New ant genus named after DESY

Researchers spot previously unknown extinct ant in 20 million-years-old amber

An international team of scientists led by Friedrich Schiller University Jena has identified a previously unknown extinct ant in a unique piece of African amber about 20 million years old. The team used DESY’s X-ray light source PETRA III to examine the critical fossil remains from 13 individual animals at a specialised measuring station operated by Helmholtz-Zentrum Hereon and realised that these could not be attributed to any known species. The new species even establishes a completely new genus of primordial ants, as the scientists from the Universities of Jena, Rennes (France) and Gdansk (Poland) as well as from Hereon report in the scientific journal Insects. The new genus was named after DESY, the new species after Hereon: With the scientific name †Desyopone hereon gen. et sp. nov., the discoverers honour the two research institutions, which had contributed significantly to this discovery with modern imaging methods.


“It is a great honour that DESY is the namesake of the new primordial ant genus,“ emphasises Christian Schroer, Leading Scientist of PETRA III at DESY. “And we are delighted that we can provide the brilliant X-ray light for such top-class research with our facility.” PETRA III is a particle accelerator that sends fast electrons on slalom paths, where they emit highly focused X-ray light that can be used to study the finest details of a wide variety of samples.

Read more on the DESY website

Image: Magnified (about 100,000 fold) representation of the extinct ant in a glass block in the Hereon measuring station at DESY’s X-ray light source PETRA III, where the original had been studied.

Credit: DESY, Marta Mayer


Natural substances show promise against coronavirus

X-ray screening identifies compounds blocking a major corona enzyme

Three natural compounds present in foods like green tea, olive oil and red wine are promising candidates for the development of drugs against the coronavirus. In a comprehensive screening of a large library of natural substances at DESY’s X-ray source PETRA III the compounds bound to a central enzyme vital for the replication of the coronavirus. All three compounds are already used as active substances in existing drugs, as the team headed by Christian Betzel from the University of Hamburg and Alke Meents from DESY reports in the journal Communications Biology. However, if and when a corona drug can be developed on the basis of these compounds remains to be investigated.

“We tested 500 substances from the Karachi Library of Natural Compounds if they bind to the papain-like protease of the novel coronavirus, which is one of the main targets for an antiviral drug,” explains the study’s main author Vasundara Srinivasan from the University of Hamburg. “A compound that binds to the enzyme at the right place can stop it from working.”

The papain-like protease (PLpro) is a vital enzyme for virus replication: When a cell is hijacked by the coronavirus, it is forced to produce building blocks for new virus particles. These proteins are manufactured as a long string. PLpro then acts like a molecular pair of scissors, cutting the proteins from the string. If this process is blocked, the proteins cannot assemble new virus particles.

Read more on the DESY website

Image: The paper’s main author Vasundara Srinivasan at an X-ray set-up to test protein crystals in the lab.

Credit: University of Hamburg, Susanna Gevorgyan

Aleksei Kotlov’s #My1stLight

Aleksei was responsible for setting up the new P66 beamline at PETRA III at DESY

Setting up the P66 beamline was a challenging time. The years of discussions, iterations, doubts, calculations, ordering of parts, and construction end at some point with commissioning of the beamline. Only then could you see the final result of your work and see that all decisions were right. To me personally it was like the birth of a baby. Suddenly you realize, that small beam spot on the sample is a big event for you and whole beamline community and to make it happen you have invested a significant part of your life.

Image: Aleksei on the P66 beamline at PETRA III

Efficient production technique for a novel ‘green’ fertiliser

Advanced milling technique produces slow-release soil nutrient crystals

A purely mechanical method can produce a novel, more sustainable fertiliser in a less polluting way. That is the result of a method optimised at DESY’s light source PETRA III. An international team used PETRA III to optimise the production method that is an adaptation of an ancient technique: by milling two common ingredients, urea and gypsum, the scientists produce a new solid compound that slowly releases two chemical elements critical to soil fertilisation, nitrogen, and calcium. The milling method is rapid, efficient, and clean—as is the fertiliser product, which has the potential to reduce the nitrogen pollution that fouls water systems and contributes to climate change. The scientists also found that their process is scalable; therefore, it could be potentially implemented industrially. The results by scientists from DESY; the Ruđer Bošković Institute (IRB) in Zagreb, Croatia; and Lehigh University in the USA have been published in the journal Green Chemistry. The new fertiliser still needs to be tested in the field.

For several years, scientists from DESY and IRB, have been collaborating to explore the fundamentals of mechanical methods for initiating chemical reactions. This method of processing, called mechanochemistry, uses various mechanical inputs, such as compressing, vibrating, or, in this case, milling, to achieve the chemical transformation. “Mechanochemistry is quite an old technique,” says Martin Etter, beamline scientist at the P02.1 beamline at PETRA III. “For thousands of years, we’ve been milling things, for example, grain for bread. It’s only now that we’re starting to look at these mechanochemical processes more intensively using X-rays and seeing how we can use those processes to initiate chemical reactions.”

Etter’s beamline is one of the few in the world where mechanochemistry can be routinely performed and analysed using X-rays from a synchrotron. Etter has spent years developing the beamline and working with users to fine-tune methods for analysing and optimising mechanochemical reactions. The result has been a globally renowned experiment setup that has been used in studying many types of reactions important to materials science, industrial catalysis, and green chemistry.

Read more on the DESY website

Image: The co-crystals of the novel fertiliser (symbolised here with gypsum) release their nutrients much more slowly

Credit: DESY, Gesine Born

 

Brilliant people support light source experiments

Academic and industrial researchers have access to world class experimental techniques at light sources around the world. Experimental time on the beamlines is extremely precious and in order to get the most out of this ‘beamtime’ scientists need expert advice and support. Today’s #LightSourceSelfie Monday Montage is a tribute to the brilliant scientists, engineers, computer scientists and other support staff who work at light sources and provide external researchers with the assistance they need to ensure their experiments are successful and they come away with useful data that will advance their scientific studies.

Monday Montage – Brilliant people support light source experiments

Light sources have demonstrated huge adaptability during the pandemic

Johanna Hakanpää is the beamline scientist for P11, one of the macromolecular crystallography beamlines at PETRAIII at DESY in Hamburg. Originally from Finland, she studied chemistry and then did her masters and PhD work in protein crystallography. Johanna was drawn to the field because she wanted to understand how life really works. Supporting health related research is important to her and Johanna is especially inspired by her son who is a patient of celiac disease. Together they hope that one day, with the help of science, he will be able to eat normally without having to think about what is contained in his food. Johanna started her light source journey as a user and was really impressed by the staff scientists who supported her during her experiments. This led her to apply for a beamline scientist position and she successfully made the transition, learning the technical aspects of the beamlines on the job.

In her #LightSourceSelfie, Johanna highlights the adaptability of light sources during the pandemic as a key strength. Being part of a team that was able to keep the lights on for users via remote experiments is a reflection of the commitment that Johanna and her colleagues have when it comes to facilitating science. Thousands of staff at light sources all around the world have shown the same commitment, ensuring scientific advances can continue. This is particularly true for vital research on the SARS-CoV-2 virus itself. Learn more about this research here: https://lightsources.org/lightsource-research-and-sars-cov-2/

Quantum Physics in Proteins

Artificial intelligence affords unprecedented insights into how biomolecules work

A new analytical technique is able to provide hitherto unattainable insights into the extremely rapid dynamics of biomolecules. The team of developers, led by Abbas Ourmazd from the University of Wisconsin–Milwaukee and Robin Santra from DESY, is presenting its clever combination of quantum physics and molecular biology in the scientific journal Nature. The scientists used the technique to track the way in which the photoactive yellow protein (PYP) undergoes changes in its structure in less than a trillionth of a second after being excited by light.

“In order to precisely understand biochemical processes in nature, such as photosynthesis in certain bacteria, it is important to know the detailed sequence of events,” Santra explains their underlying motivation. “When light strikes photoactive proteins, their spatial structure is altered, and this structural change determines what role a protein takes on in nature.” Until now, however, it has been almost impossible to track the exact sequence in which structural changes occur. Only the initial and final states of a molecule before and after a reaction can be determined and interpreted in theoretical terms. “But we don’t know exactly how the energy and shape changes in between the two,” says Santra. “It’s like seeing that someone has folded their hands, but you can’t see them interlacing their fingers to do so.”

Read more on the PETRAIII website

Image: Illustration of a quantum wave packet in close vicinity of a conical intersection between two potential energy surfaces. The wave packet represents the collective motion of multiple atoms in the photoactive yellow protein. A part of the wave packet moves through the intersection from one potential energy surface to the other, while the another part remains on the top surface, leading to a superposition of quantum states

Credit: DESY, Niels Breckwoldt

X-ray insights may enable better plastics production

Analysis helps to understand fragmentation of catalyst particles in ethylene polymerisation

An X-ray study at DESY is pointing the way towards a better understanding of plastics production. A team led by Utrecht University investigated so-called Ziegler-type catalysts, the workhorses in the world’s polyethylene and polypropylene production, at DESY’s X-ray source PETRA III. As the scientists report in the journal JACS Au, the catalyst microparticles fragment into an astonishing variety of smaller particles during polymer production. The results allow for a better finetuning of desired polymer properties and may even help to further increase polymer yield.

Polyolefins, such as polyethylene (PE) and polypropylene (PP), play an important role in everyday life. Applications range from food packaging to increase the lifetime of the product to the sterile packing of medical equipment to the insulation of electrical cables. To prepare tailored polyolefins on demand, a versatile class of catalyst materials, such as the Ziegler-type catalysts, are used that consist of very small particles containing various metals such as titanium.

The catalyst particles have typical sizes of only a few tens of micrometres (thousandths of a millimetre), that is, less than the thickness of a human hair. Thanks to these catalysts, polyethylene can be produced at ambient pressure and temperature and with enhanced material characteristics. “Polyolefin research today focusses on specifically tailoring polymer properties to the demands of customers, and this is where insights about the polymerisation process such as the ones obtained in this study are crucial,” explains Koen Bossers from Utrecht University, first author of the study.

Read more on the DESY website

Image: 434 particles were imaged simultaneously with a resolution of 74 nm and identified and characterised individually with respect to their geometrical properties and fragmentation behaviour. The displayed rendering shows a virtual cut through the tomographic data set where each identified particle is color-coded for better visualisation. Most particles are about 5-6 microns in diameter. The data has further been segmented into regions of similar electron density to separate polymer from catalyst fragments within each particle; these regions are displayed in blue, green, orange, and red and visualised via the virtual cut though the 3-D representation of the catalyst particles. This segmentation allowed for a detailed analysis of the fragmentation behaviour of each particle

Credit: Utrecht University, Roozbeh Valadian

Astonishing diversity: Semiconductor nanoparticles form numerous structures

X-ray study reveals how lead sulphide particles self-organise in real time

The structure adopted by lead sulphide nanoparticles changes surprisingly often as they assemble to form ordered superlattices. This is revealed by an experimental study at PETRA III. A team led by the DESY scientists Irina Lokteva and Felix Lehmkühler, from the Coherent X-ray Scattering group headed by Gerhard Grübel, has observed the self-organisation of these semiconductor nanoparticles in real time. The results have been published in the journal Chemistry of Materials. The study helps to better understand the self-assembly of nanoparticles, which can lead to significantly different structures.

Among other things, lead sulphide nanoparticles are used in photovoltaic cells, light-emitting diodes and other electronic devices. In the study, the team investigated the way in which the particles self-organise to form a highly ordered film. They did so by placing a drop of liquid (25 millionths of a litre) containing the nanoparticles inside a small cell and allowing the solvent to evaporate slowly over the course of two hours. The scientists then used an X-ray beam at the P10 beamline to observe in real time what structure the particles formed during the assembly.

To their surprise, the structure adopted by the particles changed several times during the process. “First we see the nanoparticles forming a hexagonal symmetry, which leads to a nanoparticle solid having a hexagonal lattice structure,” Lokteva reports. “But then the superlattice suddenly changes, and displays a cubic symmetry. As it continues to dry, the structure makes two more transitions, becoming a superlattice with tetragonal symmetry and finally one with a different cubic symmetry.” This sequence has been never revealed before in such detail.

Read more on the DESY website

Image: The lead sulphide nanoparticles, which are about eight nanometres (millionths of a millimetre) in size, initially arrange themselves into a layer with hexagonal symmetry

Credit: (Credit: University of Hamburg, Stefan Werner)

X-ray unveils the creation process of materials on several length scales

Nanostructuring often makes materials very powerful in many applications. Some nanomaterials take on the desired complex structures independently during their creation process. Scientists from the University of Hamburg, DESY, ESRF and the Ludwig Maximilians University in Munich have studied the formation of cobalt oxide crystals just a few nanometers in size and how they assemble, while they are still being formed. The results are published in Nature Communications.

Nanomaterials have special properties that make them more effective than conventional materials in various applications. In sensors and catalysts (in green energy production, such as water splitting into energy-rich hydrogen and oxygen) the important chemical processes happen at the surface. Nanostructured materials, even in small amounts, provide a very large surface and are therefore suitable for this kind of applications.

Further potential arises due to the variety of shapes and material combinations that are conceivable on the nanoscale. However, establishing the exact shape of these nanostructures can be a tedious process. Researchers focus on nanocrystals that independently form complex structures without any external influence, for example by sticking together (assembling). This increases their effectiveness in important technological applications, such as green energy generation or sensor technology.

“Often nanoparticles arrange themselves independently, as if following a blueprint, and take on new shapes,” explains Lukas Grote, one of the main authors of the study and scientist at DESY and the University of Hamburg. “Now, however, we want to understand why they are doing this and what steps they go through on the way to their final form. That is why we follow the formation of nanomaterials in real time using high-intensity X-rays. ” For some of the experiments, the researchers used the European Synchrotron Radiation Facility (ESRF) and DESY’s synchrotron radiation source PETRA III.

Read more on the ESRF website

Image: X-rays from a synchrotron radiation source are both attenuated (absorbed) and deflected (scattered) by matter. Depending on which of these interactions is measured with a certain X-ray technology, conclusions can be drawn about different stages of the development process of a nanomaterial. If you combine both X-ray absorption and X-ray scattering, you can decipher all the steps from the starting material (left) to the fully assembled nanostructures (right).

Credit: Nature Communications

Promising candidates identified for COVID drugs

A team of researchers has identified several candidates for drugs against the coronavirus SARS-CoV-2 at DESY´s high-brilliance X-ray lightsource PETRA III. They bind to an important protein of the virus and could thus be the basis for a drug against Covid-19.

In a so-called X-ray screening, the researchers, under the leadership of DESY, tested almost 6000 known active substances that already exist for the treatment of other diseases in a short amount of time. After measuring about 7000 samples, the team was able to identify a total of 37 substances that bind to the main protease (Mpro) of the SARS-CoV-2 virus, as the scientists report online today in the journal Science. Seven of these substances inhibit the activity of the protein and thus slow down the multiplication of the virus. Two of them do this so promisingly that they are currently under further investigation in preclinical studies. This drug screening – probably the largest of its kind – also revealed a new binding site on the main protease of the virus to which drugs can couple.

Read more on the DESY website

Image: In the control hutch of the PETRA III beamline P11, DESY researcher Wiebke Ewert shows on a so-called electron density map where a drug candidate (green) binds to the main protease of the corona virus (blue).

Credit: DESY, Christian Schmid

The egg in the X-ray beam

Innovative time-resolved method reveals network formation by and dynamics of proteins.

A team of scientists has been using DESY’s X-ray source PETRA III to analyse the structural changes that take place in an egg when you cook it. The work reveals how the proteins in the white of a chicken egg unfold and cross-link with each other to form a solid structure when heated. Their innovative method can be of interest to the food industry as well as to the broad field of research surrounding protein analysis. The cooperation of two groups, headed by Frank Schreiber from the University of Tübingen and Christian Gutt from the University of Siegen, with scientists at DESY and European XFEL, reports the research in two articles in the journal Physical Review Letters.

Eggs are among the most versatile food ingredients. They can take the form of a gel or a foam, they can be comparatively solid and also serve as the basis for emulsions. At about 80 degrees Celsius, egg white becomes solid and opaque. This is because the proteins in the egg white form a network structure. Studying the exact molecular structure of egg white calls for energetic radiation, such as X-rays which is able to penetrate the opaque egg white and has a wavelength that is not longer than the structures being examined.

Read more on the DESY website

Image: When heated, the proteins in the originally transparent chicken egg white form a tightly meshed, opaque network.

Credit: DESY, Gesine Born

Researchers watch nanomaterials growing in real time

For the first time, a team of scientists including from DESY has succeeded in capturing in real time the first few milliseconds in the life of a gold coating as it forms on a polymer. The team used PETRA III to observe the earliest stages in the growth of a metal-polymer hybrid material as a film of gold was applied to a polymer carrier, in a process that can be used in industrial applications. The group’s research, which it presented now in the journal Nanoscale Horizons, not only offers important new insights into how innovative hybrid nanomaterials form, it also sets a new world record in the temporal resolution achieved using GISAXS, a surface-sensitive scattering technique.

Metal-polymer materials form the basis of modern flexible electronics, such as organic field effect transistors (OFET) or novel television screens (OLED). A detailed understanding of the manufacturing process is essential in order to manufacture such composites using smaller amounts of starting materials, to make them more energy-efficient and to be able to use them more flexibly.

Read more on the DESY website

Image: Experimental setup on beamline P03: The high-brilliance X-ray beam from PETRA III (magenta) is scattered by the surface structures while gold atoms are rapidly deposited on wafer-thin layers of plastic. The deflected X-ray light is recorded using a special high-speed camera designed at DESY. The sophisticated analysis of the real-time data obtained provides clues about the change in the sizes, distances and density profile of the resulting metal-polymer boundary layer

Credit: DESY/M. Schwartzkopf

High-pressure experiments provide insight into icy planets

Research team determines compression behaviour of water ice in unprecedented detail

An international team of scientists has been using X-rays to take a look inside distant ice planets. At the PETRA III Extreme Conditions Beamline, they investigated how water ice behaves at high pressure, under conditions corresponding to those inside the planet Neptune, for example. At pressures up to almost two million times atmospheric pressure at sea level on Earth, the researchers were able to observe in unparalleled detail how water ice behaves under compression. The team, led by Hauke Marquardt from the University of Oxford, is presenting its findings in the scientific journal Physical Review B.

Planetary ices – such as water ice (H2O), methane ice (CH4) and ammonia ice (NH3) – make up large parts of the ice giants in our solar system and are very likely to occur inside many exoplanets, which are planets outside our solar system. “However, the physical properties and phase diagrams of these compounds are not sufficiently known at the pressures and temperatures that prevail inside planets,” explains Marquardt. “Previous experimental studies using X-ray diffraction in a static diamond anvil cell have contributed a great deal to our understanding of ices at high pressure, but they have been unable to adequately answer numerous questions.”

Read more on the DESY website

Image : Ice at room temperature: A mixture of water ice and liquid water in a high-pressure cell at a temperature around 25 degrees Celsius and a pressure of one gigapascal, which corresponds to 10 000 times atmospheric pressure

Credit: DESY, Hanns-Peter Liermann

Minerals let Earth’s oceans seep down deeper than expected

Amphiboles could carry the volume of the Arctic Ocean into Earth’s mantle in 200 million years

A bigger volume of the world’s oceans is seeping deeper into Earth’s mantle than expected: That is the result of a study investigating a water-bearing mineral abundant in the oceanic crust. High-pressure experiments at DESY’s X-ray source PETRA III show that the mineral glaucophane is surprisingly stable up to 240 kilometres underground, which means it also carries water down to this depth. Scientists attribute this to the gradual cooling of Earth’s interior over geological timescales. The cooler temperatures let glaucophane and possibly other water-bearing minerals survive to greater pressures, as the team headed by Yongjae Lee from Yonsei University in South Korea reports in the journal Nature Communications. The scientists estimate that in about 200 million years, an additional volume equal to the Arctic Ocean could seep deep into Earth’s mantle this way.

Read more on the DESY website

Image: In the high-pressure cell, glaucophane samples are heated and squeezed between two diamond anvils

Credit: Yonsei University, Yoonah Bang/Huijeong Hwang

Quantum beats for zeptosecond timing

A team of scientists is developing high-precision timing for quantum technologies

Quantum systems will be crucial to future technologies. However, in order to use such systems in practical applications, it is necessary to control and manipulate them with great precision. A Hamburg research team has now succeeded in controlling and measuring a quantum system with hitherto unattainable temporal precision on the PETRA III beamline P01. They managed to control and detect oscillations inside an atomic nucleus, as well as the gamma radiation emitted, to within 1.3 zeptoseconds. A zeptosecond is 0.000 000 000 000 001 seconds; the thousandth part of a billionth of a billionth of a second. The new method developed by the team makes use of the fundamental excitations that occur within a solid. Precise adjustments of this kind are important when building quantum sensors, for example, to establish extremely precise time standards or to detect minute changes. The newly developed method may also have potential applications in quantum computers or quantum communication, as a way of making specific adjustments to such systems.

Read more on the DESY website

Image: View of the experiment at the PETRA III beamline P01 (in X-ray beam direction): The sample on the round table in the centre of the picture is connected to microwave measuring tips. The X-rays emitted by the sample are analysed at the end with a detector. Electromagnets with iron yokes around the sample table generate a magnetic field at the sample location to align the magnetisation in the sample

Credit: L. Bocklage/DESY