X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure determination of aerosolized bacteriophages PR772 measured with an XFEL. The rotational invariants derived from diffraction patterns collected during multiple independent XFEL experiments facilitate the characterization of similarities and structural variations within the measured ensembles of PR772 particles. Despite modest experimental resolution, we can identify various structural features of the viruses, including the asymmetric nature of capsid distortions from the perfect icosahedral shape, density variations in the encapsulated content, and an extension at one of the capsid vertices. Rotational invariants combine structural sensitivity with applicability to forward-scattering modeling and inverse problem solving, making them powerful tools for probing the structure and temporal evolution of nano- and bioparticles using an XFEL, particularly enhancing the fidelity of structural analysis at limited experimental resolution.

Solution-phase bottom up self-assembly of nanocrystals into superstructures such as ordered superlattices is an attractive strategy to generate functional materials of increasing complexity, including very recent advances that incorporate strong interparticle electronic coupling. While the self-assembly kinetics in these systems have been elucidated and related to the product characteristics, the weak interparticle bonding interactions suggest the superstructures formed could continue to order within the solution long after the primary nucleation and growth have occurred, even though the mechanism of annealing remains to be elucidated. Here, we use a combination of Bragg coherent diffractive imaging and X-ray photon correlation spectroscopy to create real-space maps of supercrystalline order along with a real-time view of the strain fluctuations in aging strongly coupled nanocrystal superlattices while they remain suspended and immobilized in solution. By combining the results, we deduce that the self-assembled superstructures are polycrystalline, initially comprising multiple nucleation sites, and that shear avalanches at grain boundaries continue to increase crystallinity long after growth has substantially slowed. This multimodal approach should be generalizable to characterize a breadth of materials in situ in their native chemical environments, thus extending the reach of high-resolution coherent X-ray characterization to the benefit of a much wider range of physical systems.

We will discuss the impact of simulation in a Coherent Diffractive Imaging (CDI) beamline currently under construction at NSLS-II. The optical system is designed to efficiently transport brightness from source to sample, while varying the sample illumination beam size and controlling the coherence properties of the beam. Detailed forward simulations of the measured intensity arising from the interaction of a model of the sample and the known x-ray beam can be used to interpret the images provided by the CDI method. Our current activities, plans for the immediate future, and considerations of our future needs will be presented.

Click to increase image sizeClick to decrease image size AcknowledgmentsWe would like to thank P. Elleaume (ESRF) for his decision to initiate the SRW project, J. Sutter (Diamond LS) and R. Celestre (ESRF) for their contributions to SRW, M. S. del Rio, R. Barrett (ESRF), M.-E. Couprie, O. Marcouille (SOLEIL), B. Nash, R. Nagler, P. Moeller, D. Bruhwiler (RadiaSoft), A. Wojdyla, K. Goldberg (LBNL/ALS), X. Shi, L. Rebuffi (ANL/APS), Q. Shen, W.-K. Lee, P. Zschack and J. Hill (BNL/NSLS-II) for collaborations, support, and fruitful discussions. The work was supported by US DOE Contracts No. DE-SC0012704 (NSLS-II Operations) and DE-SC0011237 (SBIR), and Field Work Proposal PS-017. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at LBNL, operated under Contract No. DE-AC02-05CH11231 using NERSC award BES-ERCAP0024810.Disclosure statementNo potential conflict of interest was reported by the authors.

Bragg coherent diffractive imaging (BCDI) is a noninvasive microscopy technique that can visualize the shape and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. Its strain imaging capability relies on Fourier transform--based iterative phase retrieval algorithms, which are mostly developed under the kinematical approximation. Such approximation prohibits the application of BCDI on larger crystals, which are commonly seen in most emerging functional materials. Understanding the dynamical effect in BCDI, as well as developing a validated method for modeling BCDI at the dynamical diffraction limit, is crucial for applying BCDI to hierarchical systems that contain micron-sized crystals and grains. Here we report a comparative study on the impact of dynamical diffraction effects by comparing the reconstruction results from two measurements of the same crystal. Forward simulation is implemented to show subtle changes of interference fringes in the diffraction pattern due to the dynamical diffraction, and is compared directly with the experimental data.

We describe approaches to high-accuracy physical optics calculations used for the development of x-ray beamlines at synchrotron radiation sources, as well as simulation of experiments and processing of experimental data at some of these beamlines. We pay special attention to the treatment of the partial coherence of x rays, a topic of high practical importance for modern low-emittance high-brightness synchrotron radiation facilities. The approaches are based, to a large extent, on the works of Emil Wolf and co-authors, including the basic scalar diffraction theory and the coherent mode decomposition method. The presented simulation examples are related to the case of the novel Coherent Diffractive Imaging beamline that is currently under development at the National Synchrotron Light Source II at the Brookhaven National Laboratory.

Coherent diffractive imaging is a powerful microscopy for the recovery of the complex exit-surface wave emerging from a sample of interest by recording the intensity of the field diffracted by it. Its application requires strict adherence to the underlying assumptions, which are well met by laser-like sources. This chapter describes the imaging method, the assumptions that underlie the solution to the inverse problem that it solves, and a survey of current methods and results from laser-based experiments.

Bragg coherent diffractive imaging (BCDI) is a noninvasive microscopy technique that can visualize the morphology and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. While BCDI has been successfully applied in various studies of materials, it is less successful for highly strained crystals. Specifically, it is difficult to correctly reconstruct the electron density of a highly strained object using conventional phase retrieval algorithms. Although various algorithms have been developed to overcome this challenge, most of them require a priori knowledge that is not always available in practice. Here we report a phase retrieval workflow that can invert diffraction patterns from multiple Bragg peaks simultaneously. The workflow is explored via simulated diffraction from crystals with various strain conditions. Reconstructions from the workflow consistently demonstrate more accurate electron density maps, in comparison with the conventional method. For highly strained crystals, the workflow improves the reliability and consistency of BCDI phase retrieval significantly.

At the National Synchrotron Light Source II, a beamline has been designed that aims to meet the needs of general CDI experiments at x-ray energies between 5 and 15 keV, where access to nanoscale information can be provided in “full-field” images of micron-sized particles in Bragg- and forward-scattering geometries. Here, we present the optical design underlying the proposed beamline, which delivers a variably-sized focal spot in the micron range with independently vari

Wellbore cement is subjected to a number of mechanical, thermal and chemical stress regimes over its lifetime. Therefore, next-generation wellbore cement formulations need to be evaluated in conditions relevant to these environments. In this work, we investigate the mechanism of the alteration of a novel self-healing polymer-cement composite after exposure to a CO2-rich environment by using synchrotron-based X-ray Fluorescence (XRF), X-ray absorption near edge structure (XANES), and scanning electron microscopy coupled with energy dispersive spectroscopy. Results showed that a chemical alteration of the polymer-cement follows the rim carbonation mechanism, similar to conventional cement, although carbonation takes place to a lesser extent in polymer-cements despite the higher porosity. Along with detailed mechanistic insights on carbonation in polymer-cement composite, the performance of these in CO2-rich environment is further studied using standard compressive strength analysis.

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.

Nanoporous metals fabricated by dealloying have a unique bi-continuous, sponge-like porous structure with ultra-high surface area. The unique properties of these materials, especially nanoporous gold, have numerous potential applications in sensors and actuators and in energy-related applications such as catalytic materials, super-capacitors, and battery supports. The degree of porosity and size of the metal ligaments are critical parameters that determine many properties and thus govern the functionalities of nanoporous metals in many applications including energy storage and conversion. We used Fresnel coherent diffractive imaging combined with tomographic reconstruction to quantify the nanoscale three-dimensional spatial distribution and homogeneity of the porosity and ligament size within a bulk sample of nanoporous gold. The average porosity and its standard deviation along the axial direction through the sample were determined, as well as the characteristic feature size and its standard deviation. The result shows that free corrosion is an effective way to create homogeneous nanoporous metals with sample sizes on the order of 1 μm. [DOI: 10.1115/1.4046414]

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Over the last couple of decades, the synchrotron radiation research community has witnessed tremendous advancement in the field of X-ray imaging and microscopy. Continuing enhancement of the light ...

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μ m x 1.7 μ m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Soils regulate the environmental impacts of trace elements, but direct measurements of reaction mechanisms in these complex, multi-component systems can be challenging. The objective of this work was to develop approaches for assessing effects of co-localized geochemical matrix elements on the accumulation and chemical speciation of arsenate applied to a soil matrix. Synchrotron X-ray fluorescence microprobe (µ-XRF) images collected across 100 µm × 100 µm and 10 µm × 10 µm regions of a naturally weathered soil sand-grain coating before and after treatment with As(V) solution showed strong positive partial correlations (r' = 0.77 and 0.64, respectively) between accumulated As and soil Fe, with weaker partial correlations (r' > 0.1) between As and Ca, and As and Zn in the larger image. Spatial and non-spatial regression models revealed a dominant contribution of Fe and minor contributions of Ca and Ti in predicting accumulated As, depending on the size of the sample area analyzed. Time-of-flight secondary ion mass spectrometry analysis of an area of the sand grain showed a significant correlation (r = 0.51) between Fe and Al, so effects of Fe versus Al (hydr)oxides on accumulated As could not be separated. Fitting results from 25 As K-edge microscale X-ray absorption near-edge structure (µ-XANES) spectra collected across a separate 10 µm × 10 µm region showed ∼60% variation in proportions of Fe(III) and Al(III)-bound As(V) standards, and fits to µ-XANES spectra collected across the 100 µm × 100 µm region were more variable. Consistent with insights from studies on model systems, the results obtained here indicate a dominance of Fe and possibly Al (hydr)oxides in controlling As(V) accumulation within microsites of the soil matrix analyzed, but the analyses inferred minor augmentation from co-localized Ti, Ca and possibly Zn.

Authors: Tais Gorkhover, Anatoli Ulmer, Ken Ferguson, Max Bucher, Filipe R. N. C. Maia, Johan Bielecki, Tomas Ekeberg, Max F. Hantke, Benedikt J. Daurer, Carl Nettelblad, Jakob Andreasson, Anton Barty, Petr Bruza, Sebastian Carron, Dirk Hasse, Jacek Krzywinski, Daniel S. D. Larsson, Andrew Morgan, Kerstin Mühlig, Kenta Okamoto, Alberto Pietrini, Daniela Rupp, Mario Sauppe, Gijs van der Schot, Marcin Siebert, Jonas A. Selberg, Martin Svenda, Michelle Swiggers, Nicusor Timneanu, Daniel Westphal, Garth Williams, Alessando Zani, Henry N. Chapman, Gyula Faigel, Thomas Möller, Janos Hajdu and Christoph Bostedt