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.
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.

Breaking up buckyballs is hard to do

A new study shows how soccer ball-shaped molecules burst more slowly than expected when blasted with an X-ray laser beam.

As reported in Nature Physics, an international research team observed how soccer ball-shaped molecules made of carbon atoms burst in the beam of an X-ray laser. The molecules, called buckminsterfullerenes – buckyballs for short ­– consist of 60 carbon atoms arranged in alternating pentagons and hexagons like the leather coat of a soccer ball. These molecules were expected to break into fragments after being bombarded with photons, but the researchers watched in real time as buckyballs resisted the attack and delayed their break-up.

The team was led by Nora Berrah, a professor at the University of Connecticut, and included researchers from the Department of Energy’s SLAC National Accelerator Laboratory and the Deutsches Elektronen-Synchrotron (DESY) in Germany. The researchers focused their attention on examining the role of chemical effects, such as chemical bonds and charge transfer, on the buckyball’s fragmentation.

Using X-ray laser pulses from SLAC’s Linac Coherent Light Source (LCLS), the team showed how the bursting process, which takes only a few hundred femtoseconds, or millionths of a billionth of a second, unfolds over time. The results will be important for the analysis of sensitive proteins and other biomolecules, which are also frequently studied using bright X-ray laser flashes, and they also strengthen confidence in protein analysis with X-ray free-electron lasers (XFELs).

>Read more on the Linear Coherent Light Source at SLAC website

Image: An illustration shows how soccer ball-shaped molecules called buckyballs ionize and break up when blasted with an X-ray laser. A team of experimentalists and theorists identified chemical bonds and charge transfers as crucial factors that significantly delayed the fragmentation process by about 600 millionths of a billionth of a second.
Credit: Greg Stewart/SLAC National Accelerator Laboratory

For additional information: article published on the DESY website

Ultra-white beetle scales may be the key to more sustainable paint

An international team of researchers has managed to mimic the colour of the Cyphochilus beetle scales – one of the brightest whites in nature, thanks to the ESRF’s imaging capabilities. This could help the development of ultra-white, sustainable paints.

Cyphochilus beetle scales are one of the brightest whites in nature. Until now, researchers did not known how their ultra-white appearance is created. X-ray nanotomography experiments at the ESRF have shown that the nanostructure in their tiny scales creates the colour, not the use of pigment or dyes.
Andrew Parnell, from the University of Sheffield and corresponding author of the study said: “In the natural world, whiteness is usually created by a foamy Swiss cheese-like structure made of a solid interconnected network and air. Until now, how these structures form and develop and how they have evolved light-scattering properties has remained a mystery.”
The findings show that the foamy structure of the beetles’ scales has the right proportion of empty spaces, in a highly interconnected nano-network, which optimise the scattering of light – creating the ultra-white colouring.

>Read more on the European Synchrotron website

Image: Andrew Denison and Stephanie Burg in the experimental hutch of beamline ID16B. 

Metal particles abraded from tattooing needles travel inside the body

Allergic reactions are common side effects of tattoos and pigments have been blamed for this. Now researchers prove, for the first time, that particles, containing the allergens nickel and chromium, wear from the needle during the tattooing process, travel inside the body and could also induce allergies.

The number of tattooed people has increased substantially in recent years, with some countries revealing to have up to 24% of the population with a tattoo. Adverse reactions from tattoos are common and until now, researchers believed only inks were to blame.
“There is more to tattoos than meet the eye. It is not only about the cleanliness of the parlour, the sterilization of the equipment or even about the pigments. Now we find that the needle wear also has an impact in your body”, explains Hiram Castillo, one of the authors of the study and scientist at the ESRF.
Today, in a new study published in the journal Particle and Fibre Toxicology, scientists have shown that, surprisingly, chromium and nickel particles coming from tattoo needle wear are distributed towards the lymph nodes. Usually tattoo needles contain nickel (6–8%) and chromium (15–20%) both of which prompt a high rate of sensitization in the general population and may therefore play a role in tattoo allergies. Two years ago, the same team of researchers found that the pigments and their metal impurities are transported to the lymph nodes in a nanoform, where they can be found years after the placement of the tattoos.

>Read more on the ESRF website and watch the video below

Image: Ines Schreiver, first author (German Federal Institute for Risk Assessment (BfR), Berlin, Germany), with Julie Villanova, ESRF scientist during experiments at the ESRF ID16B beamline.
Credit: ESRF

First high-speed hard X-ray microscopic movies at a free-electron laser

New technique enables investigation of industrially relevant materials and processes in motion.

A group of researchers has for the first time performed high-speed microscopy using an X-ray laser at the European XFEL in Schenefeld near Hamburg, Germany. The method allows for observations of processes that take place at speeds up to a few kilometres per second, paving the way for 3D microscopic movies of fast phenomena, with important potential industrial applications. Such movies could show what happens during complex processes with a resolution at the sub-micrometre level, which is less than the diameter of a human hair, while also teasing out hidden internal details. While most other applications of X-ray lasers are based on the short wavelength of their X-ray flashes, making images that reach atomic resolution possible, this use takes advantage of the penetrating properties of X-rays. The resulting images, which are on the microscopic rather than atomic scale, reveal the internal structures of complex processes such as fluid cavitation at high speed. The research, which has been published in the journal Optica, was led by scientists from the Center for Free-Electron Laser Science (CFEL) in Hamburg (a collaboration between DESY, Universität Hamburg, and the Max Planck Society) and the European XFEL and involves scientists from P.J. Šafárik University in Slovakia, Lund University in Sweden, Diamond Light Source and University College London in the UK, the Karlsruhe Institute of Technology in Germany, and the European Synchrotron Radiation Facility (ESRF) in France.

>Read more on the European XFEL website

Illustration: X-ray microscopic image of a bursting glass capillary, taken at the SPB/SFX instrument at the European XFEL. The image on the left shows the image produced from the experiment. The middle version shows the direction of the motion of debris, showing the spinning glass fragments and details of turbulence in the water. The right version shows the velocity of the debris in metres per second. Download to view video here.
Credit: European XFEL

World record in tomography: watching how metal foam forms

An international research team at the Swiss Light Source (SLS) has set a new tomography world record using a rotary sample table developed at the HZB.

With 208 three-dimensional tomographic X-ray images per second, they were able to document the dynamic processes involved in the foaming of liquid aluminium. The method is presented in the journal Nature Communications.
The precision rotary sample table designed at the HZB rotates around its axis at several hundred revolutions per second with extreme precision. The HZB team headed Dr. Francisco García-Moreno combined the rotary sample table with high-resolution optics and achieved a world record of over 25 tomographic images per second using the BESSY II EDDI beamline in 2018.

>Read more on the Bessy II at HZB wesbite

Image: The precision rotary sample table designed at the HZB turns around its axis at several hundred revolutions per second with extreme precision.
Credit: © HZB

Superfluorescent emission in the UV range

Free-electron laser FLASH coaxes superfluorescent emission from the noble gas xenon

Scientists have for the first time induced superfluorescence in the extreme ultraviolet range. Superfluorescence, or superradiance, could be used to build a laser that does not require an optical resonator. The team headed by DESY’s lead scientist Nina Rohringer used DESY’s free-electron laser FLASH to stimulate xenon, a noble gas, inside a narrow tube, causing it to emit coherent radiation, like a laser. The research team is now presenting its work in the journal Physical Review Letters.

“The phenomenon of superfluorescence was first discovered in the microwave range in the 1970s, and then demonstrated for infrared and optical wavelengths too,” explains Rohringer. “In the meantime, superfluorescence has also been observed in the X-ray domain, and at one time this mechanism was believed to be a promising candidate for building X-ray lasers. Until now, however, superfluorescence had not been demonstrated in the extreme ultraviolet, or XUV, range.”

In superfluorescence, the incident light is amplified and emitted along the axis of the medium as a narrow beam of coherent radiation, like in a laser. To produce superfluorescence in the XUV spectrum, the incoming light needs to have enough energy to knock the electrons out of the inner shell of the atoms that make up the lasing medium. Redistribution within the electron shell (Auger decay) leads to a situation in which more particles find themselves in an excited state than in an unexcited state. Physicists refer to this as population inversion.

>Read more on the FLASH at DESY website

Image: The xenon superfluorescence shows up as a bright line (yellow) superimposed on the averaged free-electron laser spectrum (purple, averaged over many shots).
Credit: European XFEL, Laurent Mercadier

“Invisible ink” on antique Nile papyrus revealed by multiple methods

Researchers from the Egyptian Museum and Papyrus Collection, Berlin universities and Helmholtz-Zentrum Berlin studied a small piece of papyrus that was excavated on the island of Elephantine on the River Nile a little over 100 years ago.

The team used serval methods including non-destructive techniques at BESSY II. The researchers’ work, reported in the Journal of Cultural Heritage, blazes a trail for further analyses of the papyrus collection in Berlin.

The first thing that catches an archaeologist’s eye on the small piece of papyrus from Elephantine Island on the Nile is the apparently blank patch. Researchers from the Egyptian Museum, Berlin universities and Helmholtz-Zentrum Berlin have now used the synchrotron radiation from BESSY II to unveil its secret. This pushes the door wide open for analysing the giant Berlin papyrus collection and many more.

>Read more on the BESSY II at HZB website

Illustration: A team of researchers examined an ancient papyrus with a supposed empty spot. With the help of several methods, they discovered which signs once stood in this place and which ink was used.
Credit: © HZB

Visualizing electrostatic gating effects in two-dimensional heterostructures

Electronic and optoelectronic devices utilise electric fields to manipulate material properties, controlling band structures and band alignments across heterostructures that combine metals, semiconductors and insulators. With two-dimensional materials, 2D heterostructures (2DHS) can be fabricated with atomic precision by simply stacking layers. In these, applied out-of-plane electric fields are a powerful tool that can be used to degenerately dope semiconductors, modify electronic structure through the Stark effect, and alter band-alignments between layers. As a result, out-of-plane electric fields have been used to engineer functional architectures such as high-efficiency light-emitting diodes and tunnelling transistors, and to probe many-body phenomena.
Despite the fundamental importance of electric-field control over band structure, direct experimental measurements are challenging and have been limited. Whilst gate electrodes are routinely applied for electrical transport investigations, and many studies have reported electric-field dependent light-emission from 2DHS, these depend upon but do not directly reveal the single-particle electronic structure. Angle resolved photoemission spectroscopy (ARPES) has proven to be a powerful tool for probing the momentum-resolved valence band structure of 2D materials such as graphene and semiconducting transition metal dichalcogenides (MX2). But it is challenging to apply conventional ARPES, which typically averages over lengthscales > 100 µm, to 2DHS which are usually only a few µm across. Using the high spatial resolution and flux of the Spectromicroscopy beamline at Elettra, we have shown that submicrometre spatially resolved ARPES (µARPES) can determine band parameters and band alignments across 2DHS of mechanically exfoliated flakes. These heterostructures are similar to those used for optical spectroscopy and transport measurements, opening the way to study operating devices.

>Read more on the Elettra website

Illustration: Direct momentum-resolved electronic structure measurements of in-operando microelectronic devices.

How morphing materials store information

Experiments at SLAC’s X-ray laser reveal in atomic detail how two distinct liquid phases in these materials enable fast switching between glassy and crystalline states that represent 0s and 1s in memory devices.

Instead of flash drives, the latest generation of smart phones uses materials that change physical states, or phases, to store and retrieve data faster, in less space and with more energy efficiency. When hit with a pulse of electricity or optical light, these materials switch between glassy and crystalline states that represent the 0s and 1s of the binary code used to store information.
Now scientists have discovered how those phase changes occur on an atomic level.
Researchers from European XFEL and the University of Duisburg-Essen in Germany, working in collaboration with researchers at the Department of Energy’s SLAC National Accelerator Laboratory, led X-ray laser experiments at SLAC that collected more than 10,000 snapshots of phase-change materials transforming from a glassy to a crystalline state in real time.

>Read more on the LCLS at SLAC website

Image: The research team after performing experiments at SLAC’s Linac Coherent Light Source X-ray laser.
Credit: Klaus Sokolowski-Tinten/University of Duisburg-Essen)

Please read also the article published on the EUXFEL website:
Rigid bonds enable new data storage technology

Potassium hunting on protein factories

Amazing insights into the location of elusive potassium ions on bacterial ribosomes

Groundbreaking research at the new long-wavelength macromolecular crystallography beamline (I23) at Diamond Light Source has for the first time demonstrated the location of potassium ions in bacterial ribosomes. Ribosomes are the protein factories of cells and although they are vital for life, little was known of the sites of metal ions that are crucial for their structure and function. The work recently published in Nature Communications showcases the fantastic applications of the I23 beamline and sheds light on the important role of potassium ions.

>Read more on the Diamond Light Source website

Image: (extract, full image here) 70S ribosome elongation complex (potassium atoms rendered as green spheres).