Conference Agenda

Session
MS-80: 4th generation SR and XFEL Facilities
Time:
Friday, 20/Aug/2021:
10:20am - 12:45pm

Session Chair: Makina Yabashi
Session Chair: Sofia Diaz-Moreno
Location: Terrace 2A

130 2nd floor

Invited: Jean Susini (France)


Session Abstract

Recent advance of accelerator technologies has promoted the emergence of ultrabrilliant, coherent x-ray sources such as 4th generation synchrotron light sources and X-ray free-electron lasers (XFELs). The former renovates a vast range of scientific applications with an ultralow-emittance storage-ring source, while the latter enables ultimate “snapshot” observation using intense, femtosecond X-ray pulses. This microsymposium will focus on new scientific opportunities and perspectives enabled with these novel sources. It also covers advanced applications of X-ray absorption spectroscopy (XAS) achieved with the new sources.


Introduction
Presentations
10:20am - 10:25am

Introduction to session

Makina Yabashi, Sofia Diaz-Moreno



10:25am - 10:55am

The ultra-low emittance synchrotron storage rings: a new paradigm for matter characterization.

Jean Susini

Synchrotron SOLEIL, Gif sur Yvette, France

Over the last few years, photon science community has been experiencing a revolution with the advent of ultra-low emittance storage rings based on Multi-Bend Achromat (MBA). In addition to green fields projects MAXIV (1), SIRIUS (2), and HEPS (3) in operation, commissioning, or construction, respectively, many third-generation facilities undertook major upgrades such as ESRF-EBS (4), APS-U (5), ALS-U (6), SLS-2 (7), DLS-2 (8), etc. All are aiming to achieve unparalleled performances in terms of average spectral brilliance, coherent flux, and nano-focusing capabilities.

After an introduction of the main concepts behind this new revolutionary concept, the new characterization techniques and their potential for new applications will be discussed, for two distinct examples, including the commissioning and operation of the ESRF-EBS (6 GeV) and the project SOLEIL (2.75 GeV) upgrade:

Since 2015 the ESRF has prepared the replacement of its old storage ring based on the double-bend achromat lattice by the EBS storage ring(9) based on the newly developed HMBA lattice with seven bending magnets per cell. During a long shutdown the EBS storage ring was installed in 2019 and went into its commissioning phase in December 2019. The EBS storage ring was successfully commissioned as the first fourth generation high energy synchrotron light source during the first six month in 2020. Nominal beam parameters could be confirmed early on in the process and the beamlines resumed user operation in September 2020 as planned. The expected improvement of the key beam parameters in terms brilliance, coherence and flux were confirmed across the entire beamline portfolio. Details on the commissioning of the beamlines and the performance reached will be presented together with early scientific results.

In 2019, SOLEIL launched a CDR (10) for an upgrade of its 20 years old storage ring with the ambition to produce round electron beams with a record low emittance of less than 50 pm.rad x 50 pm.rad, hence photon beams with an exceptional brilliance exceeding by two orders of magnitude the performances of the current source. The very broad spectral range of Soleil from THz to tens of KeV is a challenge but offers unique scientific opportunities which will be discussed and illustrated by examples in materials science and biology.

[1] Tavares, P. F., et al., “Status of the MAX-IV Accelerators”, IPAC 2019 proceedings, TUYPLM3, 1185-1190 (2019).

[2] Liu, L., “SIRIUS Commissioning Results”, IPAC 2020 (2020).

[3] Jiao Y., “The HEPS Project”, Journal of Synchrotron Radiation, 25, 1611-1618 (2018).

[4] Raimondi P., “Hybrid Multi Bend Achromat: from SuperB to EBS”, 8th International Particle Accelerator Conference, May 2017, Copenhagen, Denmark, 3670-3675,10.18429/JACoW-IPAC2017-THPPA (2017).

[5] Borland, M. et al., “The Upgrade of the Advanced Photon Source”, IPAC 2018 proceedings, THXGBD1, 2872-2877 (2018).

[6] Steier, C. et al., “Design Progress of ALS-U, the Soft X-Ray Diffraction Limited Upgrade of the Advanced Light Source, IPAC 2019 proceedings, 1639-1641 (2019).

[7] Streun, A., et al., “SLS-2: the Upgrade of the Swiss Light Source”, Journal of Synchrotron Radiation, 25, 631-641 (2018).

[8] https://www.diamond.ac.uk/Home/About/Vision/Diamond-II.html

[9] Orange Book: http://www.esrf.eu/home/orange-book.html

[10] CDR SOLEIL, https://www.synchrotron-soleil.fr, to be published



10:55am - 11:15am

Ultrafast structural changes in matter induced by intense X-ray free-electron laser pulses

Ichiro Inoue1, Yuichi Inubushi1,2, Taito Osaka1, Toru Hara1, Eiji Nishibori3, Makina Yabashi1

1RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.; 2Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan; 3University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.

X-rays have become established as an invaluable probe for gaining an atomic insight into the structure of matter through various kinds of interaction processes, such as scattering, absorption, and emission of photoelectrons and fluorescence. Since these interactions were usually weak with the previous X-ray sources, X-ray irradiation was assumed not to modify matter. This situation has been altered by the recent advent of X-ray free-electron lasers (XFELs), which can generate brilliant femtosecond X-ray pulses.

When an XFEL pulse irradiates matter, photoelectrons and Auger electrons are emitted during or shortly after the irradiation of the pulse and trigger cascades of secondary electrons. If the radiation dose exceeds a critical value, the electron excitations strongly change interatomic potential surface and cause subsequent atomic disordering, and may even lead to the Coulomb explosion in the case of high X-ray dose. Given the time scale of electron cascading (typically, a few tens of fs) and inertia of atoms, the onset of atomic disordering is expected to take place behind the start of X-ray exposure. Indeed, it has been predicted that ultrafast X-ray pulse as short as ~10 fs with sufficient intensity can produce high-quality diffraction before the onset of substantial radiation damage, enabling structure determination of macromolecular nanocrystals and even individual biomolecule [1]. A deep understanding of transient XFEL interaction with matter is essential not only because of fundamental interest but for analyzing experiments with intense XFEL pulses.

Up to now, transient XFEL-matter interactions have been relying on theoretical modeling, validated by time-integrated measurements of charge states of ions and emitted fluorescence using a single XFEL pulse. To observe time-dependent X-ray interactions with matter, we developed a femtosecond X-ray pump-X-ray probe method [2] by combining nano-focusing optics [3] and twin XFEL pulses with controlled time separations [4] at SPring-8 Angstrom Compact free-electron LAser (SACLA) [5]. This method was applied to various materials (diamond [2,5], silicon [6], oxides, and protein crystals) and revealed the time scale of the electron excitations and the onset time of the structural changes.

In this talk, the XFEL-induced transient structural changes in matter revealed by the pump-probe experiments are discussed. In addition, preliminary results of the advanced pump-probe experiments using seeded-XFEL pulses [7,8] will be presented.

[1] Neutze, R., Wouts, R., Van der Spoel, D., Weckert, E., Hajdu, J. (2000). Nature 406, 752.[2] Inoue, I., Inubushi, Y., Sato, Y., Tono, K., Katayama, T., Kameshima, T., Ogawa, K., Togashi, T., Owada, S., Amemiya, Y., Tanaka, T., Hara, T., & Makina, Y. (2016). Proc. Natl. Acad. Sci. USA 113, 1492.[3] Mimura, H., Yumoto, H., Matsuyama, S., Koyama, T., Tono, K. et al., (2014). Nature Commun. 5, 3539.[4] Hara, T., Inubushi, Y., Katayama, T., Sato, T., Tanaka, H., Tanaka, T., Togashi, T., Togawa, T., Tono, K., Yabashi, M. & Ishikawa, T. (2014). Nat. Commun. 4, 2919.[5] Inoue, I., Deguchi, Y., Ziaja, B., Osaka, T., Abdullah, M. M., Jurek, Z., Medvedev, N., Tkachenko, V., Inubushi, Y., Kasai, H., Tamasaku, K., Hara. T., Nishibori, E. & Makina, Y. (2021). Phys. Rev. Lett. 126, 117403.[6] Hartley, N., Grenzer, L., Huang, L., Inubushi, Y., Kamimura, N., Katagiri, K. et al. (2021). Phys. Rev. Lett. 126, 015703.[7] Inoue, I., Osaka, T., Hara, T., Tanaka, T., Inagaki, T. et al. (2019). Nature Photon. 13, 319.[8] Inoue, I., Osaka, T., Hara, T. & Yabashi, M. (2020). J. Synchrotron Rad. 27, 1720.



11:15am - 11:35am

Pink-beam serial femtosecond crystallography for accurate structure factor determination at an X-ray free electron laser

Karol Nass1, Camila Bacellar1, Claudio Cirelli1, Florian Dworkowski1, Yaroslav Gevorkov2, Daniel James1, Philip J. M. Johnson1, Demet Kekilli1, Gregor Knopp1, Isabelle Martiel1, Dmitry Ozerov1, Alexandra Tolstikova2, Laura Vera1, Tobias Weinert1, Oleksandr Yefanov2, Joerg Standfuss1, Sven Reiche1, Christopher J. Milne1

1Paul Scherrer Institut, Forschungstrasse 111, Villigen, 5232, Switzerland; 2Center for Free-Electron Laser Science, Notkestrasse 85, Hamburg, 22607, Germany

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies [1]. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out and accurate structure factor amplitudes determined [2]. Recently, an improvement in native-SAD phasing of SFX data was demonstrated by utilizing longer wavelengths that increased the strength of the anomalous signal [3]. This reduced up to 10-fold the number of indexed images needed for successful de novo structure determination. Another approach to reduce the number of indexed images, applicable not only to de novo phasing but also to molecular replacement strategies, is to use polychromatic (pink) X-ray pulses for SFX. Theoretically, faster convergence rates of the Monte Carlo approach can be achieved by increasing the bandwidth or divergence of the X-ray pulses [4, 5].

We used the capability of the Swiss free-electron laser (SwissFEL) to generate large-bandwidth X-ray pulses (Δλ/λ = 2.2 % FWHM) and applied them in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure factor amplitudes. Compared to data measured using the same setup but X-ray pulses with typical, quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17 % FWHM), up to four fold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific break-troughs.

[1] Nass, K. (2019). Acta Cryst. D 75, 211-218.

[2] Nass, K., Meinhart, A., Barends, T. R., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R. B., Koglin, J., Liang, M., Shoeman, R. L., Williams, G., Boutet, S. & Schlichting, I. (2016). IUCrJ 3, 180-191.

[3] Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Doré, A. S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Bacellar, C., Bohinc, R., Steinmetz, M. O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M. & Milne, C. J. (2020). IUCrJ 7, 965-975.

[4] Dejoie, C., McCusker, L. B., Baerlocher, C., Abela, R., Patterson, B. D., Kunz, M. & Tamura, N. (2013). J. Appl. Cryst. 46, 791-794.

[5] White, T. A., Barty, A., Stellato, F., Holton, J. M., Kirian, R. A., Zatsepin, N. A. & Chapman, H. N. (2013). Acta Cryst. D 69, 1231-1240.

Keywords: Pink-beam; serial femtosecond crystallography; de novo protein structure determination; X-ray crystallography; SFX; SAD; single-wavelength anomalous diffraction; XFEL; large-bandwidth



11:35am - 11:55am

Towards a structural biology at organism relevant temperature and chemical conditions

John Richard Helliwell

University of Manchester, Manchester, United Kingdom

The three probes of the structure of matter in biology (X-rays, neutrons and electrons) have complementary properties and strengths. The balance between these three structural research probes, within their strengths and weaknesses, is perceived to change, even dramatically so at times. Of course for understanding biological systems the required perspectives are:- physiologically relevant temperatures and relevant chemical conditions. These remain very tough challenges because e.g. cryoEM looks never to set foot in room temperature and crystallization often requires non-physiological chemical conditions. X-ray crystallography especially from the synchrotron has brought huge improvements in analytical capability and dominates the PDB. CryoEM has also brought great advantage for structural studies of non-crystallisable complexes. Overall, integrated structural biology techniques and functional assays make a package towards physiological relevance of any given study. X-ray laser serial fsec crystallography experiments aimed at structural dynamics and neutron macromolecular crystallography aimed at determining protonation states of ionisable amino acids are both, as a spin off, yielding room temperature structures, as well as being damage free. Comparisons between room and cryo biological structures are increasing as the X-ray laser and neutron facilities expand in number and grow in capability; structural differences are being increasingly described in many papers. We need to expand these facility provisions for room temperature studies. Likewise the extremely bright sources such as ESRF2 ie "EBS" will bring a larger number of room temperature results through the serial crystallography approach but with X-ray radiation damage effects yet to be quantified.



11:55am - 12:15pm

Ultrafast dynamical diffraction wavefronts in strained Si imagined with Tele-ptychography

Angel Rodriguez-Fernandez1, Ana Diaz2, Anand H. S. Iyer3, Mariana Verezhak2, Klaus Wakonig2, Magnus H. Colliander3, Dina Carbone4

1Eu XFEL GmbH, Schenefeld, Germany; 2Paul Scherrer Institute, Villigen PSI, Switzerland; 3Chalmers University of Technology, Gothenburg, Sweden; 4MAX IV, Lund University, Lund, Sweden

Dynamical diffraction effects, also known as echoes, produced in thin crystals in both forward and diffracted directions are of highest importance for X-ray optics at ultrafast sources, as XFELs, and for the study of ultrafast phenomena in micron-sized single crystals. These echoes present delays of few fs between each other and the transmitted beam (similar as it happens with sound echoes, but in this case of electromagnetic nature and therefore with the speed of light). The delay relates to a displacement of the monochromatic diffracted beams in the transverse direction to the X-ray beam propagation [1,2]. Such echoes are used in self-seeding forward monochromators at hard xFELs.

We would like to present our work performed at NanoMAX, MAX IV laboratory, Sweden, in which we image the dynamical diffraction wavefront from a 100 um thick Si wafer [3]. The work uses the full coherence and high flux of NanoMAX, together with the technique known as tele-ptychography [4], to image the forward diffracted wavefront at a pinhole located 3 mm downstream the sample. As presented in figure 1, the data collected is reconstructed using a ptychography algorithm in the pinhole plane, obtaining amplitude and phase of the wavefront. The wavefront is propagated back to the focus where, combined to the small size of the X-ray beam provided by NanoMAX, provides a high- resolution (55 nm) image for the detection of forward diffracted echoes.

The work underline how this effect must be taken into account in the imaging and study of samples with thickness of the order of the X-ray extinction length. We also show that a strain induced in the surface can modulate the temporal delay of the dynamical diffraction waves as presented in the second figure attached. All the work is accompanied with the simulation of the effect using a self-written code, that can be used to model both temporal and static strains in single crystal samples, as well as in micro-pillars in which these dynamical effects are also present [5].

[1] A. Rodriguez-Fernandez et al., ActaCryst. A74, 75 (2018);

[ 2] Y. Shvydko and R. Lindberg, Phys. Rev. ST Accel.Beams15, 100702 (2012);

[3] A. Rodriguez-Fernandez et al., "Imaging ultrafast dynamical diffraction wavefronts in strained Si with coherent X-rays" arXiv:2012.08893 (2020)

[4] E. H. R. Tsai et al, Optics Express 34 (2016) 6441;

[5] M. Verezhak et al. "X-ray ptychographic topography, a new tool for strain imaging" PRB (2021);



Advances with EIGER2 (CdTe) detectors for Synchrotron and Laboratory

Stefan Brandstetter, Max Burian

Dectris Ltd, Baden-Daettwil , Switzerland

Hybrid photon counting (HPC) X-ray detectors are crucial ingredients for cutting-edge synchrotron research [1] by providing noise-free detection with advanced acquisition modes. In this regard, the latest HPC detector generation EIGER2 is setting new performance standards that push current horizons in X-ray science. These detectors combine all advantages of previous HPC detector generations while offering (i) 75 µm × 75 µm pixel size, (ii) kilohertz frame rates, (iii) negligible dead time (100 ns) and (iv) count rates of 107 photons per pixel.

Recently, EIGER2 detectors are available both with silicon and with CdTe sensors to provide high quantum efficiency at energies up to 100 keV. Two separately adjustable energy thresholds allow for reduction of high-energy background such as from cosmic radiation or higher harmonics radiation. For one, this active background suppression significantly improves signal-to-noise in laboratory applications where weaker signals are expected. For the other, these benefits advance established methods like crystallography and small angle X-ray scattering and empower new fields of research, such as X-ray photon correlation spectroscopy and coherent studies.

Here, we present results from detector characterization and application experiments, highlighting key properties such as count rate capability, readout and spatial resolution. We will further show the potential capabilities of newly released detector features, such as the double-gating acquisition mode for shot-to-shot background correction. Combined with characterization measurements at beamlines and in the laboratory, these results evidence how the EIGER2 detector systems will advance static and time-resolved X-ray experiments.

[1] Förster, A., et al. (2019) Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 377, 20180241.