Cornell High Energy Synchrotron Source (CHESS)

Picking up good vibrations – of proteins – at CHESS

2023/05/102023/05/18

A new method for analyzing protein crystals – developed by Cornell researchers and given a funky two-part name – could open up applications for new drug discovery and other areas of biotechnology and biochemistry.

The development, outlined in a paper published March 3 in Nature Communications, provides researchers with the tools to interpret the once-discarded data from X-ray crystallography experiments – an essential method used to study the structures of proteins. This work, which builds on a study released in 2020, could lead to a better understanding of a protein’s movement, structure and overall function.

Protein crystallography produces bright spots, known as Bragg peaks, from the crystals, providing high-resolution information about the shape and structure of a protein. This process also captures blurry images – patterns and clouds related to the movement and vibrations of the proteins – hidden in the background of the Bragg peaks.

These background images are typically discarded, with priority given to the bright Bragg peak imagery that is more easily analyzed.

Meisburger worked closely with Ando to develop the robust workflow to decode the weak background signals from crystallography experiments called diffuse scattering. This allows researchers to analyze the total scattering from crystals, which depends on both the protein’s structure and the subtle blur of its movements.

Their two-part method – which the team dubbed GOODVIBES and DISCOBALL – simultaneously provides a high-resolution structure of the protein and information on its correlated atomic movements.

GOODVIBES analyzes the X-ray data by separating the movements – subtle vibrations – of the protein from other proteins that might be moving around it. DISCOBALL independently validates these movements for certain proteins directly from the data, allowing researchers to trust the results from GOODVIBES and understand what the protein might be doing.

How a record-breaking copper catalyst converts CO2 into liquid fuels

2023/02/172023/03/06

Researchers at Berkeley Lab, collaborating with CHESS scientists at the PIPOXS beamline, have made the first real-time movies of copper nanoparticles as they evolve to convert carbon dioxide and water into renewable fuels and chemicals. Their new insights could help advance the next generation of solar fuels.

Since the 1970s, scientists have known that copper has a special ability to recycle carbon dioxide into valuable chemicals and fuels. But for many years, scientists have struggled to understand how this common metal works as an electrocatalyst, a mechanism that uses energy from electrons to chemically transform molecules into different products.

Now, a research team led by Lawrence Berkeley National Laboratory (Berkeley Lab) has gained new insight by capturing the world’s first real-time movies of copper nanoparticles (copper particles engineered at the scale of a billionth of a meter) as they convert CO₂ and water into renewable fuels and chemicals: ethylene, ethanol, and propanol, among others. The work was reported in the journal Nature.

“This is very exciting. After decades of work, we’re finally able to show – with undeniable proof – how copper electrocatalysts excel in CO₂ reduction,” said Peidong Yang, a senior faculty scientist in Berkeley Lab’s Materials Sciences and Chemical Sciences Divisions who led the study. Yang is also a professor of chemistry and materials science and engineering at UC Berkeley. “Knowing why copper is such an excellent electrocatalyst brings us steps closer to turning CO₂ into new, renewable solar fuels through artificial photosynthesis.”

Image: Artist’s rendering of a copper nanoparticle as it evolves during CO2 electrolysis: Copper nanoparticles (left) combine into larger metallic copper “nanograins” (right) within seconds of the electrochemical reaction, reducing CO2 into new multicarbon products.

Credit: Yao Yang/Berkeley Lab

Influence of alloying on slip intermittency and implications for dwell fatigue in titanium

2022/11/142023/01/04

The high precision of HEDM measurements at FAST offer new insight into the microscopic processes that cause dwell fatigue, pointing toward new alloying strategies for mitigation.

What is the discovery?

Titanium alloys exhibit a phenomenon known as dwell fatigue: when the alloys are held under persistent loads as low as 60% of yield stress, their fatigue lifetime is gradually reduced. The culprit for this degradation in performance is believed to be dislocation slip, which is an intermittent, scale bridging phenomenon, not unlike a nanoscale earthquake occurring in the alloy. Sudden dislocation slips can induce large stress bursts and initiate crack formation. In a new publication appearing in Nature Communications, a team lead by Felicity Worsnop (MIT) and David Dye (Imperial College London) has used high-energy diffraction microscopy at the FAST beamline at CHEXS to observe and quantify thousands of sudden “stress drop” events in thousands of different crystalline grains inside titanium alloys held under dwell fatigue conditions. The team was able to collect unprecedentedly precise statistics for the probability for different types of stress drop events to occur in different alloys. The figure below shows the probability for stress drops with magnitude equal to or greater than Δτ̅ and associated with the possible 3 slip modes (illustrated at right), in 4 different alloys (a – disordered Ti-7AL, low oxygen content; b – higher oxygen content; c – low oxygen, after aging; d – high oxygen, after aging). They discover that interstitial oxygen promotes slip homogeneity, with a higher frequency of smaller stress drops being observed, whereas precipitation of regions with aluminum ordering results in fewer, larger events. Basal slip is observed to be the most common of the slip modes and gives rise to the largest slip events.

Protein family shows how life adapted to oxygen

2022/10/042022/10/12

Cornell scientists have created an evolutionary model that connects organisms living in today’s oxygen-rich atmosphere to a time, billions of years ago, when Earth’s atmosphere had little oxygen – by analyzing ribonucleotide reductases (RNRs), a family of proteins used by all free-living organisms and many viruses to repair and replicate DNA.

“By understanding the evolution of these proteins, we can understand how nature adapts to environmental changes at the molecular level. In turn, we also learn about our planet’s past,” said Nozomi Ando, associate professor of chemistry and chemical biology in the College of Arts and Sciences and corresponding author of the study. “Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade” published in eLife Digest Oct. 4.

Co-first authors of the study are Audrey Burnim and Da Xu, doctoral students in chemistry and chemical biology, and Matthew Spence, Research School of Chemistry, Australian National University, Canberra. Colin J. Jackson, professor of chemistry, Australian National University, Canberra, is a corresponding author.

This undertaking involved a large dataset of 6,779 RNR sequences; the phylogeny took several high-performance computers a combined seven months (1.4 million CPU hours) to calculate. Made possible by computing advances, the approach opens up a new way to study other diverse protein families that have evolutionary or medical significance.

RNRs have adapted to changes in the environment over billions of years to conserve their catalytic mechanism because of their essential role for all DNA-based life, Ando said. Her lab studies protein allostery – how proteins are able to change activity in response to the environment. The evolutionary information in a phylogeny gives us a way to study the relationship between the primary sequence of a protein and its three-dimensional structure, dynamics and function.

Image: Tree inference on a ribonucleotide reductase (RNR) sequence dataset as included in the original report, “Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade“.

Welcome Jeney Wierman – New MacCHESS Director

2022/07/142022/07/29

Jeney Wierman started as the new MacCHESS Director on July 1st, 2022. Below is a welcome message to the whole CHESS Community.

Jeney takes over the MacCHESS directorship from Marian Szebenyi, who will be retiring later this year after 30 years at MacCHESS .

Dear CHESS Community,

It is (hopefully) no secret that I hold a very special place in my heart for CHESS, the people working here, and the community it supports. With that, I am honored and delighted to join CHESS this summer as Director of MacCHESS! First, I must thank Marian Szebenyi for continuing to work with me into the fall startup – I have large shoes to fill and appreciate the overlap support. Second, I would also like to thank all who were a part of the hiring process over the past few months, plus onboarding over the last week. Much appreciated.

Image: Jeney Wierman has started as the MacCHESS Director on July 1.

#SynchroLightAt75 – Rod MacKinnon’s Nobel Prize in chemistry

2022/06/092022/06/09

Rod MacKinnon – Nobel Prize in chemistry 2003 for work on the structure of ion channels

The structural work of MacKinnon was carried out primarily at the Cornell High Energy Synchrotron Source (CHESS) and the National Synchrotron Light Source (NSLS) at Brookhaven. At the time, CHESS was a first-generation SR source. The award for MacKinnon’s work was the second recognition of SR work by the Nobel Committee. MacKinnon acknowledges the crucial role that the two synchrotron facilities, Cornell Synchrotron (CHESS/MacCHESS) and NSLS, have played in his research on the protein crystallography of membrane channels.

Image: View showing the location of CHESS, which is underground at Cornell

Credit: Jon Reis

Nonprecious transition metal nitrides as efficient oxygen reduction electrocatalysts for alkaline fuel cells

2022/03/092022/04/11

CHEXS users have discovered a class of nonprecious metal derivatives that can catalyze fuel cell reactions about as well as platinum, at a fraction of the cost. A critical part of the fuel cell is the oxygen reduction reaction, an infamously sluggish process that is traditionally sped up by platinum and other precious metals. Now, in a new paper appearing in the journal Science Advances, a team lead by Héctor Abruña (the Émile M. Chamot Professor of Chemistry and Chemical Biology at Cornell University), have reported a new cobalt nitride catalyst material with near identical efficiency to platinum while costing 475 times less (as of February 2022). Carbon-supported cobalt nitride (Co3N/C) achieved a record-high peak power density among reported nitride cathode catalysts of 700 mW cm−2 in alkaline membrane electrode assemblies. The material was demonstrated to remain stable below 1.0V potentials inside working fuel cells, using operando x-ray spectroscopy at the PIPOXS beamline. Operando XANES and EXAFS (A,B) show dramatic changes in valence and bond lengths for potentials above 1V, while below 1V the material remains stable (C,D).

Measuring complex fluids under extreme flow conditions

2022/02/042022/02/10

Utilizing the unique focusing optics, flexible sample space, and SAXS capabilities at the FMB-beamline, a group of researchers from the National Institute of Standards and Technology measured the rheology and structure of complex fluids subjected to extreme flow velocities while confined within micrometer-sized capillaries.

What did the scientists do?

A capillary rheometer capable of producing high shear rates at the wall, previously developed for neutron scattering, was modified to expand the accessible shear rates up to 10⁷ s^-1 when using a high-flux x-ray source with small spot sizes, such as the FMB-beamline at CHESS. Using the new setup optimized for x-ray scattering, the structure and rheology of worm-like micelle solutions were measured at high shear rates to better understand the microstructural alignment, breakdown, and shear thinning rheology of these widely utilized surfactants.

Why is this important?

Worm-like micelle surfactant systems have numerous applications ranging from pharmaceutical formulations to enhanced oil recovery. The simultaneous rheology and x-ray scattering measurements will help link the changes in macroscopic rheological properties to the changes in nanoscale fluid structure such as micelle orientation and length distribution. These measurements are also important to improve rheological models, which currently fail to accurately predict the viscosity of complex fluids at high shear rates.

Image: SAXS measurements at the FMB-beamline showed distinct changes in the worm-like micelle structure under flow

Spare time hobbies and interests

2022/01/312022/01/31

Finding ways to relax and recharge your batteries is really important and helps you maintain perspective, particularly during very busy periods at work. Participants in #LightSourceSelfies told us what they like to do in their spare time. This montage, with contributors from the Australian Synchrotron, CHESS, SESAME and the APS, shows the variety of interests that people within the light source community have. If you are looking for a new way to relax and unwind, you might find an idea that appeals to you in this #LightSourceSelfie!

Enjoying your spare time away from light sources!

Nights!

2022/01/032022/01/03

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

2021/12/082021/12/08

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

2021/12/012021/12/09

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.”

Beginning your light source journey

2021/11/222021/11/23

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

2021/10/142021/10/21

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.

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

2021/08/112021/08/26

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.

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

2021/07/122021/07/28

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.

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.