Structure of an amorphous calcium carbonate phase involved in the formation of Pinctada margaritifera shells.

Some mollusc shells are formed from an amorphous calcium carbonate (ACC) compound, which further transforms into a crystalline material. The transformation mechanism is not fully understood but is however crucial to develop bioinspired synthetic biomineralization strategies or accurate marine biomineral proxies for geoscience. The difficulty arises from the simultaneous presence of crystalline and amorphous compounds in the shell, which complicates the selective experimental characterization of the amorphous fraction. Here, we use nanobeam X-ray total scattering together with an approach to separate crystalline and amorphous scattering contributions to obtain the spatially resolved atomic pair distribution function (PDF). We resolve three distinct amorphous calcium carbonate compounds, present in the shell of Pinctada margaritifera and attributed to: interprismatic periostracum, young mineralizing units, and mature mineralizing units. From this, we extract accurate bond parameters by reverse Monte Carlo (RMC) modeling of the PDF. This shows that the three amorphous compounds differ mostly in their Ca-O nearest-neighbor atom pair distance. Further characterization with conventional spectroscopic techniques unveils the presence of Mg in the shell and shows Mg-calcite in the final, crystallized shell. In line with recent literature, we propose that the amorphous-to-crystal transition is mediated by the presence of Mg. The transition occurs through the decomposition of the initial Mg-rich precursor into a second Mg-poor ACC compound before forming a crystal.

Sub-micrometric spatial distribution of amorphous and crystalline carbonates in biogenic crystals using coherent Raman microscopy.

In living organisms, calcium carbonate biomineralization combines complex bio-controlled physical and chemical processes to produce crystalline hierarchical hard tissues (usually calcite or aragonite) typically from an amorphous precursor phase. Understanding the nature of the successive transient amorphous phases potentially involved in the amorphous-to-crystalline transition requires characterization tools, which are able to provide a spatial and spectroscopic analysis of the biomineral structure. In this work, we present a highly sensitive coherent Raman microscopy approach, which allows one to image molecular bond concentrations in post mortem shells and living animals, by exploiting the vibrational signature of the different carbonates compounds. To this end, we target the ν1 calcium carbonate vibration mode and produce spatially and spectroscopically resolved images of the shell border of a mollusk shell, the Pinctada margaritifera pearl oyster. A novel approach is further presented to efficiently compare the amount of amorphous carbonate with respect to its crystalline counterpart. Finally, the whole microscopy method is used to image in vivo the shell border and demonstrate the feasibility and the reproducibility of the technique. These findings open chemical imaging perspectives for the study of biogenic and bio-inspired crystals.

Confocal Bragg ptychography for bulk specimens: a numerical demonstration.

We report on a new X-ray imaging method, which generalizes Bragg ptychography to 3D mapping of embedded crystalline volumes within thick specimens. The sample is probed by a pencil X-ray beam. The diffracted beam is magnified by an objective and passes through a slit in the image plane to be monitored by a 2D detector in the far-field of the image plane. The dimensions of the incoming beam and the slit opening define a confocal Bragg volume. Scanning the sample with respect to this probe volume, an iterative oversampling routine is used to reconstruct the shape and projected displacement field of extended internal volumes. This routine takes into account the pupil function and known aberrations of the lens. We demonstrate the method by a numerical study of a 3.5 µm grain comprising a wall of edge dislocations. With a probe volume of ∼0.12 µm3 and a compound refractive lens with a numerical aperture of 0.49×10-3 as the objective, the dislocations are fully resolved with a displacement sensitivity of ∼10 pm. The spatial resolution is 26×27×123 nm3 (rms), with the poor resolution along the optical axis being limited by the probe size. With a four times larger numerical aperture, the resolution becomes 16×8×123 nm3 (rms). The lens aberrations are found to be not critical.

Joint estimation of object and probes in vectorial ptychography.

Vectorial ptychography has been recently introduced to reconstruct the Jones matrix of an anisotropic object by means of series of ptychographic measurements performed using a set of polarized illumination probes in conjugation with various analyzers. So far, the probes were assumed to be completely known (amplitude, wavefront, state of polarization), which is rarely the case in practice. Here we address the issue of the joint estimating of the set of polarized illumination probes together with the Jones matrix of an anisotropic object in vectorial ptychography. We propose an algorithm based on a conjugate gradient strategy. Experimental results are reported, showing an improvement on the object estimate, in addition to a precise reconstruction of the probes.

Measuring Three-Dimensional Strain and Structural Defects in a Single InGaAs Nanowire Using Coherent X-ray Multiangle Bragg Projection Ptychography.

III-As nanowires are candidates for near-infrared light emitters and detectors that can be directly integrated onto silicon. However, nanoscale to microscale variations in structure, composition, and strain within a given nanowire, as well as variations between nanowires, pose challenges to correlating microstructure with device performance. In this work, we utilize coherent nanofocused X-rays to characterize stacking defects and strain in a single InGaAs nanowire supported on Si. By reconstructing diffraction patterns from the 21̅1̅0 Bragg peak, we show that the lattice orientation varies along the length of the wire, while the strain field along the cross-section is largely unaffected, leaving the band structure unperturbed. Diffraction patterns from the 011̅0 Bragg peak are reproducibly reconstructed to create three-dimensional images of stacking defects and associated lattice strains, revealing sharp planar boundaries between different crystal phases of wurtzite (WZ) structure that contribute to charge carrier scattering. Phase retrieval is made possible by developing multiangle Bragg projection ptychography (maBPP) to accommodate coherent nanodiffraction patterns measured at arbitrary overlapping positions at multiple angles about a Bragg peak, eliminating the need for scan registration at different angles. The penetrating nature of X-ray radiation, together with the relaxed constraints of maBPP, will enable the in operando imaging of nanowire devices.

Numerical study of Bragg CDI on thick polycrystalline specimens.

Bragg coherent diffraction imaging (BCDI) is a powerful X-ray imaging technique for crystalline materials, providing high resolution maps of structure and strain. The technique is typically used to study a small isolated object, and is in general not compatible with a bulk polycrystalline sample, due to overlap of diffraction signals from various crystalline elements. In this paper, we present an imaging method for bulk samples, based on the use of a coherent source. The diffracted X-ray beam from a grain or domain of choice is magnified by an objective before being monitored by a 2D detector in the far field. The reconstruction principle is similar to the case of BCDI, while taking the magnification and pupil function into account. The concept is demonstrated using numerical simulations and reconstructions. We find that by using an object-lens distance shorter than the focal length, the numerical aperture is larger than in a traditional imaging geometry, and at the same time the setup is insensitive to small phase errors by lens imperfections. According to our simulations, we expect to be able to achieve a spatial resolution smaller than 20 nm when using the objective lens in this configuration.

Quantitative imaging of anisotropic material properties with vectorial ptychography.

Following the recent establishment of the formalism of vectorial ptychography [Opt. Lett.40, 5144 (2015)OPLEDP0146-959210.1364/OL.40.005144], first measurements, to the best of our knowledge, are reported in the optical range, demonstrating the capability of the proposed method to map the four parameters of the Jones matrix of an anisotropic specimen, and therefore to quantify a wide range of optical material properties, including power transmittance, optical path difference, diattenuation, retardance, and fast-axis orientation.

Three-Dimensional Imaging of Phase Ordering in an Fe-Al Alloy by Bragg Ptychography.

We show three-dimensional images of phase ordering in a Fe_{55}Al_{45} alloy obtained by coherent x-ray diffraction Bragg ptychography. Fe-Al alloys display ordered phases where the atoms organize on sublattices resulting in the emergence of otherwise forbidden superlattice reflections. The degeneracy of the ordering results in antiphase domain boundaries that, in addition to the general lattice strain, provide phase shifts of the diffracted beam depending on the reflection. The reconstructed phase images can be separated into components originating from B2 phase domains and lattice strain by performing Bragg ptychography on both the (002) fundamental and the (001) superlattice reflections.

Ptychography in anisotropic media.

This letter describes ptychography in the context of polarized light probing anisotropic specimen (i.e., showing properties of birefringence and/or diattenuation). We established an optimization strategy using a vectorial formalism. We propose a measurement scheme using a set of linearly polarized probes and linear polarization analyzers, which allows the retrieval of the full anisotropy map of the specimen.

Noise models for low counting rate coherent diffraction imaging.

Coherent diffraction imaging (CDI) is a lens-less microscopy method that extracts the complex-valued exit field from intensity measurements alone. It is of particular importance for microscopy imaging with diffraction set-ups where high quality lenses are not available. The inversion scheme allowing the phase retrieval is based on the use of an iterative algorithm. In this work, we address the question of the choice of the iterative process in the case of data corrupted by photon or electron shot noise. Several noise models are presented and further used within two inversion strategies, the ordered subset and the scaled gradient. Based on analytical and numerical analysis together with Monte-Carlo studies, we show that any physical interpretations drawn from a CDI iterative technique require a detailed understanding of the relationship between the noise model and the used inversion method. We observe that iterative algorithms often assume implicitly a noise model. For low counting rates, each noise model behaves differently. Moreover, the used optimization strategy introduces its own artefacts. Based on this analysis, we develop a hybrid strategy which works efficiently in the absence of an informed initial guess. Our work emphasises issues which should be considered carefully when inverting experimental data.

4th generation synchrotron source boosts crystalline imaging at the nanoscale.

New 4th-generation synchrotron sources, with their increased brilliance, promise to greatly improve the performances of coherent X-ray microscopy. This perspective is of major interest for crystal microscopy, which aims at revealing the 3D crystalline structure of matter at the nanoscale, an approach strongly limited by the available coherent flux. Our results, based on Bragg ptychography experiments performed at the first 4th-generation synchrotron source, demonstrate the possibility of retrieving a high-quality image of the crystalline sample, with unprecedented quality. Importantly, the larger available coherent flux produces datasets with enough information to overcome experimental limitations, such as strongly deteriorated scanning conditions. We show this achievement would not be possible with 3rd-generation sources, a limit that has inhibited the development of this otherwise powerful microscopy method, so far. Hence, the advent of next-generation synchrotron sources not only makes Bragg ptychography suitable for high throughput studies but also strongly relaxes the associated experimental constraints, making it compatible with a wider range of experimental set-ups at the new synchrotrons.

Amorphous-to-crystal transition in the layer-by-layer growth of bivalve shell prisms.

Biomineralization integrates complex physical and chemical processes bio-controlled by the living organisms through ionic concentration regulation and organic molecules production. It allows tuning the structural, optical and mechanical properties of hard tissues during ambient-condition crystallisation, motivating a deeper understanding of the underlying processes. By combining state-of-the-art optical and X-ray microscopy methods, we investigated early-mineralized calcareous units from two bivalve species, Pinctada margaritifera and Pinna nobilis, revealing chemical and crystallographic structural insights. In these calcite units, we observed ring-like structural features correlated with a lack of calcite and an increase of amorphous calcium carbonate and proteins contents. The rings also correspond to a larger crystalline disorder and a larger strain level. Based on these observations, we propose a temporal biomineralization cycle, initiated by the production of an amorphous precursor layer, which further crystallizes with a transition front progressing radially from the unit centre, while the organics are expelled towards the prism edge. Simultaneously, along the shell thickness, the growth occurs following a layer-by-layer mode. These findings open biomimetic perspectives for the design of refined crystalline materials. STATEMENT OF SIGNIFICANCE: Calcareous biominerals are amongst the most present forms of biominerals. They exhibit astonishing structural, optical and mechanical properties while being formed at ambient synthesis conditions from ubiquitous ions, motivating the deep understanding of biomineralization. Here, we unveil the first formation steps involved in the biomineralization cycle of prismatic units of two bivalve species by applying a new multi-modal non-destructive characterization approach, sensitive to chemical and crystalline properties. The observations of structural features in mineralized units of different ages allowed the derivation of a temporal sequence for prism biomineralization, involving an amorphous precursor, a radial crystallisation front and a layer-by-layer sequence. Beyond these chemical and physical findings, the herein introduced multi-modal approach is highly relevant to other biominerals and bio-inspired studies.

Revealing nano-scale lattice distortions in implanted material with 3D Bragg ptychography.

Small ion-irradiation-induced defects can dramatically alter material properties and speed up degradation. Unfortunately, most of the defects irradiation creates are below the visibility limit of state-of-the-art microscopy. As such, our understanding of their impact is largely based on simulations with major unknowns. Here we present an x-ray crystalline microscopy approach, able to image with high sensitivity, nano-scale 3D resolution and extended field of view, the lattice strains and tilts in crystalline materials. Using this enhanced Bragg ptychography tool, we study the damage helium-ion-irradiation produces in tungsten, revealing a series of crystalline details in the 3D sample. Our results lead to the conclusions that few-atom-large 'invisible' defects are likely isotropic in orientation and homogeneously distributed. A partially defect-denuded region is observed close to a grain boundary. These findings open up exciting perspectives for the modelling of irradiation damage and the detailed analysis of crystalline properties in complex materials.

Introduction to the special issue on high-resolution X-ray diffraction and imaging.

The latest virtual special issue of Journal of Applied Crystallography features some highlights of the 13th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP 2016), held in Brno, Czech Republic, in September 2016.

Ageing dynamics of ion bombardment induced self-organization processes.

Instabilities caused during the erosion of a surface by an ion beam can lead to the formation of self-organized patterns of nanostructures. Understanding the self-organization process requires not only the in-situ characterization of ensemble averaged properties but also probing the dynamics. This can be done with the use of coherent X-rays and analyzing the temporal correlations of the scattered intensity. Here, we show that the dynamics of a semiconductor surface nanopatterned by normal incidence ion beam sputtering are age-dependent and slow down with sputtering time. This work provides a novel insight into the erosion dynamics and opens new perspectives for the understanding of self-organization mechanisms.

Ion beam sputtered surface dynamics investigated with two-time correlation functions: a model study.

Ion beam sputtering is a widely used technique to obtain patterned surfaces. Despite the wide use of this approach on different materials to create surface nanostructures, the theoretical model to explain the time evolution of the erosion process is still debated. We show, with the help of simulations, that two-time correlation functions can serve to assess the validity of different models. These functions can be measured experimentally with the x-ray photon correlation spectroscopy technique.