X-ray Free-electron Laser Applications Research Articles

Helium-electrospray improves sample delivery in X-ray single-particle imaging experiments

Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements have the potential to significantly increase the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.

Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses.

The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.

Femtosecond imaging of giant-hemeprotein with XFEL pulses

Outrunning radiation damage, extremely intense femtosecond pulses of x-ray free-electron lasers (XFELs) open up the possibility of imaging the structure and dynamics of macromolecules frozen in time at room temperature. Single-Particle Imaging (SPI) of uncrystallized macromolecules at high-resolution is one of the most-desired foundational applications of XFELs and one of the ultimate goals of SPI is to image the light-induced ultrafast (ps/fs) dynamics in single-macromolecules. Biological proteins exhibiting photoinduced ultrafast dynamics are in the range of tens to few-hundreds of kDa, which are too small for SPI with the photon flux of current generation XFELs. Ideally, one needs MDa-sized, strongly scattering, photoactive proteins for such challenging endeavours to discern the signal above the background scattering and to obtain difference-maps with sufficient quality to elucidate photoinduced changes empirically. Photoactive proteins are sparse in nature and MDa-sized photoactive macromolecules are extremely rare. We have found one such rare MDa-sized photoactive, porphyrin-containing, large-metalloprotein-complex, the giant-hemeprotein—erythrocruorin (Ery) and show that Ery is likely suitable for validating the ultimate potential of SPI. We present the cryoEM characterization of stability of Ery in the unique experimental conditions of XFEL-SPI together with simulated single-molecule diffraction and 3D intensity reconstruction using expand-maximize-compress (EMC) algorithm and propose a potential SPI roadmap to demonstrate the imaging of ps/fs resolved bio-functional dynamics in Ery with XFEL pulses. Also, here we report the first in-solution ensemble fluctuation scattering results of Ery with the microfocus hard x-ray FEL pulses at the Linac Coherent Light Source (LCLS), USA—a step towards single-molecule imaging of Ery in-solution with nanofocus. We envisage that the robust giant-hemeprotein Ery could likely be an archetype biological macromolecular system enabling the imaging of light-induced ultrafast (ps/fs) dynamics such as protein-quake following heme-doming in isolated single-proteins—“the Holy Grail” of XFEL-SPI.

Numerical characterization of quasi-steady thermal load for thin crystal at cryogenic temperature with nondiffusive heat transfer

With dramatically improved brightness and repetition rate, the thermal load for crystal optics in x-ray free-electron laser applications has also significantly increased. To mitigate the thermal load, one effective method is cryogenic cooling. However, the emerging nondiffusive heat transfer phenomenon at cryogenic temperature may cause design failure if overlooked. To evaluate the optical performance of thin crystal optics under thermal load at cryogenic temperature, an integrated numerical tool is presented and applied to characterize the thermal load on thin crystals with nondiffusive phenomena accounted. Significant thermally induced distortion of the rocking curve is observed from numerical simulation, leading to potential seed power reduction in hard x-ray self-seeding application. Cryogenic cooling is confirmed necessary by simulation to handle the thermal load at high repetition rate operation.

EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm

Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.

Femtosecond laser produced periodic plasma in a colloidal crystal probed by XFEL radiation

With the rapid development of short-pulse intense laser sources, studies of matter under extreme irradiation conditions enter further unexplored regimes. In addition, an application of X-ray Free-Electron Lasers (XFELs) delivering intense femtosecond X-ray pulses, allows to investigate sample evolution in IR pump - X-ray probe experiments with an unprecedented time resolution. Here we present a detailed study of the periodic plasma created from the colloidal crystal. Both experimental data and theory modeling show that the periodicity in the sample survives to a large extent the extreme excitation and shock wave propagation inside the colloidal crystal. This feature enables probing the excited crystal, using the powerful Bragg peak analysis, in contrast to the conventional studies of dense plasma created from bulk samples for which probing with Bragg diffraction technique is not possible. X-ray diffraction measurements of excited colloidal crystals may then lead towards a better understanding of matter phase transitions under extreme irradiation conditions.

X-ray mirror surface figure correction with nanometre precision controlled by layer stresses simulated by FEA.

Hard X-rays with energies higher than several kiloelectronvolts can be focused to spot sizes below 10 nm with the present synchrotron beamlines, offering unique advantages for the chemical, elemental and structure analysis of matter. Nevertheless, a surface precision on the nanometre scale for the focusing optics is required and remains the main hurdle limiting X-ray analytical techniques with single-nanometre spatial resolution. On the other hand, to preserve the wavefront properties of coherent X-ray beams, precise control of the reflective mirror surface quality at the nanometre scale is demanded for X-ray free-electron laser applications. In this work, the surface shape of a multilayer-coated X-ray mirror is controlled by layer stresses. The desired surface profile of the mirror is differentiated to its second order to obtain its corresponding curvature profile. With a step size of 1 mm along the mirror length, different coating thicknesses are applied to create different layer thermal stresses from uniform temperature change. The mirror surface profile can be obtained by integrating the curvature profile to its second order and further corrected by moving constant values for the slope and height. The technical process is simulated by finite element analysis (FEA). A case study showed that the residual slope error and the residual height error between the desired shape and the FEA result are 0.22 µrad (r.m.s.) and 1.42 nm (r.m.s.), respectively.

Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 1020 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 1020 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.

Observation of femtosecond X-ray interactions with matter using an X-ray–X-ray pump–probe scheme

Resolution in the X-ray structure determination of noncrystalline samples has been limited to several tens of nanometers, because deep X-ray irradiation required for enhanced resolution causes radiation damage to samples. However, theoretical studies predict that the femtosecond (fs) durations of X-ray free-electron laser (XFEL) pulses make it possible to record scattering signals before the initiation of X-ray damage processes; thus, an ultraintense X-ray beam can be used beyond the conventional limit of radiation dose. Here, we verify this scenario by directly observing femtosecond X-ray damage processes in diamond irradiated with extraordinarily intense (∼10(19) W/cm(2)) XFEL pulses. An X-ray pump-probe diffraction scheme was developed in this study; tightly focused double-5-fs XFEL pulses with time separations ranging from sub-fs to 80 fs were used to excite (i.e., pump) the diamond and characterize (i.e., probe) the temporal changes of the crystalline structures through Bragg reflection. It was found that the pump and probe diffraction intensities remain almost constant for shorter time separations of the double pulse, whereas the probe diffraction intensities decreased after 20 fs following pump pulse irradiation due to the X-ray-induced atomic displacement. This result indicates that sub-10-fs XFEL pulses enable conductions of damageless structural determinations and supports the validity of the theoretical predictions of ultraintense X-ray-matter interactions. The X-ray pump-probe scheme demonstrated here would be effective for understanding ultraintense X-ray-matter interactions, which will greatly stimulate advanced XFEL applications, such as atomic structure determination of a single molecule and generation of exotic matters with high energy densities.

Effect of slope errors on the performance of mirrors for x-ray free electron laser applications.

In this work we point out that slope errors play only a minor role in the performance of a certain class of x-ray optics for X-ray Free Electron Laser (XFEL) applications. Using physical optics propagation simulations and the formalism of Church and Takacs [Opt. Eng. 34, 353 (1995)], we show that diffraction limited optics commonly found at XFEL facilities posses a critical spatial wavelength that makes them less sensitive to slope errors, and more sensitive to height error. Given the number of XFELs currently operating or under construction across the world, we hope that this simple observation will help to correctly define specifications for x-ray optics to be deployed at XFELs, possibly reducing the budget and the timeframe needed to complete the optical manufacturing and metrology.

Numerical study of the laser-tip coupling in surface plasmon assisted stacked-double-gate field emitter arrays

Recently, sub-wavelength-pitch stacked double-gate metal nanotip arrays have been proposed to realize high current, high brightness electron bunches for ultrabright cathodes for x-ray free-electron laser applications. With the proposed device structure, ultrafast field emission of photoexcited electrons is efficiently driven by vertical incident near infrared laser pulses, via near field coupling of the surface plasmon polariton resonance of the gate electrodes with the nanotip apex. In this work, in order to gain insight in the underlying physical processes, the authors report detailed numerical studies of the proposed device. The results indicate the importance of the interaction of the double-layer surface plasmon polariton, the position of the nanotip, as well as the incident angle of the near infrared laser pulses.

Femtosecond all-optical synchronization of an X-ray free-electron laser.

Many advanced applications of X-ray free-electron lasers require pulse durations and time resolutions of only a few femtoseconds. To generate these pulses and to apply them in time-resolved experiments, synchronization techniques that can simultaneously lock all independent components, including all accelerator modules and all external optical lasers, to better than the delivered free-electron laser pulse duration, are needed. Here we achieve all-optical synchronization at the soft X-ray free-electron laser FLASH and demonstrate facility-wide timing to better than 30 fs r.m.s. for 90 fs X-ray photon pulses. Crucially, our analysis indicates that the performance of this optical synchronization is limited primarily by the free-electron laser pulse duration, and should naturally scale to the sub-10 femtosecond level with shorter X-ray pulses.

Research at the NSF STC for Biology with X-ray lasers

"The NSF BioXFEL Science and Technology Center (STC) is a new consortium of six research campuses devoted to the application of x-ray free-electron lasers (XFELs) to structural biology. Over the last four years a variety of approaches have been made to the observation of protein structure and dynamics for various classes of proteins. The Linac Coherent Light source at SLAC, the first hard-Xray EXFEL, provides intense coherent hard X-ray pulses at 120 Hz which vaporize protein when focussed to a sub-micron beam. Atomic-resolution Bragg diffraction patterns are nevertheless obtained using 50 fs pulses prior to the onset of significant damage, in this ""diffract-then-destroy"" mode, which outruns radiation damage. This use of short pulses instead of freezing samples to reduce radiation damage therefore opens the way to the study of protein dynamics at room temperature in a native environment. I'll review the work of several groups using a range of approaches to different types of sample, including the following: 1. Differences between the frozen sychrotron structure of GPCR proteins and the RT XFEL structure [1]. 2. Pump-probe dynamic structures in Photosynthesis [2]. 3. XFEL study of 2D protein crystals [3]. 4. Prospects for improved resolution in XFEL imaging from single particles such as viruses, where patterns can be obtained from a single virus. 5. New ideas - the Lipid Cubic Phase injector (which allows protein nanocrystals to be studied also at sychrotrons) [4], prospects for fast Laue diffraction using coherent attosecond X-ray lasers, ab-initio phasing [5], the use of angular correlation functions for analysis of fast solution scattering, and two-color opportunites for serial femtosecond crystallography (SFX). See [6] for a recent review of the field. 1. W.Liu et al Science 342, 1521 (2013) 2. A.Aquila et al Optics Express 20, 2706 (2012) 3. M.Frank et al IUCrJ (2014) In press. 4. U.Weierstall et al Nature Comms. (2014) In press. 5. J. Spence et al Optics Express 19, 2866 (2011). 6. J. Spence et al Rep. Prog. Phys. 75, 102601 (2012)."

X-ray pump optical probe cross-correlation study of GaAs

Ultrafast dynamics in atomic, molecular and condensed-matter systems are increasingly being studied using optical-pump, X-ray probe techniques where subpicosecond laser pulses excite the system and X-rays detect changes in absorption spectra and local atomic structure(1-3). New opportunities are appearing as a result of improved synchrotron capabilities and the advent of X-ray free-electron lasers(4,5). These source improvements also allow for the reverse measurement: X-ray pump followed by optical probe. We describe here how an X-ray pump beam transforms a thin GaAs specimen from a strong absorber into a nearly transparent window in less than 100 ps, for laser photon energies just above the bandgap. We find the opposite effect-X-ray induced optical opacity-for photon energies just below the bandgap. This raises interesting questions about the ultrafast many-body response of semiconductors to X-ray absorption, and provides a new approach for an X-ray/optical cross-correlator for synchrotron and X-ray free-electron laser applications.

Low-flux measurements with Cornell's LCLS integrating pixel array detector

Next generation light sources are revolutionizing x-ray science by delivering ultra-intense, hard x-ray pulses many orders of magnitude brighter and shorter in duration than previously achievable. Maximizing the scientific potential of these light sources requires the development of suitable detectors. Experiments such as coherent x-ray imaging of single particles require detectors that can record extremely high instantaneous flux rates produced by femtosecond x-ray pulses (i.e. thousands of photons incident on a single pixel of an area detector in a few femtoseconds) while also being able to accurately distinguish single photon events so that many thousands of frames of data can be used to reconstruct extremely low flux information (e.g. less than 1/1000 photons per pixel per frame). This paper presents data from an integrating pixel array detector (PAD) possessing the ability to record high- and low-flux x-ray data at an X-ray Free Electron Laser (XFEL). Methods are presented to process extremely low-flux data (less than 1/10000 8-keV x-rays per pixel per frame) to accurately recover diffraction patterns from thousands of frames. The data were collected using a detector developed by Cornell for the Linac Coherent Light Source (LCLS) at SLAC National Lab. A copy of this detector was delivered to SLAC in the middle of 2008. The ASIC developed for this detector was used by SLAC as the basis for the CS-PAD (Cornell SLAC-PAD) being used on the Coherent X-ray Imaging beamline at the LCLS. These methods extend beyond XFEL applications because they allow for the suppression of dark accumulation noise which typically limits the low-flux capability of integrating detectors on conventional x-ray sources.

Diffraction before destruction

Two recent reports demonstrate the first applications of X-ray free-electron lasers to look at biological structures.

Radiation Properties of SPring-8 XFEL (SACLA) and Developments in User-experiment Facilities

An X-ray free electron laser (XFEL) has been constructed at the SPring-8 site and will be open for users at the beginning of 2012. Fundamental experimental facilities for user experiments have been developed; for example, photon beamline, beam diagnostics systems, two dimensional X-ray detectors, and a femtosecond laser system which is synchronized to XFEL pulses. Extensive researches using SPring-8 and a prototype free electron laser (SCSS test accelerator) have been performed for developing experimental techniques for XFEL applications.