Nights!

Experimental time at light sources is very precious. When a synchrotron or X-ray Free Electron Laser (XFEL) is in operating mode the goal is to allocate as many experimental shifts to external scientists and in-house research as possible. This includes night shifts! So, how do light source users survive the night shifts? #LightSourceSelfies brings you top tips from scientists based at, or using, 5 light sources in our collaboration – the ESRF, Advanced Light Source (ALS), ANSTO’s Australian Synchrotron, CHESS and the PAL XFEL.

Light source users don’t have to be experts

Aeriel Murphy-Leonard, Assistant Professor at The Ohio State University, was studying magnesium alloys in graduate school when she first heard about synchrotron sources. Aeriel’s first thought was that a synchrotron sounded like something out of a Marvel film!

In her brilliant #LightSourceSelfie, Aeriel describes how she was able to conduct her first experiment at CHESS, the synchrotron at Cornell University in New York. Having recovered from the initial alarm that the synchrotron is located under the university’s soccer fields, Aeriel had an amazing experience and describe the wonderful support she received, and expertise she gained, during this and subsequent user visits to CHESS. Aeriel says, “One thing I’ve learned that’s very valuable about CHESS, or just synchrotrons in general, is that you don’t have to be an expert. I think that’s the biggest takeaway I would like to give in this video is that you do not have to be an expert. I had no idea what it was, did not even understand, and I was able to learn from the beamline scientists and what I’ve always enjoyed about CHESS as a facility is that it’s very educational focused. You can come in not an expert and leave with a lot of expertise.”

Aeriel is passionate about supporting young professionals, particularly those from minority groups. She shares her experiences in her lifestyle blog (https://aerielviews.blog/), which is aimed at young professionals, particularly those that are in graduate school or professional school.

Wild blue wonder: X-ray beam explores food color protein

A natural food colorant called phycocyanin provides a fun, vivid blue in soft drinks, but it is unstable on grocery shelves. Cornell’s synchrotron is helping to steady it.

In food products, the natural blues tend to be moody.

A fun food colorant with a scientific name – phycocyanin – provides a vivid blue pigment that food companies crave, but it can be unstable when placed in soft drinks and sport beverages, and then lose its hues under fluorescent light on grocery shelves.

With the help of physics and the bright X-ray beams from Cornell’s synchrotron, Cornell food scientists have found the recipe for phycocyanin’s unique behavior and they now have a chance to stabilize it, according to new research published Nov. 12 in the American Chemical Society’s journal BioMacromolecules.

“Phycocyanin has a vibrant blue color,” said Alireza Abbaspourrad, the Youngkeun Joh Assistant Professor of Food Chemistry and Ingredient Technology in the Department of Food Science in the College of Agriculture and Life Sciences. “However, if you want to put phycocyanin into acidified beverages, the blue color fades quickly due to thermal treatment.”

Read more on the Chess Website

Image: A natural food colorant called phycocyanin provides a fun, vivid blue in soft drinks, but it is unstable on grocery shelves. Cornell’s synchrotron is helping to steady it.

Credit: CHESS Cornell Chronicle High Energy

Beginning your light source journey

Scientists who use synchrotrons such as the Advanced Light Source in California and CHESS at Cornell University, along with staff scientists at Free Electron Lasers in South Korea (the PAL-XFEL) and California (LCLS at SLAC), reflect on how they felt the first time they used a light source facility to conduct research experiments.  The expertise available from the staff scientists who work on the beamlines is also highlighted in this #LightSourceSelfie video.

Testing quantum electrodynamics prediction with surprising results

Echoing classical physics, quantum electrodynamics predicts the release of a spectral continuum of electromagnetic radiation upon the sudden acceleration of charged particles in quantum matter. Despite apparent theoretical success in describing sister nuclear processes, known as internal bremsstrahlung, following nuclear beta decay and K capture, the situation of the photoejection of an electron from an inner shell of an atom, intraatomic bremsstrahlung (IAB), is far from settled.

What is the discovery?
This paper addresses the experimental situation by applying a fluorescence coincidence technique to pluck the anticipated signal out of noise, taking advantage of the intense incident photon flux of a contemporary synchrotron radiation source; exploits advanced x-ray detectors which provide arrival time as well as energy information, and employs extraordinarily thin metal targets to minimize secondary effects. The surprising result is that in testing for the radiation expected from the innermost shell of copper with a 46 keV incident x-ray beam no such signal was observed at a sensitivity level that is over five sigmas below the predicted rate, taking into account the expected secondary signal, and below four sigmas if no particular secondary modeling is assumed.  In this work observations were made in the scattered photon energy range of 3 to 7 keV.

Read more on the CHESS website

Image: Schematic of the Scattering Chamber. A is the one element detector, B is the Kapton film covered main beam exit port, C is the helium (1 Atm.) filled chamber (input and output helium supply lines and chamber cover not shown), D is the target mount, E is the four-element detector, F is the Kapton film covered incident beam port.

Grain-scale deformation of a high entropy alloy


New research that exploited the unique strengths of the FAST beamline produced some of the first measurements of individual grain deformation in high entropy alloys. This data can help form accurate predictions of damage and failure processes in these emerging materials, critical for understanding their performance in real-world applications.

Grains and strains | A subset of the thousands of indexed grains are shown, along with their axial elastic strains (top) and maximum resolved sheer stress (bottom), at 4 positions indicated on the stress-strain curve. This microscopic detail is only available via high-energy x-ray techniques.

What is the discovery?


Conventional alloys are made primarily of one metal element, with a small substitution of other atoms to tune the properties (for example, 7.5% Cu and 92.5% Ag produces sterling silver). Recently, new types of high entropy alloys (HEAs) have been discovered, which are made by mixing many different metallic elements in nearly-equal proportions. HEAs can exhibit remarkably different properties from conventional alloys. In a new paper, a team lead by Jerard Gordon from the University of Michigan reports a high-energy x-ray study of the HEA made from mixing equal amounts of Co, Cr, Fe, Mn, and Ni. The team was able to use far-field high-energy diffraction microscopy (ff-HEDM) to understand the microscopic response of thousands of individual crystal grains in their sample when it is deformed under load. They were also able to compare the results with detailed crystal-plasticity models.

Read more on the CHESS website

Image: Grains and strains | A subset of the thousands of indexed grains are shown, along with their axial elastic strains (top) and maximum resolved sheer stress (bottom), at 4 positions indicated on the stress-strain curve. This microscopic detail is only available via high-energy x-ray techniques.

In situ spectroscopy as a probe of electrocatalyst performance

Hydrogen fuel cells generally require expensive and scarce platinum catalysts in order to function. Researchers have created highly reactive platinum-nickel nanowires with the potential to reduce the amount of platinum required in fuel cells. Research at PIPOXS examines the atomic-level mechanisms of this catalyst, forming a foundation for the development and commercialization of more efficient fuel cell technology.

What is the new discovery?


The oxygen reduction reaction (ORR) is an important and often limiting component of hydrogen fuel cell operation.  To facilitate this reaction, platinum-based catalysts are often used to increase its rate, though the expense and limited availability of Pt present challenges to its widespread use.  In this work, researchers selectively replaced a portion of the nickel atoms of nickel nanowires with platinum to create platinum-nickel nanowires (PtNi-NWs) as high surface area catalysts that reduced the total amount of platinum required.  These PtNi-NWs were found to be highly active, and so operando x-ray absorption spectroscopy and extended x-ray absorption fine structure (EXAFS) experiments were conducted at the PIPOXS beamline to assess the electronic and geometric changes occurring in these catalysts during their use.   These data enabled the researchers to determine that the Pt formed an alloy with the Ni in the NW and that its interaction with oxygen remained constant regardless of the external potential applied.  

Read more on the CHESS website

Image: Schematic showing the electrochemical cell used for the operando measurements, and how the EXAFS data can be used to deduce the chemistry happening during this reaction.

Rotation and axial motion system IV (RAMS IV) load frame

In spring 2021, the fourth generation of Rotation and Axial Motion System (RAMS IV) load frame was commissioned with X-rays at the Structural Materials Beamline (SMB)

WHAT DID THE SCIENTISTS DO?

The main objectives of commissioning were to enable communication between the existing control system of the beamline (SPEC) and the new control system of RAMS IV (Aerotech), and to synchronize triggering of X-ray detectors with positions of the rotation stages on RAMS IV. To this end, a number of new scripts were written and tested for both SPEC and Aerotech for executing commands, exchanging experimental parameters, interlocking and “handshaking” between the two systems. During the last few days of commissioning, a series of X-ray measurements were performed on a sample mounted on RAMS IV to test the main functionalities of the new load frame.

WHAT ARE THE BROADER IMPACTS OF THIS WORK?

The RAMS load frame series collectively form the gold standard for high-impact, precision in-situ X-ray mechanical testing at high-energy synchrotrons. The longstanding collaboration between Air Force Research Laboratory (AFRL) and Pulseray Inc. has delivered a new design and controls system.

Two RAMS IV frames were built: (1) a CHESS design for in-situ X-ray studies, and (2) an AFRL design for ex-situ studies. The AFRL machine can be used for ex-situ proof-of-concept, preparatory loading, or longer mechanical loading tests that can complement and inform work that is done in situ on the CHESS machine.

RAMS IV is optimized for simultaneous tension, torsion, and fatigue loading. Torsion and fatigue loadings are new features over the second generation of RAMS (RAMS II) that has been (and is still being) used with many user experiments at CHESS.

Read more on the CHESS website

Image: Staff Scientists Kelly Nygren and Peter Ko worked in tandem with AFRL to commission the RAMS IV

Virus recognition skills

A virus recognizes the starting point on the DNA to be packaged inside its protein shell

A bacteriophage – a virus that attacks bacteria – assembles into an infectious species using a powerful nanomachine to stuff its DNA into a protein shell. In several types of phage, this genome packaging motor is composed of several copies of large and small terminase subunits (TerL and TerS, respectively) that attach to a portal into the protein procapsid. 

Figure 1. Envelope of NV1 TerS from SAXS data, overlaid with modeled structure with open HTHs. Circle highlights one HTH motif.

The Cingolani group (Thomas Jefferson U) has now determined the structure of TerS from the Pseudomonas phage PaP3. Phage DNA to be packaged contains multiple copies of the genome, but just one copy is needed to fill a procapsid. Terminases attempt to package this one copy by various methods; in PaP3 a termination signal is provided by the interaction of a specific sequence in the DNA (the cos sequence) with TerS.

A crystal structure of PaP3 TerS reveals a nonameric ring of mixed alpha/beta composition, sitting atop a 9-stranded beta-barrel. Projecting out from the ring are spokes tipped with helix-turn-helix (HTH) DNA-binding domains. In the crystal, with no DNA present, the HTH domains are packed tightly against the inner parts of the nonamer (a “closed” form). Crystals of TerS from the related NV1 phage were also studied; their quality was not as good but the same conformation was found.  BioSAXS coupled to size-exclusion chromatography, at CHESS, was then used to examine the PaP3 TerS structure, and that of the related NV1 protein, in solution. Both turned out to be ~25% larger than predicted from the crystal structure. The molecular envelope determined from SAXS data for NV1 clearly showed protuberances on the outside of the nonameric ring that did not match the crystal structure. However, by rotating the HTH domain of each monomer about an obvious hinge region, an “open” model could be built that fit the SAXS envelope well (Figure 1). 

Read more on the CHESS website

Image: Figure 1. Envelope of NV1 TerS from SAXS data, overlaid with modeled structure with open HTHs. Circle highlights one HTH motif.

Fe Cations Control the Plasmon Evolution in CuFeS2 Nanocrystals

Research on the synthesis of CuFeS2, an exciting semiconductor, outlines a method to verify its phase purity and investigate its properties.

Plasmonic semiconductor nanocrystals have become an appealing avenue for researching nanoscale plasmonic effects due to their wide spectral range (visible to infrared) and great tunability compared to traditional precious metal nanocrystals. CuFeS2 is an exciting semiconductor that has a prominent plasmon absorption band in the visible range (∼498 nm). In this work, the researchers determined the origin of the plasmonic behaviour in CuFeS2 by characterizing the nucleation and growth stages of the reaction through a series of ex situ and in situ probes (e.g., X-ray absorption spectroscopy and X-ray emission spectroscopy). They showed that the plasmon formation is driven by band structure modification from Fe(II) incorporation into the nanocrystals. Mixed oxidation state of Cu(I)/Cu(II) and Fe(II)/Fe(III) was observed.  Using these results, the researchers proposed a reaction mechanism for synthesis of CuFeS2 and outlined a method to verify the phase purity of the material.

Read more on the CHESS website

Measuring interfaces in 3D printing

3D printing (3DP) leads to many defects and interfaces within printed parts. Failure during performance in the road-to-road and layer-by-layer processed parts appears at these interfaces and defects. Understanding the root cause of these limitations is key. 

Only by mapping the sample via µ-beam SAX was it possible to determine the source of a peculiar defect and interface morphology. To the surprise of the scientists the alignment of nanoparticles is not uniform and not random within roads and layers of an epoxy carbon fiber reinforced composite and explains some of the achieved mechanical properties and microscopy results.

Read more on the Cornell High Energy Synchrotron Source (CHESS) website

Image: 3D printing degree of orientation

Credit: CHESS

Preparation and characterization of mesoscale single crystals

What did the Scientists Discover?
Single crystals are materials with periodic structure that extends across macroscopic distances as a coherent lattice free of grain boundaries. By isolating and studying their properties, bulk single crystals have revolutionized our fundamental understanding of materials from semiconductors to biomacromolecules, fueling innovations from microelectronic devices to pharmaceutical compounds. In contrast, our understanding of many mesostructured materials is still in its infancy in part due to the lack of available single crystals. Block copolymer self-assembly of mesostructured systems presented here is a promising method to prepare periodic 10–100 nm structures with coherent orientation over macroscopic lengths enabling their study.

Why is this important?
The method presented here can prepare macroscopic bulk single crystals with other block copolymer systems, suggesting that the method is broadly applicable to block copolymer materials assembled by solvent evaporation. It is expected that such bulk single crystals will enable fundamental understanding and control of emergent mesostructure-based properties in block-copolymer-directed metal, semiconductor, and superconductor materials.

>Read more on the CHESS website

Image: (extract, full image see here) Representative SAXS patterns with log scale colors from locations as indicated in (c), exhibiting polycrystalline (e), multi-(three) crystalline (f), and single crystal (g) behavior. Diagonal bars across bottom are shadows from photodiode wire.

Researchers use CHESS to map protein motion

Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins.

And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins. And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Their paper, “Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal,”published March 9 in Nature Communications.
As a structural biologist, Nozomi Ando, M.S. ’04, Ph.D. ’08, assistant professor of chemistry and chemical biology, is interested in charting the motion of proteins, and their internal parts, to better understand protein function. This type of movement is well known but has been difficult to document because the standard technique for imaging proteins is X-ray crystallography, which produces essentially static snapshots.

>Read more on the CHESS website
>Read also: Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Image: This slice through the three-dimensional diffuse map shows intense peaks resulting from lattice vibration, as well as cloudy features caused by internal protein motions.

Twisting the helix: salt dependence of conformations of RNA duplexes

Ribonucleic acid (RNA) is a macromolecule essential in various biological roles in coding, decoding, regulation and expression of genes. Its biological functions depend critically on its structure and flexibility. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, Cornell researchers used X-ray scattering at CHESS to quantify these variations. Their results quantify the substantial and solution-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation.

>Read more on the CHESS website

Image: Left: Experimental X-ray scattering curves for RNA duplexes in solutions containing dfferent concentrations of KCl and MgCl2. Right: RNA conformations resulting form the experimental data in comparison with the canonical RNA structure.

Welcome back users!

This month marks the official start of user operation at CHESS and all three partner programs: The NSF funded CHEXS, as well as MacCHESS supported by NIH and NYSTAR, and the Materials Solutions Network at CHESS, or MSN-C, funded by the Air Force Research Lab (AFRL), all welcomed users to new hutches and beamlines. 

Louise Debefve stands outside a hutch on the experimental floor of the Cornell High Energy Synchrotron Source, CHESS. She is preparing the experimental equipment for some of the first data to be collected at CHESS since the completion of the CHESS-U upgrade. The platinum samples that she is about to study at the new beamlines will provide insights into the catalytic function of the element, enabling for example the generation of cleaner energy powering everything from cars to laptops.

But for now, Louise is happy to just be using the X-rays again, a familiar occurrence for the former graduate student, who spent years developing her research of catalysts through the use of X-rays at SSRL. As a postdoc at CHESS, Louise initially found herself right in the middle of the feverish construction of the upgrade, with no X-rays available for research.

>Read more on the CHESS website

Image: Louise Debefve, right, works with Chris Pollock and Ken Finkelstein at the new PIPOXS station.

The driving force behind Cornell Compact Undulators at CHESS

Researchers at CHESS are working to further improve the already impressive CHESS Compact Undulator, or CCU.

Within the new NSF-funded CHEXS award, Sasha Temnykh is developing a new driving mechanisms that will add variable gap control and even better tuning of the device, both desirable qualities for a variety of experimental needs.

Undulators are critical devices for the creation of brilliant X-rays at CHESS and other lightsources around the world. With the recent CHESS-U upgrade, the Cornell Electron Storage Ring, CESR, is now outfitted with seven new insertion devices. As the beam circulates around CESR, it passes through a series of alternating magnets in the undulators, resulting in X-rays that are roughly 20 times brighter than those produced prior to the upgrade, making CHESS an even more powerful X-ray source.

Researchers at CHESS lead by Sasha Temnykh are working continuously to improve the already impressive CHESS Compact Undulator, or CCU. The CCUs are about ten times more compact, lighter, and less expensive compared to conventional insertion devices typically used at other lightsource. They also require a significant shorter fabrication time. Nine CCUs have already been constructed in industry from the Cornell-held patent, and according to KYMA, the manufacturer of the CCU, other labs are starting to show interest in the device.

>Read more on the CHESS website

Image: Sasha Temnykh is the driving force behind the Cornell Compact Undulator design and development.