Category: DESY

An algorithm for sharper protein films

An algorithm for sharper protein films

Proteins are biological molecules that perform almost all biochemical tasks in all forms of life. In doing so, the tiny structures perform ultra-fast movements. In order to investigate these dynamic processes more precisely than before, researchers have developed a new algorithm that can be used to evaluate measurements at X-ray free-electron lasers such as the SwissFEL more efficiently. They have now presented it in the journal Structural Dynamics.

Sometimes, when using the navigation system while travelling by car, the device will locate you off the road for a short time. This is due to the inaccuracy of the GPS positioning, which can be as much as several metres. However, the algorithm in the sat nav will soon notice this and correct the trajectory displayed on the screen, i.e. put it back on the road.

A comparable principle for addressing unrealistic motion sequences has now been successfully applied by a team of researchers led by PSI physicist Cecilia Casadei. However, their objects of investigation are about a billion times smaller than a car: proteins. These building blocks of life fulfil crucial functions in all known organisms. In doing so, they often perform ultra-fast movements. Analysing these movements precisely is crucial for our understanding of proteins which can help us produce new medical agents, amongst other things.

How to “film” proteins…

To further improve the understanding of protein movements, Casadei, together with other PSI researchers, a researcher at DESY in Hamburg and other colleagues at the University of Wisconsin in Milwaukee, USA, has developed an algorithm that evaluates data obtained in experiments at an X-ray free-electron laser (XFEL). An XFEL is a large-scale research facility that delivers extremely intense and short flashes of laser-quality X-ray light. Here, a method called time-resolved serial femtosecond X-ray crystallography (TR-SFX) can be used to study the ultra-fast movements of proteins.

The measurements are very complex for several reasons: the proteins are much too small to be imaged directly, their movements are incredibly fast, and the intense pulse of X-ray light of an FEL completely destroys the proteins. On the experimental level, TR-SFX already solves all these problems: no individual molecule is measured, but rather a large number of identical protein molecules are induced to grow together in a regular arrangement to form protein crystals. When the FEL X-ray light shines on these crystals, the information is captured in time before the crystals and their proteins are destroyed by the pulse of light. The raw data from the measurements are available as so-called diffraction images: light spots that are created by the regular arrangement of the proteins in the crystal and registered by a detector.

Read more on the PSI website

Image: Physicist Cecilia Casadei was part of an international team that developed a new analysis algorithm. With their method, called “low-pass spectral analysis”, the data collected when proteins are measured at X-ray free-electron lasers can be evaluated more efficiently than before.

Credit: Paul Scherrer Institute/Mahir Dzambegovic

ExPaNDS webinar series to showcase achievements and look to the future

ExPaNDS webinar series to showcase achievements and look to the future

We’re pleased to announce our upcoming topic-based webinars which will take place during the coming month before the end of our grant in February 2023. The webinar topics have been selected with the help of our work package leaders and some of the highlighted use cases taken directly from the PaN community throughout our grant.

The series will provide a great opportunity to showcase some of the outcomes of our grant to the PaN facility user communities. We will present some key findings from the recently conducted data consultation, which was sent to over 14,000 PaN facility users.

The ongoing work of ExPaNDS has been very important to the PaN community and we have invited senior community figures to discuss the future needs and requirements for their respective discipline or technique to keep the momentum going beyond the grant.

We will have flash talks from our work packages with focus being on FAIR, data catalogue services, data analysis and an overview of the PaN training platform.

Read more on the ExPaNDS website

Image: Chairman of the DESY Board of Directors – Professor Dr Helmut Dosch

European Young Chemists’ Award for Sebastian Weber

European Young Chemists’ Award for Sebastian Weber

In recognition of Sebastian’s PhD thesis on hard X-ray microscopy, tomography, and application of synchrotron radiation in catalysis research

Sebastian Weber, a recent PhD graduate at the Institute for Chemical Technology and Polymer Chemistry (ITCP) / Institute for Catalysis Research and Technology (IKFT) at Karlsruhe Institute of Technology (KIT), was awarded the Gold Medal in the PhD category of the European Young Chemists‘ Award. The award is presented every two years during the EuChemS Chemistry Congress on behalf of the Società Chimica Italiana (SCI) and the European Chemical Society (EuChemS). The prize highlights excellent research from young / early stage researchers across all fields of chemistry and chemical sciences. During his PhD phase, Sebastian Weber studied materials used in heterogeneous catalysis with a broad range of spatially-resolved X-ray characterisation methods, in order to gain a deeper understanding of the structure and function of catalysts. The project made extensive use of synchrotron radiation, specifically X-ray microscopy and tomography as emerging methods in catalysis research. This success on the European level highlights the leading role which synchrotron science has to play in the study of matter.

Catalysis plays a crucial role in sustainable chemical production, chemical energy conversion and storage, among many others, and is a key technology area in synchrotron radiation research. During his PhD work at Karlsruhe Institute of Technology, Sebastian Weber studied catalysts for CO2 methanation using spatially-resolved characterisation tools including X-ray microscopy and tomography. These diverse X-ray imaging methods were exploited to study the 3D structure of catalytic materials over a range of length scales, addressing various levels of hierarchical structural features which are critical to understanding catalyst performance. This topic is a special focus of the Young Investigator Group of Dr. Thomas Sheppard at KIT, who supervised and secured funding for the project, within the wider group of Prof. Jan-Dierk Grunwaldt.

Only a handful of research groups worldwide are currently active in the field of X-ray microscopy applied to catalysis research, highlighting the emerging role of this vibrant research field. During his PhD work, Sebastian Weber in particular worked to develop applications of hard X-ray ptychography and ptychographic X-ray tomography (PXCT) to study catalyst pore structures, structural evolution under reaction conditions, and the effects of catalyst deactivation. These methods routinely reach spatial resolution below 50 nanometres (0.001 x diameter of a human hair), and have been applied so far on samples up to 50 micron in diameter (ca. the diameter of a human hair). The further development of ptychography holds excellent potential for catalysis and materials research, particularly in the age of fourth generation light sources with improved coherence and decreased source emittance. The project resulted in several high quality publications in leading chemistry and materials journals, reflecting the knowledge gained regarding 3D structure of catalysts, and the potential for development of improved catalysts in future.

Sebastian Weber recently completed his doctorate with the title “Revealing Porosity and Structure of Ni-based Catalysts for Dynamic CO2 Methanation with Hard X-rays”, earning a distinction from KIT. Now his work was further recognised by securing the Gold Medal of the European Young Chemists’ Award at PhD level. The award is presented every two years during the EuChemS Chemistry Congress on behalf of the Società Chimica Italiana (SCI) and the European Chemical Society (EuChemS). The prize highlights excellent research from young / early stage researchers across all fields of chemistry and chemical sciences, and is therefore a highly competitive prize. After a pre-selection phase based on scientific excellence, the six finalists each held a presentation at the EuChemS Chemistry Congress in Lisbon, Portugal. The award not only highlights the excellent contribution of Sebastian Weber to the field of chemical sciences, but promotes in front a broad audience the essential role of synchrotron radiation in delivering future insights and innovations across the field of natural sciences.

Related articles on this research can be found in the Diamond Annual Review 2021-2022, “X-ray ptychography investigates coking of solid catalysts in 3D”, p.66-67, and on the DESY website

Image: Award ceremony during the 8th EuChemS Chemistry Congress in Lisbon, Portugal, Sebastian Weber (KIT, left), Prof. Floris Rutjes (President of the European Chemical Society, middle) and Prof. Angela Agostiano (Chair of the EYCA Award Committee, right).

Graphics: EYCA

Gerold Rosenbaum’s #My1stLight – First Synchrotron X-ray Diffraction Pattern

Gerold Rosenbaum’s #My1stLight – First Synchrotron X-ray Diffraction Pattern

August 1970:  First Synchrotron X-ray Diffraction Recorded at DESY

In order to verify that we could get the flux from the 7.5 GeV synchrotron DESY we had calculated actually onto a small specimen, I designed and we had built an in-vacuum, remote-controlled, focusing x-ray monochromator which we were allowed to insert into the vacuum-ultraviolet beamline of the F41 group at DESY. Preparing for the last trip to DESY from our home lab at Heidelberg, my supervisor Ken Holmes told me to pack a muscle fiber and put it into the beam. Being a physicist by education, I asked why, we measure the flux and X-rays are X-rays and do the same whether from a synchrotron or from a tube at home. Ken: “Not for biologists.” Good that I followed his advice. Thus, I recorded the first synchrotron X-ray diffraction pattern (in the universe – as I like to brag and nobody can dispute this).

There it is and it shows the same pattern as with a home source. So, biologists and everybody else could be confident in what synchrotrons promised.

Credit: The results of the flux verifications were published in Nature in April 1971:

Karen Appel’s #My1stLight

Karen Appel’s #My1stLight

Karen was a beamline scientist at DESY and is currently a beamline scientist at the European XFEL

My first synchrotron experiment was at beamline L at DORIS at DESY, which at that time just set up the possibility to do micro-focus X-ray fluorescence measurements. The first experiment I was involved in was headed by the group of Prof Schenk at the Institute of Mineralogy of the University of Kiel  and focused on minerals that were formed at high pressures and high temperatures. At that moment, I was a PhD student at the University of Bonn, working on metamorphic rocks and isotope geochemistry of rocks and got involved in the experiment, because I was interested in analytical methods that could be applied to minerals that were formed at high pressures and temperatures. Besides some connections through my earlier studies, my main interest was to learn about this new method of X-ray fluoresence. We investigated the chemical trace element composition (Rare Earth elements) of minerals that were formed during metamorphic processes and commonly show a gradient of the element distribution, which is related to the metamorphic formation process. 

As we were simply providing the samples, we had the chance to have a close look at the instrumentation. Having worked with commercial machines so far, I remember that I was very much impressed by the modular set- up of a beamline and this one-day experience motivated me to apply for a job that was offered from GFZ Potsdam that included a main part in experimental work at beamline L.

Later, as a postdoc, my experiences led me into the van Gogh experiment, where we used the polychromatic mode at beamline L and were able to detect the elemental distributions of a van Gogh painting. Now I am working at the High Energy Density Science instrument at the European XFEL, studying extreme states of matter, allowing me to work as a beamline scientist and also pursue my own scientific interests.

Image (above): Karen and her colleague working at the experimental station at the beamline L of DORIS III.

Credit: DESY

Image: DE: Die Experimentierstation HED (High Energy Density Science) dient der Erforschung von Materie unter extremen Druck- und Temperaturbedingungen oder sehr starken elektromagnetischen Feldern. Zu den wissenschaftlichen Anwendungen gehört die Untersuchung von Zuständen, wie sie im Inneren astrophysikalischer Objekte wie Exoplaneten bestehen, von Phasenzuständen unter extremem Druck, von Plasmen mit hoher Dichte oder von Phasenübergängen komplexer Feststoffe unter dem Einfluss starker Magnetfelder. EN: The HED experiment station will be used to study matter under extreme conditions of pressure, temperature, or electromagnetic fields. Scientific applications will be studies of matter occurring inside astrophysical objects such as exoplanets, of new extreme-pressure phases and solid-density plasmas, and of phase transitions of complex solids in high magnetic fields.

Credit: European XFEL / Jan Hosan

Gerold Rosenbaum’s #My1stLight

Gerold Rosenbaum’s #My1stLight

From Gerold Rosenbaum – Advanced Photon Source user

A Playful Use of the Last 10 Minutes of a Run Turns Out to be Very Educational

In 1967, after finishing data collection on the DESY XUV beamline on the polarizer/polarization analyzer I had built for my diploma thesis, there were 15 minutes to go before the synchrotron was to be shut down. Since I always wanted to know how good the vacuum had to be for working in the XUV, I suggested to bleed up the 1-m-long sample chamber to 1/10000 atm or 0.08 torr. The playful use of the last 10 minutes of the run turned out to be an impressive demonstration of the superiority of the continuous spectrum of synchrotron radiation over other XUV sources (paired with a high-resolution monochromator). The very low intensity below 800 Å, even though at the peak of the monochromator spectrum, told me clearly where vacuum-UV starts.

Journal reference: R.P. Godwin, “Synchrotron radiation as a light source,” Springer-Verlag Tracts in Modern Physics 51, p.66, 1969.

Image:

When vibrations increase on cooling: Anti-freezing observed

When vibrations increase on cooling: Anti-freezing observed

An international team has observed an amazing phenomenon in a nickel oxide material during cooling: Instead of freezing, certain fluctuations actually increase as the temperature drops. Nickel oxide is a model system that is structurally similar to high-temperature superconductors. The experiment, which was carried out at the Advanced Light Source (ALS) in California, shows once again that the behaviour of this class of materials still holds surprises.

In virtually all matter, lower temperatures mean less movement of its microscopic components. The less heat energy is available, the less often atoms change their location or magnetic moments their direction: they freeze. An international team led by scientists from HZB and DESY has now observed for the first time the opposite behaviour in a nickel oxide material closely related to high-temperature superconductors. Fluctuations in this nickelate do not freeze on cooling, but become faster.

Read more on the HZB website

Image: The development of this speckle pattern over time reveals microsocopic fluctuations in the material.

Credit: © 10.1103/PhysRevLett.127.057001

Ultrafast lasers protect a DNA building block from destruction

Ultrafast lasers protect a DNA building block from destruction

An international research team led by DESY researcher Francesca Calegari and with the key participation of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) has demonstrated that ultrashort laser pulses can be used to protect one of the DNA building blocks against destruction induced by vacuum ultraviolet (VUV) radiation. The research group unveiled that a second laser flash in the infrared, timed shortly (only a few millionths of billions of a second) after the first VUV flash, prevented the adenine molecule to disintegrate, therefore stabilising it. The group presents their work in the journal Communications Chemistry published by Nature publishing group.

High energy radiation can cause irreparable damage to our own biological molecules – such as DNA – leading to mutations and potentially cell death. Damage is often occurring as a consequence of the molecular ionisation, inducing the fragmentation of the DNA subunits. So far, protection against radiation damage has hardly been achieved, as the photo-induced dissociation process could not be stopped. In their ultra-short-time experiments, Francesca Calegari´s research group and collaborators have discovered that, by taking advantage of mechanisms that take place on extremely fast time scales, it is indeed possible to protect the molecule.

Read more on the DESY website

image: Artist´s impression of the ultrafast stabilisation of adenine against dissociation: When the molecule is ionised by VUV radiation it undergoes dissociation, however, by taking advantage of a charge migration mechanism and by properly timing a second infrared laser pulse it is possible to stabilise it via a second ionisation event.

Credit: U. De Giovannini MPSD

Experimental mini-accelerator achieves record energy

Experimental mini-accelerator achieves record energy

Coupled terahertz device significantly improves electron beam quality

Scientists at DESY have achieved a new world record for an experimental type of miniature particle accelerator: For the first time, a terahertz powered accelerator more than doubled the energy of the injected electrons. At the same time, the setup significantly improved the electron beam quality compared to earlier experiments with the technique, as Dongfang Zhang and his colleagues from the Center for Free-Electron Laser Science (CFEL) at DESY report in the journal Optica. “We have achieved the best beam parameters yet for terahertz accelerators,” said Zhang. “This result represents a critical step forward for the practical implementation of terahertz-powered accelerators,” emphasized Franz Kärtner, who heads the ultrafast optics and X-rays group at DESY.
Terahertz radiation lies between infrared and microwave frequencies in the electromagnetic spectrum and promises a new generation of compact particle accelerators. “The wavelength of terahertz radiation is about a hundred times shorter than the radio waves currently used to accelerate particles,” explained Kärtner. “This means that the components of the accelerator can also be built to be around a hundred times smaller.” The terahertz approach promises lab-sized accelerators that will enable completely new applications for instance as compact X-ray sources for materials science and maybe even for medical imaging. The technology is currently under development.

> Read more on the DESY website

Image: The two-stage miniature accelerator is operated with terahertz radiation (shown here in red). In a first step (left) the electron bunches (shown in blue) are compressed, in a second step (right) they are accelerated. The two individual elements are each about two centimetres wide. Credit: DESY, Gesine Born