Category: Cornell High Energy Synchrotron Source (CHESS)

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

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

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

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

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

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

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

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!

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

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. 

Synergistic Co−Mn oxide catalyst for oxygen reduction reactions

Synergistic Co−Mn oxide catalyst for oxygen reduction reactions

Researchers employed synchrotron-based X-ray absorption spectroscopy (XAS) at CHESS to investigate the synergistic interaction of bimetallic Co1.5Mn1.5O4/C catalysts… under real-time operando electrochemical conditions.

Identifying the catalytically active site(s) in the oxygen reduction reaction (ORR) is critical to the development of fuel cells and other technologies. Researchers employed synchrotron-based X-ray absorption spectroscopy (XAS) at CHESS to investigate the synergistic interaction of bimetallic Co1.5Mn1.5O4/C catalysts – which exhibit impressive ORR activity in alkaline fuel cells – under real-time operando electrochemical conditions. Under steady state conditions, both Mn and Co valences decreased at lower potentials, indicating the conversion from Mn-(III,IV) and Co(III) to Mn(II,III) and Co(II), respectively. Changes in the Co and Mn valence states are simultaneous and exhibited periodic patterns that tracked the cyclic potential sweeps.

>Read more on the CHESS website

Image: Schematic of the in situ XAS electrochemical cell. Working electrode (WE, catalyst on carbon paper) and counter electrode (CE, carbon rod) were immersed in 1 M KOH solution. The reference electrode was connected to the cell by a salt bridge to minimize IR drops caused by the resistance in the thin electrolyte layer within the X-ray window.

Disorder raises the critical temperature of a cuprate superconductor

Disorder raises the critical temperature of a cuprate superconductor

The origin of high-temperature superconductivity remains poorly understood to date. Over the past two decades, spatial oscillations of the electronic density known as charge-density waves (CDWs) have been found to coexist with high-temperature superconductivity in most prominent cuprate superconductors. The debate on whether CDWs help or hinder high-temperature superconductivity in cuprates is still ongoing. In principle, disorder at the atomic scale should strongly suppress both high-temperature superconductivity and CDWs. In this work, however, we find that disorder created by irradiation increases the superconducting critical temperature by 50% while suppressing the CDW order, showing that CDWs strongly hinder bulk superconductivity. We show that this increase occurs because the CDWs could be frustrating the superconducting coupling between atomic planes.

>Read more on the CHESS website

Image:  In an ideal system, orthogonal charge-spin stripes in adjacent layers prevent Josephson coupling between layers. Left: In the presence of disorder, distorted stripes around defects are not orthogonal, which reestablishes Josephson coupling between layers and increases TC.

Study offers new target for antibiotic resistant bacteria

Study offers new target for antibiotic resistant bacteria

As antibiotic resistance rises, the search for new antibiotic strategies has become imperative. In 2013, the Centers for Disease Control estimated that antibiotic resistant bacteria cause at least 2 million infections and 23,000 deaths a year in the U.S.; a recent report raised the likely mortality rate to 162,044.
New Cornell research on an enzyme in bacteria essential to making DNA offers a new pathway for targeting pathogens. In “Convergent Allostery in Ribonucleotide Reductase,” published June 14 in Nature Communications, researchers used the MacCHESS research stations at the Cornell High Energy Synchrotron Source (CHESS) to reveal an unexpected mechanism of activation and inactivation in the protein ribonucleotide reductase (RNR).

Understanding the “switch” that turns RNR off provides a possible means to shut off the reproduction of harmful bacteria.
RNRs take ribonucleotides, the building blocks of RNA, and convert them to deoxyribonucleotides, the building blocks of DNA. In all organisms, the regulation of RNRs involves complex mechanisms, and for good reason: These mechanisms prevent errors and dangerous mutations.

>Read more on the CHESS website

Image: William Thomas, a graduate student in the field of chemistry and chemical biology, collects data on ribonucleotide reductase.

PREM students outfitting and upgrading CHESS x-ray beamlines

PREM students outfitting and upgrading CHESS x-ray beamlines

CHESS is fortunate to have three graduate students visiting from Puerto Rico. Supported by the NSF-PREM CiE2M – the Center for Interfacial Electrochemistry of Energy Materials – a partnership of The University of Puerto Rico, Rio PiedrasCampus (UPRRP), Universidad Metropolitana (UMET) and Universidad del Turabo (UT), and CHESS. 

This group forms an educational and innovative collaborative materials research effort to bring together a diverse and talented scientific community with experience and expertise in electro-chemistry, solid-state and inorganic chemistry, and synchrotron-based techniques to character energy materials in operando conditions at CHESS.  
The students have become an integral part of the team building out and commissioning new X-ray beamlines at the upgraded CHESS facility. New to them was learning good ultra-high vacuum (UHV) practices, using tools like torque wrenches to set vacuum seals, and using an RGA to find chemical contamination in optics boxes (“was really interesting!”). They have also studied the design of beamline components in each sector: apertures, safety bricks and power filters required to deliver X-rays to experimental hutches.
Melissa’s favorite activity was assembling components for Sector 4 X-ray monochromator. “It is like a puzzle to solve. There are many different plates and bolts and it is a real challenge to assemble based on the 3D CADmodel. There is a correct order to do things. It was fun to install water cooled components in the vacuum chamber,” she says.

>Read more on the CHESS website

Image: Brenda, Joesene, Melissa, and Alan Pauling (right) of CHESS proudly display their ultra-high vacuum assembly and installation in the Sector 2 cave of the new CHESS beamline. The students have worked hand-in-hand with CHESS staff to assemble, test and prepare the X-ray beampipes in three different sectors of CHESS. 

Biofortification of field-grown cassava

Biofortification of field-grown cassava

Micronutrient deficiency, sometimes called the “hidden hunger,” causes severe health problems in hundreds of millions of people worldwide, and is particularly damaging to children, in whom it can impair both physical and cognitive development.

Biofortification is one of the most promising tools available for alleviating this problem, but is a multifaceted challenge involving not only creating nutrient-rich crop varieties, but also ensuring bioavailability of these nutrients, protecting against increased uptake of toxins such as cadmium, and adoption by affected populations.

In an open-access paper published this week in Nature Biotechnology, a team led by researchers at the Donald Danforth Center for Plant Science in St. Louis reports successful development of an iron- and zinc- fortified variety of cassava, representing a substantial leap forward in this effort. The interdisciplinary effort reports that the new variety accumulates 7-18 times greater iron and 3-10 times greater zinc than controls, and includes detailed evaluation of the accessibility of these nutrients after being prepared for food. Adoption of this cassava variety could provide up to half of the iron and two-thirds of the zinc required for women and children among particular West African populations who rely on cassava for a substantial fraction of overall diet.

>Read more on the CHESS website

Image: X-ray Fluorescence images, obtained at CHESS, comparing localization of Fe, Zn, and Ca in the stems and storage roots of several genetically distinct varieties of Cassava; (from Narayanan et al, doi: 10.1038/s41587-018-0002-1). Scale bars: 1 mm.

Intermittent plasticity in individual grains

Intermittent plasticity in individual grains

A study using high energy x-ray diffraction.

Understanding the behavior of metals undergoing deformation is critical to design for fuel efficiency, performance and safety/crashworthiness. Traditional engineering analysis treats metal deformation as a smooth motion, like a fluid, when in reality the flow is intermittent at finer length scales. Use of a new detector enabled the study of these intermittent bursts of deformation at the scale of individual crystals in a loaded test sample.
A metal component is polycrystalline, composed of many crystals or grains. At the scale of millimeters, the deformation of a metal appears to proceed smoothly, whereas at the microscopic scale the underlying processes occurring in individual grains proceed in fits and starts. In this collaboration between researchers at Cornell University, the University of Illinois at Urbana-Champaign, the Air Force Research Laboratory and the Advanced Photon Source of Argonne National Laboratory, a high-speed detector was used to study these microscale deformation bursts in a grain-by-grain manner.

>Read more on the CHESS website

Image: The MM-PAD is shown with the vacuum cover and x-ray window removed. The 2×3 arrangement of detector modules are the brownish squares in the center.  Each module consists of 128×128 square pixels, where each pixel is 150µm of a side. Each module is roughly 2 cm x 2 cm in size. There is a 5 pixel wide (0.75 mm) inactive area between adjacent modules. (This photo is of an MM-PAD with Si, instead of CdTe sensors; otherwise, the two types of MM-PADs look identical.)

Conclusion of the construction project: CHESS-U.

Conclusion of the construction project: CHESS-U.

Fourteen months ago, Lt. Gov. Kathy Hochul came to the Cornell High Energy Synchrotron Source (CHESS) to announce a $15 million grant from the New York State Upstate Revitalization Initiative.

The URI funding was for an upgrade project – dubbed “CHESS-U” – which would arm CHESS with enhanced X-ray capabilities, keeping it a leading synchrotron source in the U.S. The project was also expected to create dozens of jobs, both at Cornell and across the region.
On Jan. 17, Hochul returned to Wilson Laboratory, the home of CHESS, to proclaim the project complete in an event that drew local lawmakers, stakeholders from Cornell, and representatives from several local and regional manufacturers whose contributions were on display during a short tour of the new experiment hutches and other equipment.
There is still some work to be done related to the project, and the linear accelerator and synchrotron beams – which were turned off for CHESS-U on June 4, 2018 – aren’t scheduled to be turned back on until Jan. 23. The event marked the official end of the construction project, for which crews worked double shifts over the final six months of 2018 in order to minimize downtime. In addition, wall and ceiling segments for most of the new experiment hutches were built off-sight at Advanced Design Consulting of Lansing and shipped to CHESS for installation. Beamlines will gradually be recommissioned in the coming months.

>Read more on the CHESS website

Image: CHESS Director Joel Brock, left, takes Lt. Gov. Kathy Hochul on a tour of the new construction at the Cornell High Energy Synchrotron Source during an event Jan. 17 to mark the conclusion of the $15 million upgrade project, known as CHESS-U.
Credit: Jason Koski/Cornell Brand Communications