Science Programme

The SPB/SFX instrument utilizes the highly-coherent, ultrafast (femtosecond), highly-intense X-ray FEL pulses for single-particle X-ray coherent diffractive imaging and X-ray crystallography of primarily biological samples smaller than 1 µm, such as crystals of macromolecules and macromolecular complexes or cells, organelles, and viruses.

The goal is to achieve (near-)atomic resolution determination of static structures or ultrafast structural dynamics (millisecond to femtosecond timescale) in these specimens. Although the main scope of SPB/SFX is with regard to biological specimens, all or similar techniques can be applied to the investigation of non-biological samples as well.

Key research projects

Coherent diffractive imaging of non-crystalline biological samples

One of the main research topics performed at SPB/SFX is utilizing the ultra-intense, ultrashort, and highly-coherent XFEL pulses for exploring the limits of coherent diffractive imaging of non-crystalline biological samples. Ultrashort exposures in the range of only a few up to several hundreds of femtoseconds allow a “diffraction-before-destruction” approach which results in virtually damage-free diffraction data, thereby allowing for radiation doses far above the conventional radiation damage limits. At SPB/SFX, experiments will explore the prospects and limits of this technique in terms of how low a signal can be used, how small a sample, and what is the best resolution to be achieved. The ultimate goal is to explore the feasibility of achieving near-atomic resolution from samples of the size down to single biological macromolecules. While the instrument is under construction, the SPB/SFX team pursue these scientific goals at other XFEL facilities worldwide.

Serial femtosecond crystallography

X-ray crystallography is still contributing the major number of macromolecular structures in the Protein Data Bank. At SPB/SFX, serial X-ray crystallography will be performed with macromolecular crystals of the size in the range of a few micrometres across or even below 1 µm, delivered within the continous stream of a liquid jet.

Serial femtosecond crystallography naturally bridges the gap between conventional X-ray crystallography (such as at synchrotrons) and serial femtosecond coherent diffractive imaging of non-crystalline particles (see above). It is in particular promising for previously inaccessible small crystals—samples where circumventing the conventional radiation damage limit by "diffraction-before-destruction" is mandatory for sufficient signal-to-noise at high resolution and the study of fast dynamics in regimes previously inaccessible by diffraction-based methods.

Dynamics in biological systems

One of the major scientific scopes of the SPB/SFX instrument will be diffraction studies of fast and irreversible dynamic processes in primarily biological systems, either of crystalline or non-crystalline nature. For all reaction initiation methods, utilizing the European XFEL and the “diffract-before-destroy” scheme for high-resolution snapshot patterns of samples at room temperature provides great opportunities for future time-resolved diffraction studies.

The general concept is to initiate a process or reaction through a variety of different methods and subsequently probe the induced structural changes by an X-ray diffraction snapshot. Here, the ultrashort X-ray pulse duration paired with synchronized, ultrafast optical or near-infrared lasers in principle allows for time resolutions in the range of some tens to hundreds of femtoseconds for snapshot imaging of ultrafast evolving reactions and changes, such as basic chemical and radiation damage processes, or laser-induced photolysis in biological systems for example. On the picosecond to nanosecond timescales, fast conformational dynamics of biological systems have barely been studied by diffraction methods, and here the European XFEL offers a unique opportunity, either for crystallographic or solution/WAXS studies. Timescales of micro- to milliseconds in enzyme-substrate mixing experiments can be achieved with liquid jet sample delivery and/or mixing systems. The small crystals used in XFEL serial crystallography greatly reduce diffussion times and enable the study of irreversible enzyme-substrate reactions not amenable by synchrotron crystallography.

Start-to-end simulation of X-ray FEL single-particle imaging experiment

The “Holy Grail” of protein structure determination is to forgo the use of crystals and be able to determine the structure from a stream of single particles. The group is developing a start-to-end simulation of serial, femtosecond, single particle experiments at European XFEL’s SPB/SFX instrument. The idea is to simulate the entire experiment, beginning from the X-ray source at the undulator to the end of the reconstruction process to determine the fidelity of a given measurement strategy for various experimental parameters. The group also aims to provide their start-to-end simulation to the public in order to build a user-base and also contribute to the scientific development of this field.

The simulation workflow currently involves six modules. The pipeline is a linear chain of modules starting from modeling of 1) the FEL source, 2) propagation and optics, 3) photon matter interaction, 4) coherent diffraction, 5) orientation recovery, and 6) phase retrieval. Most of the development effort has been on design and implementation of the interfaces. It is envisaged that the simulation will be a key tool for testing the feasibility of proposed experiments and guiding the experimental setup at the upstream interaction region of the SPB/SFX instrument.

 

Basic design of the start-to-end simulation suite.

Characterization of X-ray FEL photon beams—wavefront characterization and more

To inform and support the rapid development of existing and new methods in diffractive imaging, there is a strong need for the characterization of the FEL source and the source wave field. Quantitative knowledge of intensity and phase of the wave front on a shot-to-shot basis is a requirement to fully exploit the potential of single-particle coherent diffractive imaging. The group has performed both average and single-shot wavefront characterizations at synchrotron and FEL light sources in the past and will continue this route at the SPB/SFX instrument.