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

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

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)

Research and tinkering – SwissFEL in 2019

The newest large research facility at the Paul Scherrer Institute, SwissFEL, has been completed. Regular operation began in January 2019.

Henrik Lemke, head of the SwissFEL Bernina research group in the Photon Science Division, gives a first interm report.

Mr. Lemke, you have just published a technical article in which you report on the experience so far with SwissFEL. How would you sum it up?

With SwissFEL, we are entering new territory at PSI. It is one of only five comparable facilities on this scale worldwide. This means we still need to gain experience, because we are doing a lot of things for the first time. On January 1 this year we began regular operation. Research groups from other institutions have already been here, and they have successfully conducted experiments with us, just like PSI researchers themselves. These were already a big success. In parallel to this operation, we are also further optimising the facility and the experimental setup. This will enable us to join ranks with the comparable facilities and, in addition, develop particular methods into specialities of SwissFEL.

>Read more on the SwissFEL website

Image: Lemke at the experiment station Bernina of SwissFEL
Credit: Paul Scherrer Institute/Mahir Dzambegovic

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

A laser for penetrating waves

Research team develops a new principle to generate terahertz radiation

The “Landau-level laser” is an exciting concept for an unusual radiation source. It has the potential to efficiently generate so-called terahertz waves, which can be used to penetrate materials as well as for future data transmission. So far, however, nearly all attempts to make such a laser reality have failed. An international team of researchers has now taken an important step in the right direction: In the journal Nature Photonics (DOI: 10.1038/s41566-019-0496-1), they describe a material that generates terahertz waves by simply applying an electric current. Physicists from the German research center Helmholtz-Zentrum Dresden-Rossendorf (HZDR) played a significant role in this project.
Like light, terahertz waves are electromagnetic radiation, in a frequency range between microwaves and infrared radiation. Their properties are of great technological and scientific interest, as they allow fundamental researchers to study the oscillations of crystal lattices or the propagation of spin waves. Simultaneously “terahertz waves are of interest for technical applications because they can penetrate numerous substances that are otherwise opaque, such as clothing, plastics and paper,” Stephan Winnerl from HZDR’s Institute of Ion Beam Physics and Materials Research explains. Terahertz scanners are already used today for airport security checks, detecting whether passengers are concealing dangerous objects under their clothing – without having to resort to harmful X-rays.
>Read more on the FELBE at HZDR website

Image: An international research team has been able to show that it is relatively easy to generate terahertz waves with an alloy of mercury, cadmium and tellurium. To examine the behavior of the electrons in the material, the physicists use the free-electron laser FELBE at HZDR. Circularly polarized terahertz pulses (orange spiral) excite the electrons (red) from the lowest to the next higher energy level (parabolic shell). The energy gap of these so-called Landau levels can be adjusted with the help of a magnetic field. Credit : HZDR / Juniks

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

Coherent soft x-ray pulses from an echo-enabled free-electron laser

The free-electron laser (FEL) FERMI is a unique facility, providing users with laser-like pulses in the XUV spectral range. At FERMI, the generation of highly coherent pulses, with tunable spectro-temporal properties, relies on the so-called high-gain harmonic generation (HGHG) technique. In the latter, a (single) infrared seed laser is used to shape the electron-beam properties and trigger the amplification process. Amplification occurs at one selected harmonic, h, of the seed. However, in HGHG, the seed energy required to prepare the electron beam for FEL emission becomes larger and larger for higher harmonics (i.e., shorter FEL wavelengths). For high harmonics, the resulting strong electron-beam energy modulation reduces the FEL gain, limiting the scheme to h<15 (wavelengths of about 10-20 nm) for a single HGHG scheme, or to h of the order of 60-70 (i.e., 4-5 nm), in case of two-stage HGHG. Moreover, at such high h, the sensitivity to the shape of the electron-beam phase space becomes critical and may severely affect the FEL radiation in terms of longitudinal coherence, pulse energy, and shot-to-shot stability. In addition, the HGHG scheme cannot cover the whole harmonic range, as the final harmonic number is a product between the harmonic numbers of the individual stages. Last, but not least, the two-stage setup uses a relatively large portion of the e-beam to accommodate the double seeding process, which makes the implementation double-pulse operation difficult.
The drawbacks of the two-stage HGHG can be overcome by using a recently proposed technique called echo-enabled harmonic generation (EEHG), where the electron-beam is shaped using two seed lasers to enable FEL emission at high harmonics. The method requires a much weaker energy modulation compared to HGHG and is also intrinsically less sensitive to the initial electron-beam imperfections, making it a strong candidate for producing highly stable, nearly fully coherent, and intense FEL pulses, down to soft x-ray wavelengths.

>Read more on the FERMI at Elettra website

Image:  The EEHG scheme together with the e-beam phase space at different stages of the evolution. The 1st seed laser with a wavelength λ1 imprints a sinusoidal energy modulation with an amplitude ΔE<3σE,  σE is the initial uncorrelated energy spread, onto the relativistic e-beam in the 1st modulator. After passing through a strong 1st chicane, the electrons with different energies move relative to each other, resulting in a striated phase space with multiple energy bands. Importantly, the energy spread within a single band is much smaller than σE. The electrons then pass through the 2nd modulator, where their energy is again periodically modulated using a 2nd seed laser with λ2λ1 and ΔE2≈ΔE1. After traversing a weaker 2nd chicane, the e-beam phase space is rotated, transforming the sinusoidal energy modulation into a periodic density modulation, with high-frequency components. As the energy spread within a single band is much smaller than σE, only a moderate ΔE2 is required to reach very high harmonics. The e-beam is then injected into the radiator, tuned to emit light at a high harmonic of the 2nd seed laser.

Ghostly X-ray images could provide key info for analyzing X-ray laser experiments

SLAC researchers say their new method could make it easier to study interactions of ultrabright X-rays with matter

X-ray free-electron lasers (XFELs) produce incredibly powerful beams of light that enable unprecedented studies of the ultrafast motions of atoms in matter. To interpret data taken with these extraordinary light sources, researchers need a solid understanding of how the X-ray pulses interact with matter and how those interactions affect measurements.
Now, computer simulations by scientists from the Department of Energy’s SLAC National Accelerator Laboratory suggest that a new method could turn random fluctuations in the intensity of laser pulses from a nuisance into an advantage, facilitating studies of these fundamental interactions. The secret is applying a method known as “ghost imaging,” which reconstructs what objects look like without ever directly recording their images.

>Read more on the LCLS at SLAC website

Image: SLAC researchers suggest using the randomness of subsequent X-ray pulses from an X-ray laser to study the pulses’ interactions with matter, a method they call pump-probe ghost imaging.
Credit: Greg Stewart/SLAC National Accelerator Laboratory

Towards X-ray transient grating spectroscopy at SwissFEL

The high brilliance of new X-ray sources such as X-ray Free Electron Laser opens the way to non-linear spectroscopies.

These techniques can probe ultrafast matter dynamics that would otherwise be inaccessible. One of these techniques, Transient Grating, involves the creation of a transient excitation grating by crossing X-ray beams on the sample. Scientists at PSI have realized a demonstration of such crossing by using an innovative approach well suited for the hard X-ray regime. The results of their work at the Swiss Free Electron Laser have been published in the journal Optics Letters.
Non-linear optics is an important field of physics where the non-linear response of matter in extreme electromagnetic fields is studied and exploited for novel applications. It has been widely used for creating new laser wavelengths (Sum/Difference Frequency Generation – S/DFG) as well as for studying a variety of properties such as charge, spin, magnetic transfer as well as heat diffusion. A broad class of non-linear spectroscopy is Four Wave Mixing (FWM) where three laser beams are overlapped in space and time in a sample and a fourth beam with different wavelength and angle is detected, background free. This allows studying specific transitions and selectively excite the sample tuning the incoming beams’ wavelength while studying their dynamics by controlling the relative time delays between the laser pulses. Transient Grating (TG) spectroscopy is a special case of degenerate FWM where two of the incoming beams have the same wavelength and are crossed at the sample creating an interference pattern, or transient grating, which excites the sample as long as the field is present. When the TG impinges on the material, its index of refraction is locally perturbed and electrons exposed to the radiation are excited. These electrons then transfer their extra energy to the lattice and the heat is then dissipated by the system. A third beam, delayed with respect to the pump TG, probes the dynamics of this excitation.

>Read more on the SwissFEL at PSI website

Image: Layout depicting the experimental conditions at the Alvra experimental station. (Find all the details here)

A timely solution for the photosynthetic oxygen evolving clock

XFEL Hub collaboration reveals the intermediates of the photosynthetic water oxidation clock

A large international collaborative effort aided by the XFEL Hub at Diamond Light Source has generated the most detailed time-resolved studies to date of a key protein involved in photosynthesis. The pioneering work, recently published in Nature, shows how photosystem II harnesses light energy to produce oxygen – insights that could direct a next generation of photovoltaic cells. 
>Read more on the Diamond Light Source website

Image: this figure is issued from a video you can watch here.

New insight into a puzzling magnetic phenomenon

ImagUsing an X-ray laser, researchers watched atoms rotate on the surface of a material that was demagnetized in millionths of a billionth of a second.

More than 100 years ago, Albert Einstein and Wander Johannes de Haas discovered that when they used a magnetic field to flip the magnetic state of an iron bar dangling from a thread, the bar began to rotate.

Now experiments at the Department of Energy’s SLAC National Accelerator Laboratory have seen for the first time what happens when magnetic materials are demagnetized at ultrafast speeds of millionths of a billionth of a second: The atoms on the surface of the material move, much like the iron bar did. The work, done at SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, was published in Nature earlier this month.

>Read more on the LCLS at SLAC website

Image: Researchers from ETH Zurich in Switzerland used LCLS to show a link between ultrafast demagnetization and an effect that Einstein helped discover 100 years ago.
Credit: Dawn Harmer/SLAC National Accelerator Laboratory

In-situ single-shot diffractive fluence mapping for x-ray FEL pulses

Free-electron lasers (FEL) for the extreme-ultraviolet (XUV) and x-ray regime opened up the possibility to investigate and exploit non-linear processes in the interaction of x-rays with matter. Such processes are of considerable interest in numerous research fields, owing to the huge impact of non-linear techniques on optics and spectroscopy in the visible and near-visible spectral range. Generating and understanding non-linear effects requires sophisticated control of the sample illumination. This is especially challenging at FEL sources, where variations of the spatial fluence distribution on a single-shot basis are common. Moreover, the focused spot often exhibits a complex internal structure due to diffraction artefacts from the focusing optics. These factors cause considerable uncertainties with respect to the effective fluence on a solid sample for scattering experiments in the forward direction.
We demonstrate a flexible solution for true in-situfluence monitoring on solid samples in transmission-type diffraction experiments. Our concept measures the detailed beam footprint on the actual sample under study. The image of the illumination is recorded simultaneously with the specimen’s primary scattering signal on a two-dimensional detector. This is facilitated by a shallow grating structure of only a few nanometer depth that is lithographically fabricated into the sample carrier membrane. Such membranes are routinely used in transmission-type diffraction experiments as a transmissive structural support for thin-film or sparsely dispersed samples. The grating structure forms a diffractive optical element that maps the spatial fluence distribution on the sample to a configurable position on the detector.

>Read more on the Elettra Sincrotrone Trieste website

Image: Figure 1.  a) Single-shot diffraction image of a sample with grating-based fluence monitor and ferromagnetic domains on a logarithmic false-color scale. The ring-shaped structure is due to the magnetic domains, while the fluence monitor grating gives rise to the brighter patterns on the image diagonals. Both grating patterns are equivalent images of the beam footprint on the sample. b) Enlarged detail of the diffracted fluence map on the sample on a linear false-color scale. c) AFM image of a single-shot damage crater in the sample’s silicon substrate. The pattern observed matches the in-situ measured beam footprint very well, but belongs to a different FEL shot. Scale bars are 10µm. Adapted from M. Schneider et al., Nature Communications 9, 214 (2018)

First experiments reveal unknown structure of antibiotics killer

DESY-led international collaboration obtains first scientific results from European XFEL

An international collaboration led by DESY and consisting of over 120 researchers has announced the results of the first scientific experiments at Europe’s new X-ray laser European XFEL. The pioneering work not only demonstrates that the new research facility can speed up experiments by more than an order of magnitude, it also reveals a previously unknown structure of an enzyme responsible for antibiotics resistance. “The groundbreaking work of the first team to use the European XFEL has paved the way for all users of the facility who greatly benefit from these pioneering experiments,” emphasises European XFEL managing director Robert Feidenhans’l. “We are very pleased – these results show that the facility works even better than we had expected and is ready to deliver new scientific breakthroughs.” The scientists present their results, including the first new protein structure solved at the European XFEL, in the journal Nature Communications.

“Being at a totally new class of facility we had to master many challenges that nobody had tackled before,” says DESY scientist Anton Barty from the Center for Free-Electron Laser Science (CFEL), who led the team of about 125 researchers involved in the first experiments that were open to the whole scientific community. “I compare it to the maiden flight of a novel aircraft: All calculations and assembly completed, everything says it will work, but not until you try it do you know whether it actually flies.”

The 3.4 kilometres long European XFEL is designed to deliver X-ray flashes every 0.000 000 220 seconds (220 nanoseconds). To unravel the three-dimensional structure of a biomolecule, such as an enzyme, the pulses are used to obtain flash X-ray exposures of tiny crystals grown from that biomolecule. Each exposure gives rise to a characteristic diffraction pattern on the detector. If enough such patterns are recorded from all sides of a crystal, the spatial structure of the biomolecule can be calculated. The structure of a biomolecule can reveal much about how it works.

>Read more on the DESY website and on the European XFEL website

Image: Artist’s impression of the experiment: When the ultra-bright X-ray flashes (violet) hit the enzyme crystals in the water jet (blue), the recorded diffraction data allow to reconstruct the spatial structure of the enzyme (right).
Credit: DESY/Lucid Berlin

First serial crystallography experiments performed at BioMAX

BioMAX has successfully performed the first serial crystallography experiments at the beamline. This new method is performed at room temperature which allows structural biologists to study their molecules at more biologically relevant conditions. The technique can also be used on smaller crystals which will alleviate some of the restrictions for molecules such as membrane proteins, that do not typically form large crystals. Eventually, it is hoped that this technique will allow users at the BioMAX and MicroMAX beamlines to take snapshots of the dynamic states of proteins in rapid succession giving a dynamic view of protein movement and activity.

The serial crystallography technique promises to be very useful to users of both synchrotrons and XFELs. Over the course of one experiment, users were able to measure between 20 and 50 crystals every second, resulting in 20 TB of data from just 3 proteins. BioMAX hopes to quickly master this complex technique in order to offer it to users as soon as possible. It also gives us a glimpse of what will be possible at the newly funded MicroMAX beamline.

>Read more on the MAX IV Laboratory website

Image: BioMAX serial crystallography setup using a High Viscosity Extrusion (HVE) injector specially designed for the BioMAX endstation by Bruce Doak of the Max Planck Institute for Medical Research, Heidelberg, and fabricated at that institute.