First insight into the development of a new transcriptomic tool in French Corsica harbors.

Coastal harbor areas are subjected to a myriad of contamination sources with largely unknown effects. Such complex chemical mixtures are difficult to monitor but transcriptomics is a promising approach for such biomonitoring. The present study was designed to verify the use of the Coastal Biosensor for Endocrine Disruption (C-BED) assay, previously developed to detect emerging contaminants and their effects on Mytilus edulis, on another mussel species, Mytilus galloprovincialis. Mussels were caged on St-Florent harbor (contaminated) and on Revellata Bay (reference) for three months. A classical multibiomarkers approach was coupled to the C-BED assay. The results of both approaches were analysed using the Integrated Biomarkers Responses (IBR) and compared to each other. Both approaches demonstrated a higher contamination and probable endocrine disruption of mussels in St-Florent, compared to the reference station. These results confirm that the C-BED assay provides an innovative method to expand our ability to detect emerging contaminants.

Improvement of precision in refinements of structure factors using convergent-beam electron diffraction patterns taken at Bragg-excited conditions.

A local structure analysis method based on convergent-beam electron diffraction (CBED) has been used for refining isotropic atomic displacement parameters and five low-order structure factors with sin θ/λ ≤ 0.28 Å-1 of potassium tantalate (KTaO3). Comparison between structure factors determined from CBED patterns taken at the zone-axis (ZA) and Bragg-excited conditions is made in order to discuss their precision and sensitivities. Bragg-excited CBED patterns showed higher precision in the refinement of structure factors than ZA patterns. Consistency between higher precision and sensitivity of the Bragg-excited CBED patterns has been found only for structure factors of the outer zeroth-order Laue-zone reflections with larger reciprocal-lattice vectors. Correlation coefficients among the refined structure factors in the refinement of Bragg-excited patterns are smaller than those of the ZA ones. Such smaller correlation coefficients lead to higher precision in the refinement of structure factors.

A new electron diffraction approach for structure refinement applied to Ca3Mn2O7.

The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.

Detecting minute amounts of nitrogen in GaNAs thin films using STEM and CBED.

Nitrogen (N) is a common element added to GaAs for band gap engineering and strain compensation. However, detection of small amounts of N is difficult for electron microscopy as well as for other chemical analysis techniques. In this work, N in GaAs is examined by using different transmission electron microscopy (TEM) techniques. While both dark-field TEM imaging using the composition sensitive (002) reflections and selected area diffraction reveal a significant difference between the doped thin-film and the GaAs substrate, spectroscopy techniques such as electron energy loss and energy dispersive X-ray spectroscopy are not able to detect N. To quantify the N content, quantitative convergent beam electron diffraction (QCBED) is used, which gives a direct evidence of N substitution and As vacancies. The measurements are enabled by the electron energy-filtered scanning CBED technique. These results demonstrate a sensitive method for composition analysis based on quantitative electron diffraction.

Holographic reconstruction of the interlayer distance of bilayer two-dimensional crystal samples from their convergent beam electron diffraction patterns.

The convergent beam electron diffraction (CBED) patterns of twisted bilayer samples exhibit interference patterns in their CBED spots. Such interference patterns can be treated as off-axis holograms and the phase of the scattered waves, meaning the interlayer distance can be reconstructed. A detailed protocol of the reconstruction procedure is provided in this study. In addition, we derive an exact formula for reconstructing the interlayer distance from the recovered phase distribution, which takes into account the different chemical compositions of the individual monolayers. It is shown that one interference fringe in a CBED spot is sufficient to reconstruct the distance between the layers, which can be practical for imaging samples with a relatively small twist angle or when probing small sample regions. The quality of the reconstructed interlayer distance is studied as a function of the twist angle. At smaller twist angles, the reconstructed interlayer distance distribution is more precise and artefact free. At larger twist angles, artefacts due to the moiré structure appear in the reconstruction. A method for the reconstruction of the average interlayer distance is presented. As for resolution, the interlayer distance can be reconstructed by the holographic approach at an accuracy of ±0.5 Å, which is a few hundred times better than the intrinsic z-resolution of diffraction limited resolution, as expressed through the spread of the measured k-values. Moreover, we show that holographic CBED imaging can detect variations as small as 0.1 Å in the interlayer distance, though the quantitative reconstruction of such variations suffers from large errors.

The importance of temporal and spatial incoherence in quantitative interpretation of 4D-STEM.

Recent developments in pixelated detectors, when combined with aberration correction of probe forming optics have greatly enhanced the field of scanning electron diffraction. Differential phase contrast is now routine and deep learning has been proposed as a method to extract maximum information from diffraction patterns. This work examines the effects of temporal and spatial incoherence on convergent beam electron diffraction patterns and demonstrates that simple center of mass measurements cannot be naively interpreted. The inclusion of incoherence in deep learning data sets is also discussed.

Comparative study on the specimen thickness measurement using EELS and CBED methods.

Two thickness measurement methods using an electron energy loss spectroscopy (EELS) and 10a convergent beam electron diffraction (CBED) were compared in an Fe-18Mn-0.7C alloy. The thin foil specimen was firstly tilted to satisfy 10a two-beam condition. Low loss spectra of EELS and CBED patterns were acquired in scanning transmission electron microscopy (STEM) and TEM-CBED modes under the two-beam condition. The log-ratio method was used for measuring the thin foil thickness. Kossel-Möllenstedt (K-M) fringe of the [Formula: see text] diffracted disk of austenite was analyzed to evaluate the thickness. The results prove the good coherency between both methods in the thickness range of 72 ~ 113 nm with a difference of less than 5%.

Mesoscopic quantitative chemical analyses using STEM-EDX in current and next generation polycrystalline Ni-based superalloys.

Quantitative chemical analyses of Ni3Al based hardening precipitates (γ') in polycrystalline Ni based superalloys have been conducted using energy dispersive X-ray spectroscopy (EDX), coupled with a scanning transmission electron microscope (STEM). The aim of the current investigation is (1) to evaluate the accuracy of calibration (k factor determinations and absorption corrections using a combination of differential X-ray absorption (DXA) and convergent beam electron diffraction (CBED)) by comparing with thermodynamic calculations and (2) to demonstrate the importance of the EDX chemical analysis by taking advantage of its unique capabilities to analyse sub-micron scale chemistries within a mesoscopic field of view under STEM. Our experimental findings show good agreement with the mole fraction ratio of γ' to the disordered γ matrix predicted using the Lever rule on a thermodynamically stabilised unimodal superalloy, RR1000. The significance of analysing a statistically viable number of samples in thermodynamically metastable superalloys and the chemical fluctuations found in coarse γ', sized above 200 nm on a scale of a few hundred nanometres in the context of solving a complex morphological evolution of γ' particles is demonstrated.

The application of convergent beam electron diffraction (CBED) analysis on transformation-induced plasticity (TRIP) steels.

Convergent beam electron diffraction (CBED) in transmission electron microscopy (TEM) was applied to determine local carbon concentrations in low-carbon transformation-induced plasticity (TRIP) steels. High-order Laue-zone (HOLZ) lines were experimentally obtained for comparison with simulation results. A new procedure for calculating carbon content is thus proposed. Retained austenite (RA) is classified into three types by morphology; the relationship between the carbon content and the corresponding RA morphology is discussed based on CBED results. Furthermore, results of X-Ray diffractometry measurements are also used for comparison.

Thickness and Stacking Sequence Determination of Exfoliated Dichalcogenides (1T-TaS2, 2H-MoS2) Using Scanning Transmission Electron Microscopy.

Layered transition metal dichalcogenides (TMDs) have attracted interest due to their promise for future electronic and optoelectronic technologies. As one approaches the two-dimensional (2D) limit, thickness and local topology can greatly influence the macroscopic properties of a material. To understand the unique behavior of TMDs it is therefore important to identify the number of atomic layers and their stacking in a sample. The goal of this work is to extract the thickness and stacking sequence of TMDs directly by matching experimentally recorded high-angle annular dark-field scanning transmission electron microscope images and convergent-beam electron diffraction (CBED) patterns to quantum mechanical, multislice scattering simulations. Advantageously, CBED approaches do not require a resolved lattice in real space and are capable of neglecting the thickness contribution of amorphous surface layers. Here we demonstrate the crystal thickness can be determined from CBED in exfoliated 1T-TaS2 and 2H-MoS2 to within a single layer for ultrathin ≲9 layers and ±1 atomic layer (or better) in thicker specimens while also revealing information about stacking order-even when the crystal structure is unresolved in real space.

Identification of Phase Boundaries and Electrical Properties in Ternary Potassium-Sodium Niobate-Based Ceramics.

A large piezoelectric constant (d33) of ∼480 pC/N was attained in new ternary (1-x-y)K0.5Na0.5Nb0.96Sb0.04O3-xBaSnO3-yBi0.5Na0.5ZrO3 ceramics by forming rhombohedral-orthorhombic-tetragonal (R-O-T) phase boundary using the variations of x and y, and such a phase boundary was successfully confirmed by the convergent beam electron diffraction (CBED) patterns. For (1-x)K0.5Na0.5Nb0.96Sb0.04O3-xBaSnO3, the orthorhombic (O) phase is well-maintained for 0 ≤ x ≤ 0.015, and both the R and T phases can be introduced to (0.99-y)K0.5Na0.5Nb0.96Sb0.04O3-0.01BaSnO3-yBi0.5Na0.5ZrO3 with y = 0.025-0.04 by simultaneously tailoring their compositions (x and y); then, R-O-T multiphases can be well-established. The CBED patterns strongly support the existence of R-O-T multiphases in the ceramics with y = 0.035. When the phase transitions endure from O to R-O-T, their piezoelectric activity endures a leapfrog development from ∼165 to ∼480 pC/N. In the region of the R-O-T phase boundary, a large d33 of ∼480 pC/N was attained in the ceramics with x = 0.01 and y = 0.035. In addition, the ceramics with x = 0.01 and y = 0.04 possess a high strain of ∼0.274% due to the multiphases coexistence. According to the variations of dielectric and ferroelectric properties, the enhancement in εr and Pr plays a part in the improved d33 except for the R-O-T phase boundary. We believe that the (K, Na)NbO3 ternary systems can be used to promote piezoelectric activity by forming new phase boundaries.

Post-thinning using Ar ion-milling system for transmission electron microscopy specimens prepared by focused ion beam system.

We investigate Ar ion-milling rates and Ga-ion induced damage on sample surfaces of Si and GaAs single crystals prepared by focused ion beam (FIB) method for transmission electron microscopy observation. The convergent beam electron diffraction technique with Bloch simulation is used to measure the thickness of the Ar-ion milled samples to calculate the milling rates of Si and GaAs single crystals. The measurement shows that an amorphous layer is formed on the sample surface and can be removed by further Ar-ion milling. In addition, the local symmetry breaking induced by FIB is investigated using quantitative symmetry measurement. The FIBed-GaAs sample shows local symmetry breaking after FIB milling, although the FIBed-Si sample has no considerable symmetry breaking.

Towards a full retrieval of the deformation tensor F using convergent beam electron diffraction.

A new method to retrieve the local lattice parameters and rotations in a crystal from off-axis convergent beam electron diffraction (CBED) patterns is presented and validated using Bloch wave dynamical simulations. The originality of the method is to use both the diffracted and transmitted beams and to use kinematical approximations in the fitting algorithm. The study is based on the deformation gradient tensor F which includes rotation and strain. Working on simulated images it is shown that (i) from a single direction of observation, seven parameters out of the nine parameters of F can be determined with an accuracy of 3 × 10(-4) for the normal strain parameters εxx, εyy, and εzz, (ii) the unit cell volume can only be retrieved if the diffracted and transmitted beams are both included in the fitting and (iii) all the nine parameters of F can be determined by combining two directions of observation separated by about 20°.

FDES, a GPU-based multislice algorithm with increased efficiency of the computation of the projected potential.

While the computational complexity of calculation of the projected potential in the multislice algorithm through reciprocal space scales quadratically with the number of atoms A per slice, a pure real-space calculation scales linearly with A. A hybrid strategy is introduced that has a theoretical complexity of O(AlogA), but that, when measured, outperforms both the reciprocal-space and the real-space approach by approximately an order in A and a large factor, respectively. This strategy is implemented in a new program, dubbed forward dynamical electron scattering (FDES), which simulates high resolution transmission electron microscopy images, diffraction patterns and convergent beam electron diffraction patterns. FDES attains a further increase in speed by running on a graphics processing unit and is made available to the community as open software.

Determination of three-dimensional strain state in crystals using self-interfered split HOLZ lines.

An experimental method to measure the strain through the thickness of a crystal is demonstrated. This enables the full three-dimensional stress-strain state of a crystal at the nanoscale to be determined taking the current practice from two-dimensional strain state determination. Knowing the 3D strain state is desired by crystal growers in order to improve their crystal's quality. This method involves combining electron diffraction with electron interferometry in a transmission electron microscope. The electron diffraction uses a split higher order Laue zone (HOLZ) line and the electron interferometry uses an electron biprism.

Automated CBED processing: sample thickness estimation based on analysis of zone-axis CBED pattern.

An automated processing of convergent beam electron diffraction (CBED) patterns is presented. The proposed methods are used in an automated tool for estimating the thickness of transmission electron microscopy (TEM) samples by matching an experimental zone-axis CBED pattern with a series of patterns simulated for known thicknesses. The proposed tool detects CBED disks, localizes a pattern in detected disks and unifies the coordinate system of the experimental pattern with the simulated one. The experimental pattern is then compared disk-by-disk with a series of simulated patterns each corresponding to different known thicknesses. The thickness of the most similar simulated pattern is then taken as the thickness estimate. The tool was tested on [0 1 1] Si, [0 1 0] α-Ti and [0 1 1] α-Ti samples prepared using different techniques. Results of the presented approach were compared with thickness estimates based on analysis of CBED patterns in two beam conditions. The mean difference between these two methods was 4.1% for the FIB-prepared silicon samples, 5.2% for the electro-chemically polished titanium and 7.9% for Ar(+) ion-polished titanium. The proposed techniques can also be employed in other established CBED analyses. Apart from the thickness estimation, it can potentially be used to quantify lattice deformation, structure factors, symmetry, defects or extinction distance.

Direct atomic structure determination by the inspection of structural phase.

A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

Digital electron diffraction--seeing the whole picture.

The advantages of convergent-beam electron diffraction for symmetry determination at the scale of a few nm are well known. In practice, the approach is often limited due to the restriction on the angular range of the electron beam imposed by the small Bragg angle for high-energy electron diffraction, i.e. a large convergence angle of the incident beam results in overlapping information in the diffraction pattern. Techniques have been generally available since the 1980s which overcome this restriction for individual diffracted beams, by making a compromise between illuminated area and beam convergence. Here a simple technique is described which overcomes all of these problems using computer control, giving electron diffraction data over a large angular range for many diffracted beams from the volume given by a focused electron beam (typically a few nm or less). The increase in the amount of information significantly improves the ease of interpretation and widens the applicability of the technique, particularly for thin materials or those with larger lattice parameters.

Strain measurement at the nanoscale: Comparison between convergent beam electron diffraction, nano-beam electron diffraction, high resolution imaging and dark field electron holography.

Convergent beam electron diffraction (CBED), nano-beam electron diffraction (NBED or NBD), high resolution imaging (HRTEM and HRSTEM) and dark field electron holography (DFEH or HoloDark) are five TEM based techniques able to quantitatively measure strain at the nanometer scale. In order to demonstrate the advantages and disadvantages of each technique, two samples composed of epitaxial silicon-germanium layers embedded in a silicon matrix have been investigated. The five techniques are then compared in terms of strain precision and accuracy, spatial resolution, field of view, mapping abilities and ease of performance and analysis.