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

Using European XFEL to shed light on photosynthesis

First membrane protein studied at European XFEL

In a paper now published in Nature Communications an international group of scientists show that the fast X-ray pulse rate produced by the European XFEL can be used to study the structure of membrane proteins such as those involved in the process of photosynthesis. These results open up eagerly awaited experimental opportunities for scientists studying these types of proteins.

Large proteins and protein complexes are difficult to study with traditional structural biology approaches. Large protein complexes, such as those that sit across cell membranes and regulate traffic in and out of cells, are difficult to crystalize and generally only produce small crystals that are hard to analyse. The extremely fast X-ray pulses generated by European XFEL now enable scientists to collect large amounts of data from a stream of small crystals to develop detailed models of the 3D structure of these proteins.

>Read more on the European XFEL website

Image (extract, full illustration in the article): Graphic shows the basic design of a serial femtosecond crystallography experiment at European XFEL. X-ray bursts strike crystallized samples resulting in diffraction patterns that can be reassembled into detailed images.
Credit: Shireen Dooling for the Biodesign Institute at ASU

All SQS experiment stations up and running

Three new experiment stations expand the scientific possibilities in the field of soft X-ray science.

The soft X-ray instrument for Small Quantum Systems (SQS) welcomed its first users at the end of 2018. Now, almost a year later, the SQS team and collaborators have completed their ambitious plan to install and commission all three experiment stations, each specifically designed for different types of experiments and samples, ranging from atoms and small molecules to large clusters, nanoparticles and biomolecules. We look at how the instrument has developed during the past year, how important collaboration has been for the success of SQS so far, and what lies ahead.

>Read more on the European XFEL website

Image: SQS scientist Rebecca Boll makes final adjustments on the AQS experiment station before the first users arrive at the end of 2018.
Credit: European XFEL

Q&A with Sakura Pascarelli, new scientific director at European XFEL

European XFEL’s new scientific director talks about her career, her new role and her love for swimming.

On 1 September Sakura Pascarelli joined the European XFEL from the ESRF. In her role as scientific director she is responsible for the development of the four hard X-ray instruments. She spoke to Rosemary Wilson about her career, her new role and her love for swimming.

How did you get into science?

I spent part of my childhood in Burma and Indonesia. The American school system there enabled you to do lessons at your level, meaning you stayed interested and engaged. I really liked maths which I did with kids a few years older than me. I remember also doing experiments. I liked seeing things explode and break and try to understand why. Later on in Italy, I studied physics – not because I was particularly talented, but because I enjoyed it.

You joined ESRF at a time when the facility was still being built. What parallels can you see between that time, and now here at European XFEL?

I went to the ESRF to build one of the first beamlines there. We didn’t know what we would be able to discover or measure with this new machine. Here at European XFEL I see some of that same excitement. That opportunity taught me so much about instrumentation, and coordinating the construction of a beamline. But it is a different world now. Back then a good scientist with a solid background in physics, X-ray optics or instrumentation, could build a group and build a beamline. That is not possible here. This is so much more complicated. Here you need experts in X-rays, lasers, electronics, detectors. We don’t really know how to measure a femtosecond pulse let alone synchronise it with another laser! To run these instruments we need group leaders who are really good managers. This is so important. It is no longer enough for someone to be just a good scientist. At European XFEL we need to make sure the groups are well structured, well managed and that the people are happy. That might be difficult in the beginning when things don’t work, but when people see that their work is recognized, satisfaction and productivity increases.

>Read more on the European XFEL website

Image: European XFEL

Two years of user operation in numbers

1200 users, 60 experiments and 6 petabytes of data since operation began.

September 1 marks two years since the official opening and start of user operation at European XFEL. With the scheduled expansion from two to six operational instruments, the facility has expanded its experimental capacity and possibilities significantly during the past two years. At the same time, both the performance of the X-ray free-electron laser and instruments was continually improved. The scientific community shows strong interest in experiments at the new facility, with a total of 363 submitted proposals during this period, of which 98 were awarded beamtime. In total, 1200 users from across the world came to Schenefeld for their research. As the facility continues to be developed, even more time will be available for user experiments in the future.

>Read more on the European XFEL website

Image: Laser installation on the European XFEL campus in 2017 highlighting the five underground tunnels.
Credit: The European XFEL (Germany)

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

Third user run successfully completed, fourth starting soon

Around 600 scientists visit the facility for experiments during user period.

The third user experiment period at European XFEL, which ran from November 2018, was successfully completed in June 2019. The X-ray beam was available for experiments for a total of 18 weeks. Twenty-eight user experiments were carried out at all six instruments, and 599 users were welcomed to the facility.

While only two instruments were operational at the beginning of the run, a further four started operation during the period, so that all six instruments were operational by the end of the run. Many other systems also had to first be prepared so that everything worked together. This included the accelerator and electron beam system, which could distribute the beam on demand to the different light sources. Other systems that were optimized to reach the goal of parallel operation of all three beamlines included the X-ray optics and diagnostic systems in the tunnels, elements at the instruments themselves that deal with the X-ray beam and specimen delivery, detectors, and software and data storage systems.

>Read more on the European XFEL website

Picture: The MID experiment station was one of the four to begin user operation during user run 3.
Credit: European XFEL / Jan Hosan

Fastest soft X-ray camera in the world installed at European XFEL

DSSC detector will expand scientific capabilities of soft X-ray instruments

At European XFEL near Hamburg the world’s fastest soft X-ray camera has successfully been put through its paces. The installation, commissioning and operation of the unique detector marks the culmination of over a decade of international collaborative research and development. The so-called DSSC detector, designed specifically for the low energy regimes and long X-ray wavelengths used at the European XFEL soft X-ray instruments, will significantly expand the scientific capabilities of the instrument for Spectroscopy and Coherent Scattering (SCS) where it is installed. It will enable ultrafast studies of electronic, spin and atomic structures at the nanoscale making use of each X-ray flash provided by European XFEL. At the end of May, the first scientific experiments using the DSSC were successfully conducted at SCS.

> Read more on the European XFEL website

Image: European XFEL management and staff celebrate the successful installation and commissioning of the DSSC detector at the SCS instrument. The DSSC can be seen behind the group in the centre of the photo. From left to right European XFEL managing director Nicole Elleuche, Detector group leader Markus Kuster, European XFEL managing director Robert Feidenhans’l, DSSC consortium leader Matteo Porro, detector scientist Monica Turcato, SCS group leader Andreas Scherz. Copyright European XFEL

European XFEL plans ultrahigh-speed network connection to Poland

Data from experiments will also be processed at partner institute NCBJ in Otwock-Świerk.

European XFEL and the National Center for Nuclear Research (NCBJ) in Otwock-Świerk near Warsaw plan to establish the first ultrahigh-speed connection for research data between Germany and Poland. The aim is for the new Supercomputing Center at NCBJ to be used for the processing and analysis of data generated at the European XFEL. The dedicated network connection between the DESY Computer Center, which hosts European XFEL’s primary data, and NCBJ will feature a data transfer rate of 100 gigabits per second (Gbit/s). With the exception of the higher-speed connection to DESY, that is approximately 100 times faster than the current typical Internet connection between European XFEL and other research institutes, through which the transfer of data for an average experiment at the facility would take about a month. In comparison, household high-speed Internet connections can typically manage about 250 Mbit/s for a download. This makes this new connection at least 400 times faster.
For the installation of the new high-speed data connection, the German National Research and Education Network (DFN), the Supercomputing and Networking Center at the Institute for Bioorganic Chemistry in Poznań (PSNC), the Research and Academic Computer Network National Research Institute (NASK), and Deutsches Elektronen-Synchrotron (DESY) will also take part alongside European XFEL and NCBJ. At the end of May this year, the partners signed a Memorandum of Understanding that will serve as the basis and starting point for establishing the new high-speed connection. It can largely be built on existing technical infrastructure, but certain specific components will have to be added. For example, the connection between the German and Polish research networks will be enabled by the European University Viadrina in Frankfurt an der Oder and the neighbouring Polish city of Słubice.

>Read more on the European XFEL website

Image: At European XFEL at peak user operation times, up to a petabyte of data can be produced per week.
Credit:  European XFEL / Jan Hosan

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

All six European XFEL instruments now operational

User experiments started at instrument for High Energy Density.

The first experiments have now started at the instrument for High Energy Density (HED) experiments. HED is the sixth and thereby last instrument of European XFEL’s current design configuration to start user operation. With six instruments on three SASE beamlines operational, European XFEL now has the capacity to host three times as many user experiments as compared to when operation began in 2017.
HED combines hard X-ray FEL radiation and the capability to generate matter under extreme conditions of pressure, temperature or electric field. HED will be used for studies of matter occurring inside exoplanets, of new extreme-pressure phases and solid-density plasmas, and of structural phase transitions of complex solids in high magnetic fields. The HED instrument is built in close collaboration with the HiBEF consortium led by Helmholtz Zentrum Dresden-Rossendorf (HZDR).
Next operation goals involve further increasing the capabilities and experiment portfolio of the instruments, increasing the amount of beamtime available for users at the six instruments and achieving successful parallel user operation of all three SASE beamlines. Parallel user operation is expected to start later this year.

>Read more on the European XFEL website

Image: The first users at the HED instrument.
Credit: European XFEL

Getting the timing right for molecular movies

Jitter effects measured at European XFEL

Scientists have long dreamed of being able to film the details of chemical and biological reactions by taking, and stitching together snapshots of these processes. Getting the timing of the individual shots of the movies just right is dependent on a number of factors including understanding the timing variation, or so-called ‘jitter’, of the laser beams used to take the images. In an experiment published now in the journal Optics Letters, scientists describe how they measured the jitter at the SPB/SFX instrument at European XFEL and demonstrate how this unavoidable and undesirable effect might be overcome. The knowledge gained from these movies could lead to new technological innovations and developments.
Biological and chemical reactions happen extremely quickly and filming them requires an extremely fast and precise camera. Much like a fast exposure time can be used to capture a series of images showing details of the movements a sprinter makes during a race, so the extremely short bursts of X-rays produced by facilities such as European XFEL are short and frequent enough to capture the sequence of molecular movements that happen during a reaction. To make a molecular movie, scientists can, for example, first kick-start the reaction they want to film by hitting their sample of choice with a laser. Then, the intense X-ray laser is used to take a sequence of images of the molecular process as it unfolds. Getting the timing of the two lasers just right is crucial for the success of these types of experiments, however, at these speeds, it is not trivial.

>Read more on the European XFEL website
Image: The SPB/SFX instrument at European XFEL.
Credit: European XFEL

Low background noise crucial for single particle imaging experiments

Model experiment brings scientists a step closer to SPI at European XFEL

Taking snapshots of single molecules with X-rays has long been a dream for many scientists. Such experiments have successfully been computationally modelled, but have never been practically demonstrated before.
In a model experiment carried out at the European Synchrotron Radiation Facility (ESRF), European XFEL scientists, together with international collaborators, have now come one step closer to successfully carrying out so-called single particle imaging experiments (SPI) at X-ray laser facilities such as European XFEL. In a paper published today in the journal from the International Union of Crystallography (IUCrJ), scientists demonstrate experimentally that, in principle, a 3D structure can indeed be obtained from many tens of thousands of very weak images, using X-rays with similar properties as produced at X-ray free-electron lasers such as European XFEL.

>Read more on the European XFEL website

Image: Reconstruction of the 3D electron density. (a) Reconstruction from the result derived by EMC. The electron density projected along an axis perpendicular to the drawing plane is shown here. (b) Reconstruction from the reference Fourier volume. Again, the projected electron density is shown. (c) 3D iso-surface rendering of the reconstructed electron density shown in panel (a). The threshold of the iso-surface has been set to 0.2, given a normalized density with values between 0 and 1. (d) Scanning electron micrograph from the original sample.
Image source

Sakura Pascarelli appointed scientific director at European XFEL

Italian physicist will be responsible for scientific development of hard X-ray instruments

The Italian physicist Dr. Sakura Pascarelli will be the new scientific director at European XFEL. Pascarelli will join European XFEL on 1 September from the European Synchrotron Radiation Facility, ESRF in Grenoble, France. She succeeds Andreas Schwarz who retired at the end of 2018. As one of three scientific directors, Pascarelli will be responsible for the four short-waved hard X-ray instruments at European XFEL: FXE for studying extremely fast processes, SPB/SFX for investigating biomolecules and biological samples, HED for studying matter under extreme pressures and temperatures, and MID for investigating nanostructures or irregularly ordered materials such as glass, liquids and biological substances. In addition, Pascarelli will also be responsible for developing the scientific research program for these experiment stations.

>Read more on the European XFEL website

Image: Sakura Pascarelli
Credit: Chantal Argoud (ESRF)

Two more experiment stations start user operation

Facility double experiment capacity.

Two additional experiment stations—or instruments—have now started operation at European XFEL. The instruments for Small Quantum Systems (SQS) and Spectroscopy and Coherent Scattering (SCS) welcomed their first user groups for experiments last week and this week respectively. With the successful start of operation of the new instruments, European XFEL has now doubled its capacity to conduct research. With the first three groups coming to the new instruments in 2018, the total number of users who will have visited the facility in 2018 will reach over 500.
The two already operational instruments, SPB/SFX and FXE, have been used to examine biomolecules or biological processes and ultrafast reactions respectively since September 2017. In the future, two of the four now operational instruments will be run in parallel in twelve hour shifts. Two more instruments are scheduled to start user operation in the first half of 2019.

>Read more on the European XFEL website

Image: Scientists at the SQS instrument.
Credit: European XFEL / Jan Hosan

Capturing the strongest X-ray beam on Earth

First images of the European XFEL beam

At European XFEL scientists use intense X-rays to take pictures of the smallest particles imaginable. The European XFEL X-ray beam is a billion times brighter than other traditional X-ray sources, but since X-rays are invisible to the naked eye, it is not usually possible to see the X-ray beam. Working together with a professional photographer, scientists at the largest X-ray laser in the world located in Schenefeld near Hamburg, have now managed to capture an image of the intense European XFEL X-ray beam. The pictures were taken as the X-ray beam entered the experiment area in the FXE instrument hutch at the end of a journey that started in a 3.4km long underground tunnel.

On the images published today, the X-ray beam appears as a thin blue stripe. What we are actually seeing, however, is glowing nitrogen molecules which the X-ray beam has caused to light up as it travels through the air thereby interacting with the molecules.

>Read more on the European XFEL website

Image: The European XFEL beam.
Credit: European XFEL