suck in electrons from neighboring carbon and hydrogen atoms, and those electrons were also ejected, one by one.

Rather than losing 47 electrons, as would be the case for an isolated iodine atom, the iodine in the smaller molecule lost 54, including the ones it grabbed from its neighbors – a level of damage and disruption that’s not only higher than would normally be expected, but significantly different in nature.

Results Feed Into Theory to Improve Experiments

“We think the effect was even more important in the larger molecule than in the smaller one, but we don’t know how to quantify it yet,” Rudenko said. “We estimate that more than 60 electrons were kicked out, but we don’t actually know where it stopped because we could not detect all the fragments that flew off as the molecule fell apart to see how many electrons were missing. This is one of the open questions we need to study.”

For the data analyzed to date, the theoretical model provided excellent agreement with the observed behavior, providing confidence that more complex systems can now be studied, said LCLS Director Mike Dunne. “This has important benefits for scientists wishing to achieve the highest-resolution images of biological molecules to inform the development of better pharmaceuticals, for example,” he said. “These experiments will also guide the development of a next-generation instrument for the LCLS-II upgrade project, which will provide a major leap in capability due to the increase in repetition rate from 120 pulses per second to 1 million.”

SLAC LCLS-II

The theory work for the study was led by Robin Santra of the Center for Free-Electron Laser Science at DESY and the University of Hamburg in Germany. Other research institutions contributing to the study were Tohoku University in Japan; Max Planck Institute for Nuclear Physics, Max Planck Institute for Medical Research, Hamburg Center for Ultrafast Imaging and the National Metrology Institute (PTB) in Germany; the University of Science and Technology in Beijing; Aarhus University in Denmark; Sorbonne University in France; the DOE’s Argonne National Laboratory and Brookhaven National Laboratory; the University of Chicago; and Northwestern University. Funding for the research came from the DOE Office of Science and from the German Research Foundation (DFG).

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

From DESY: “Profiling FLASH electron bunches on a femtosecond scale”

DESY

2017/05/26
No writer credit found

Scientists use external seeding to monitor few-femtosecond slices of ultra-relativistic electron bunches.

The success of FELs, having a transformative impact on science with X-rays, relies on the capability of analysing and controlling ultra-relativistic electron beams on femtosecond timescales. One major challenge is to extract tomographic electron slice parameters for each bunch instead of projected electron beam properties. A team of scientists has developed an elegant method to derive the slice emittance from snapshots of electron bunches with femtosecond resolution. Mapping of electron slice parameters and seeded FEL pulse profiles is an important ingredient for both, today’s large scale facilities and future compact table-top FELs and creates new opportunities for tailored photon beam applications. The project team headed by Jörg Rossbach from the University of Hamburg, DESY photon scientist Tim Laarmann and DESY accelerator physicist Jörn Bödewadt, reports its work in the journal Scientific Reports.

View into the seeding area of FLASH (photo: Dirk Nölle).

DESY/FLASH

Since 2005, DESY´s free-electron laser FLASH in Hamburg delivers ultra-short high-brilliance photon pulses to a wide range of scientific users. The light pulses are generated by electron bunches that are accelerated to a velocity close to the speed of light. These bunches have lengths of less than 100 μm, the diameter of a human hair. After acceleration, they traverse a series of magnets with alternating polarities, the undulator, and emit bright, soft X-ray light. While a synchrotron light source like PETRA III works very similar, a free-electron laser makes use of a further phenomenon: “During the emission process, different parts of the electron bunch organize themselves into thin microbunches with a distance of the wavelength of the emitted light,” explains principal author and PhD student Tim Plath. “Several parts of the bunch undergo this process with slightly different wavelengths and phases leading to a spiky structure of the spectrum. It is in the nature of this spontaneous amplification process that the properties are slightly different from shot to shot. This process is called self-amplified spontaneous emission (SASE) and is routinely used at many FEL facilities”.

Experimental setup of the seeding experiment at FLASH. From left: The beam comes from the linear accelerator and is overlapped with an external seed laser. In the modulator the laser imprints an energy modulation on the electron bunch that gets transformed to a density modulation by the bunching chicane. The formed microbunches can then coherently emit radiation in the radiator. The experimental setup is followed by a diagnostic for the photons and the rf deflector that can diagnose the electron bunch distribution (picture: Tim Plath, UHH/DESY).

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.