World Science Day spotlight: Collaborating to tackle SARS-CoV-2

Science facilities worldwide have been working around the clock to drive forward SARS-CoV-2 research to alleviate the suffering that the COVID-19 pandemic is currently causing.

Today (November 10), in recognition of World Science Day for Peace and Development, the collective efforts of thousands of scientists and technical experts is being marked through this year’s focus – “Science for and with Society in dealing with the global pandemic.”

At the start of the pandemic, the facilities that make up the Lightsources.org collaboration were swift to ensure that rapid access was available for researchers working on SARS-CoV-2. This has led to a large body of research being undertaken at synchrotrons and free electron lasers.  The aims have been varied and include mapping the structure of the virus; finding binding sites for drugs to lock into; screening existing drugs to establish if they have a role to play in treating patients; understanding the impact of the virus on the lungs; and understanding the immune response so vaccines can be designed to illicit an immune response in the body.

A dedicated, regularly updated, web page – Lightsource research for SARS-CoV-2 – draws together all this research, along with other publications and resources.  It also includes links for researchers wishing to gain rapid access for their SARS-CoV-2 experiments.

The World Science Day for Peace and Development was created as a follow-up to the World Conference on Science, organised jointly by UNESCO and the International Council for Science in Budapest (Hungary) in 1999.

By linking science more closely with society, World Science Day for Peace and Development aims to ensure that citizens are kept informed of developments in science. It also underscores the role scientists play in broadening our understanding of the remarkable, fragile planet we call home and in making our societies more sustainable.

Learn more about World Science Day for Peace and Development on the UNESCO website

Image: World Science Day for Peace and Development 2020 poster

Credit: UNESCO

Understanding more about the ExPaNDS project

Diamond is a key collaborator in this European project, which will be mapping the data behind the thousands of published scientific papers

ExPaNDS is the European Open Science Cloud (EOSC) Photon and Neutron Data Service, which is a collaboration project between ten national Photon and Neutron Research Infrastructures (PAN RIs). This ambitious project will create opportunities for facilities’ users to access the data behind the thousands of successful published scientific papers generated by Europe’s PaN RIs – which every year create petabytes of data.
ExPaNDS will link all relevant data catalogues to ensure that any scientific research communities have access to both the raw data collected that is linked to their session(s) at these facilities, and the relevant peer review articles produced as a direct result of their usage.

The project brings together a network of ten national PaN RIs from across Europe as well as EGI, a federated e-Infrastructure set up to provide advanced computing services for research. In order to do this, ExPaNDS will develop a common ontology for all the elements of these catalogues, a roadmap for the back-end architecture, functionalities and a powerful taxonomy strategy in line with the requirement of the EOSC user community.

>Read more on the Diamond Light Source website
>Find more news on the ExPaNDS website

ExPaNDS presentation video

Helping to grow more food in Africa

University of Saskatchewan scientists help farmers in West Africa improve crops.

Derek Peak and Abimfoluwa Olaleye are using Canadian Light Source at the University of Saskatchewan (Usask) to help farmers in Nigeria and the Republic of Benin to grow vegetables less expensively and more sustainably. The USask researchers and their team recently published a paper in Soil Systems that explores the effects of an innovative farming practice, fertilizer microdosing, on two vegetable systems in both countries.

“The overall idea was to scale up good, innovative ideas to solve food security problems in the regions,” says Peak. “We combine agricultural studies out in the field with socio-economic studies and development work.” Olaleye’s interest in the project is both scientific and personal. “Anything agriculture always gets my interest, it’s something I’m passionate about. And helping people is a big bonus. My dad was a farmer back in Nigeria, so I picked up on that,” he says.

>Read more on the Canadian Light Source website

Image: Abimfoluwa Olaleye (right) and Taylor Procyshen, a graduate student who helped with the project, working in the laboratory together.

SESAME: the doors are closed, but open for science

Quarantine and curfew are affecting many activities in Jordan and abroad, but although SESAME’s doors have been closed since March 18th, the staff have been anything but inactive, devoting a great deal of their time at home to science and work.

With two new papers just published in the past few weeks, Messaoud Harfouche, the XAFS/XRF Beamline Scientist, keeps himself busy helping more users obtain results from the data taken at the beamline. “During these weeks, I am dealing with six projects at the same time, two from Egypt, two from Pakistan, one from Iran, and one from Jordan” he says. Given the difficulty of XAFS analysis and the complexity of some software packages, the degree of involvement in each project may vary from suggesting the best path in data analysis to full collaboration, implying result interpretation and participation in drafting a scientific paper. “Moreover”, continues Messaoud, “my own research projects were also in my drawer, waiting to be worked out. With willpower and a little perseverance, curfew may turn out to be very beneficial”.

On another front, scientists from synchrotron radiation laboratories in different points in Europe (ELETTRA in Italy, ESRF in France and SOLARIS in Poland) and SESAME in Jordan are collaborating at a distance on raytracing simulations for the Technical Design Report (TDR) of SESAME’s BEATS (BEAmline for Tomography at SESAME) beamline which is approaching finalization, and from their respective homes Matteo Altissimo (ELETTRA), Alexander Rack (ESRF), Tomasz Kolodziaj (SOLARIS), and Gianluca Iori (SESAME) are constantly in touch with each other. In parallel, from their homes, too, team members of SESAME’s technical sector have been collaborating in the final design of the front end and experimental station of the beamline. BEATS is SESAME’s hard X-ray tomography beamline that is expected to come on stream in 2022.

>Read more on the SESAME website

Picture: As in the case of thousands of researchers worldwide, computer screens and notebooks are currently the main tools for the work of SESAME’s staff.

Accoustic spin waves: towards a new paradigm of on-chip communication

For the first time researchers have observed directly sound-driven spin waves (magnetoacoustic waves) and have revealed its nature.

Results show that these magnetization waves can go up to longer distances (up to centimeters) and have larger amplitudes than the commonly known spin waves. The study, published in Phys. Rev. Lett., is carried out by researchers from the University of Barcelona (UB), the Institute of Materials Science of Barcelona (ICMAB-CSIC), and the ALBA Synchrotron, in collaboration with the Paul-Drude-Institut in Berlin.

Researchers have observed directly and for the first time magnetoacoustic waves (sound-driven spin waves), which are considered as potential information carriers for novel computation schemes. These waves have been generated and observed on hybrid magnetic/piezoelectric devices. The experiments were designed by a collaboration between the University of Barcelona (UB), the Institute of Materials Science of Barcelona (ICMAB-CSIC) and the ALBA Synchrotron. The results show that magnetoacoustic waves can travel over long distances -up to centimeters- and have larger amplitudes than expected.

>Read more on the ALBA website

Image: TOP: A propagating and a standing magnetization wave in ferromagnetic Nickel, driven by magnetoelastic coupling to a surface acoustic wave in a piezoelectric LiNbO3substrate. The images combine line profiles (color indicating the local magnetization direction) at different delay times between the probing X-ray pulse and the electrical SAW excitation.
BOTTOM: Scheme of the strain caused by the surface acoustic waves (SAWs) in the piezoelectric (in green color scale) and magnetic modulation in the ferromagnetic material (in orange-cyan color scale).

How a new electrocatalyst enables ultrafast reactions

The work provides rational guidance for the development of better electrocatalysts for applications such as hydrogen-fuel production and long-range batteries for electric vehicles.

The oxygen evolution reaction (OER) is the electrochemical mechanism at the heart of many processes relevant to energy storage and conversion, including the splitting of water to generate hydrogen fuel and the operation of proposed long-range batteries for electric vehicles. Because the OER rate is a limiting factor in such processes, highly active OER electrocatalysts with long-term stability are being sought to increase reaction rates, reduce energy losses, and improve cycling stability. Catalysts incorporating rare and expensive materials such as iridium and ruthenium exhibit good performance, but an easily prepared, efficient, and durable OER catalyst based on earth-abundant elements is still needed for large-scale applications.

Key insight: shorter O-O bonds
In an earlier study, a group led by John Goodenough (2019 Nobel laureate in chemistry) measured the OER activities of two compounds with similar structures: CaCoO3 and SrCoO3. They found that the CaCoO3 exhibited higher OER activity, which they attributed to its shorter oxygen–oxygen (O-O) bonds. Inspired by this, members of the Goodenough group have now analyzed a metallic layered oxide, Na0.67CoO2, which has an even more compact structure than CaCoO3. X-ray diffraction (XRD) experiments performed at the Advanced Photon Source (APS) confirmed that the shortest O-O separation in Na0.67CoO2 is 2.30 Å, compared to 2.64 Å for CaCoO3. The researchers then compared the OER performance of Na0.67CoO2 with IrO2, Co3O4, and Co(OH)2. They found that Na0.67CoO2 exhibited the highest current density, the lowest overpotential (a measure of thermodynamic energy loss), and the most favorable Tafel slope (sensitivity of the electric current to applied potential). The Na0.67CoO2 also showed excellent stability under typical operating conditions.

>Read more on the Advanced Light Source website

Image: (extract, full image here) A new electrocatalyst prepared for this study, Na0.67CoO2, consists of two-dimensional CoO2 layers separated by Na layers (not shown). The Co ions (blue spheres) have four different positions (Co1-Co4), and the distorted Co–O octahedra have varying oxygen–oxygen (O-O) separations (thick red lines connecting red spheres). All of the O-O bonds are shorter than 2.64 Å (the length of the corresponding bonds in a comparable material), and the shortest bonds are less than 2.40 Å. It turns out that O-O separation has a strong effect on the oxygen evolution reaction (OER) in this material.

Growing an international community for agricultural synchrotron research

Dr. Chithra Karunakaran’s passion for agriculture has taken her around the world and helped her to grow an international agricultural imaging research community from Saskatoon. 

Given that the Canadian Light Source (CLS) is situated on the University of Saskatchewan (USask) campus, renowned for agriculture, and surrounded by some of the finest farm land in the country, it’s little wonder it has developed a reputation for outstanding agriculture-related research. Location is only part of the story though; some credit has to go to an engineer determined to apply advanced synchrotron techniques to the study of what we grow and what we eat.

The view from Agriculture Science Manager Dr. Chithra Karunakaran’s office window is dominated by the USask College of Agriculture and Bioresources, which also owns the research greenhouse located across the street from the CLS. Both are part of what she termed “the right ecosystem” needed to expand ag research at the facility, a project she has devoted herself to since she arrived in Saskatoon. The key has been adapting beamline techniques to serve the needs of plant, soil and food scientists.

>Read more on the Canadian Light Source website

Image: Karunakaran working with synchrotron science equipment. 

Scientists observe ultrafast birth of free radicals in water

What they learned could lead to a better understanding of how ionizing radiation can damage material systems, including cells.

Understanding how ionizing radiation interacts with water—like in water-cooled nuclear reactors and other water-containing systems—requires glimpsing some of the fastest chemical reactions ever observed.

In a new study conducted at the Department of Energy’s SLAC National Accelerator Laboratory, researchers have witnessed for the first time the ultrafast proton transfer reaction following ionization of liquid water. The findings, published today in Science, are the result of a world-wide collaboration led by scientists at the DOE’s Argonne National Laboratory, Nanyang Technological University, Singapore (NTU Singapore) and the German research center DESY.

The proton transfer reaction is a process of great significance to a wide range of fields, including nuclear engineering, space travel and environmental remediation. This observation was made possible by the availability of ultrafast X-ray free electron laser pulses, and is basically unobservable by other ultrafast methods. While studying the fastest chemical reactions is interesting in its own right, this observation of water also has important practical implications.

>Read more on the LCLS at SLAC website

Image: X-rays capture the ultrafast proton transfer reaction in ionized liquid water, forming the hydroxyl radical (OH) and the hydronium (H3O+) ion. Credit: Argonne National Laboratory

Covalent Organic Framework (COF‐1) under pressure

Covalent Organic Frameworks (COF’s) form a family of polymeric materials composed only by light elements. The absence of metal atoms in their structure makes COF’s distinctly different compared to their relatives, Metal Organic Framework materials (MOF’s). Historically first COF structure (named COF-1) was reported back in 2005 by Cote et al., (Science 310 (2015) 1166).  It consists of benzene rings linked by B3Ointo hexagon-shaped 2D sheets which are stacked into a layered structure, resembling in this respect the structure of graphite composed by graphene layers. By analogy with graphene the single layer of COF material could be named as COFene since it represents a true 2D material composed by carbon, hydrogen, boron and oxygen. Unlike graphite, COF-1 is porous material with relatively high surface area which makes it promising for various applications, e.g. for energy storage devices, as a sorbents for gas storage or for membranes.  However, little was known about mechanical properties of COF’s or single layered COFenes except for few theoretical estimations. Unlike graphite or MOF’s, no high pressure studies were available for COFs. The study by A. Talyzin group from Umeå University (Sweden) performed at Elettra at the Xpress beamline and SOLEIL synchrotrons in collaboration with the Technical University of Dresden (Germany) and the Chalmers University (Sweden) is first to evaluate compressibility and pressure limits for stability of COF-1 structure.

>Read more on the Elettra website

Picture: schematics of the high pressure experiments involving diamond anvil cell

Scientists probe Earth’s deep mantle in the laboratory

Extreme conditions experiments sharpen view of our planet’s interior

Simulating the conditions 2700 kilometres deep underground, scientists have studied an important transformation of the most abundant mineral on Earth, bridgmanite. The results from the Extreme Conditions Beamline at DESY’s X-ray light source PETRA III reveal how bridgmanite turns into a structure known as post-perovskite, a transformation that affects the dynamics of Earth’s lower mantle, including the spreading of seismic waves. The analysis can provide an explanation for a range of peculiar seismic observations, as the team headed by Sébastien Merkel from the Université de Lille in France report in the Journal Nature Communications.
Bridgmanite is a magnesian-iron mineral ((Mg,Fe)SiO3) with a crystal structure that is not stable under ambient conditions. It forms about 660 kilometres below the surface of the Earth, and microcrystalline grains found as inclusions in meteorites are the only samples ever recovered on the surface. “In order to study bridgmanite under the conditions of the lower mantle, we had to produce the mineral first,” explains Merkel. To do so, the scientists compressed tiny amounts of iron-magnesium-silicon-oxide in a diamond anvil cell (DAC), a device that can squeeze samples with high pressure between two small diamond anvils.

Image: The crystal structures of bridgmanite (left) and post-perovskite (right).

Credit: Université de Lille, Sébastien Merkel
>Read more on the PETRA III (DESY) website

Translucency of graphene to van der Waals forces

If in the infinitely large it is the gravitational force that determines the evolution in space and time of planets, stars and galaxies, when we focus our observation on the atomic scale other are the forces that allow materials to exist. These are forces that, like a “special glue”, allow atoms and molecules to aggregate to form living and non-living systems. Among them we find one that, although discovered 150 years ago by Johannes Diderik van der Waals (vdW), still carries with it some aspects of ambiguity. Van der Waals was the first to reveal its origin and to give a first and simple analytical description, even though it took more than a century, with the new discoveries of quantum field theory, to be able to fully understand its quantum character and its relation to the vacuum energy and Casimir force. And only in the last 30 years it has been realized how much this force pervades the natural world. One of the wonders is represented by the geckos, who use these forces to climb vertical and smooth walls thanks to the vdW forces, which are enhanced because of the multitude of hairs present in each finger of their legs. These forces are also known to affect the stability of the double helix of the DNA and are also responsible for the interactions between different groups of amino acids.
What makes the vdW force unique is the fact that it is the weakest of the inter-atomic and inter-molecular forces present in nature and therefore it remains extremely difficult to measure with great accuracy. At the same time, even the inclusion of these force in the most accurate methods of calculation has not yet found a universal solution and the different approaches used by theoretical physicists and chemists to take them into account can sometimes lead to conflicting results.

>Read more on the Elettra website

Image:   CO desorption from Gr/Ir(111). (a) Selected spectra of the uptake corresponding to θCO=0.08 ML (bottom) and 0.30 ML (top). (b) TP-XPS C 1s core level spectra showing its evolution during thermal desorption of CO from Gr/Ir(111). (c) Comparison of CO coverage evolution as a function of temperature for selected CO initial coverages. 

Asia-Oceania Forum for Synchrotron Radiation Research in Tawain

The Asia-Oceania Forum for Synchrotron Radiation Research (AOFSRR) was formally established in 2006. The current members include Australia, China, India, Japan, Malaysia, New Zealand, South Korea, Singapore, Taiwan, Thailand, and Vietnam. Its objective is to strengthen collaboration among the synchrotron radiation (SR) facilities and to promote SR sciences and accelerator-based research in the Asia-Oceania region.

Image: Students performed experiments and analyzed data at various endstations.

Read more on the NSRRC website

First molecular movies at European XFEL

Scientists show how to use extremely short X-ray pulses to make the first movies of molecular processes at the European XFEL.

In a paper published today in Nature Methods, scientists show how to effectively use the high X-ray pulse repetition rate of the European XFEL to produce detailed molecular movies. This type of information can help us to better understand, for example, how a drug molecule reacts with proteins in a human cell, or how plant proteins store light energy.

Traditional structural biology methods use X-rays to produce snapshots of the 3D structure of molecules such as proteins. Although valuable, this information does not reveal details about the dynamics of biomolecular processes. If several snapshots can be taken in fast enough succession, however, these can be pasted together to make a so-called molecular movie. The high repetition rate of the extremely short X-ray pulses produced by the European XFEL makes it now possible to collect large amounts of data to produce movies with more frames than ever before. An international group of scientists have now worked out how to make optimal use of the European XFEL’s very high X-ray repetition rate to make these molecular movies at the facility in order to reveal unprecedented details of our world.

>Read more on the European XFEL website

Image: Artistic visualisation of a serial crystallography experiment. A stream of crystalline proteins are struck by an optical laser that initiates a reaction. Following a short delay the X-ray laser strikes the crystals. The information recorded about the arrangement of the atoms in the protein is used to reconstruct a model of the structure of the protein.
Credit: European XFEL / Blue Clay Studios

The mechanism of the most commonly used antimalarial drugs unveiled

For centuries, quinoline has been an effective compound in antimalarial drugs, although no one knew its mode of action in vivo.

Today, a team led by the Weizmann Institute has discovered its mechanism in infected red blood cells in near-native conditions, by using the ESRF, Alba Synchrotron and BESSY. They publish their results in PNAS.

Malaria remains one of the biggest killers in low-income countries. Estimates of the number of deaths each year range from 450,000 to 720,000, with the majority of deaths happening in Africa. In the last two decades, the malaria parasite has evolved into drug-resistant strains. “Recently, the increasing geographical spread of the species, as well as resistant strains has concerned the scientific community, and in order to improve antimalarial drugs we need to know how they work precisely”, explains Sergey Kapishnikov, from the University of Copenhagen, in Denmark, and the Weizmann Institute, in Israel, and leader of the study.

Plasmodium parasite, when infecting a human, invades a red blood cell, where it ingests hemoglobin to grow and multiply. Hemoglobin releases then iron-containing heme molecules, which are toxic to the parasite. However, these molecules crystallise into hemozoin, a disposal product formed from the digestion of blood by the parasite that makes the molecules inert. For the parasite to survive, the rate at which the heme molecules are liberated must be slower or the same as the rate of hemozoin crystallization. Otherwise there would be an accumulation of the toxic heme within the parasite.

>Read more on the ESRF website

Image (taken from BESSY II article): The image shows details such as the vacuole of the parasites (colored in blue and green) inside an infected blood cell.
Credit:
S. Kapishnikov

Two other institutes, BESSY II at HZB and ALBA Synchrotron, have participated in this research. Please find here their published articles:

> X-ray microscopy at BESSY II reveal how antimalaria-drugs might work

> The mechanism of the most commonly used antimlalarial drugs in near- native conditions unveiled

Worldwide scientific collaboration develops catalysis breakthrough

A new article  just published in Nature Catalysis shows the simple ways of controlling the structure of platinum nanoparticles and tuning their catalytic properties. 

Research led by Cardiff Catalysis Institute (CCI) in collaboration with scientists from Lehigh University, Jazan University, Zhejiang University, Glasgow University, University of Bologna, Research Complex at Harwell (RCaH), and University College London have combined their unique skills to develop and understand using advanced characterisation methods (particularly TEM and B18 at Diamond Light Source), how it is possible to use a simple preparation method to control and manipulate the structures of metal nanoparticles. These metal nanoparticles are widely used by industry as innovative catalysts for the production of bulk chemicals like polymers, liquid fuels (e.g., diesel, petrol) and other speciality chemicals (pharmaceutical products).

>Read more on the Diamond Light Source website

Image: Andy Beale works at Diamond Light Source.