Abstract: We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments.

Abstract: A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt.

Abstract: In computed tomography, the reconstruction is typically obtained on a voxel grid. In this work, however, we propose a mesh-based reconstruction method. For tomographic problems, 3D meshes have mostly been studied to simulate data acquisition, but not for reconstruction, for which a 3D mesh means the inverse process of estimating shapes from projections. In this paper, we propose a differentiable forward model for 3D meshes that bridge the gap between the forward model for 3D surfaces and optimization. We view the forward projection as a rendering process, and make it differentiable by extending recent work in differentiable rendering. We use the proposed forward model to reconstruct 3D shapes directly from projections. Experimental results for single-object problems show that the proposed method outperforms traditional voxel-based methods on noisy simulated data. We also apply the proposed method on electron tomography images of nanoparticles to demonstrate the applicability of the method on real data.

Abstract: The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and structural biology. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and fairly accurate, especially for scanning TEM (STEM) annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory, which was previously mainly required for holography. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We argue that a physically better justified ab initio description of the scattering potential is both useful and viable for an increasing number of systems, and we expect such simulations to steadily gain in popularity and importance.

Abstract: We introduce a facile approach to transfer thin films and other mechanically sensitive TEM samples inside a FIB with minimal introduction of stress and bending. The method is making use of a pre-synthetized flexible freestanding Ag nanowire attached to the tip of a typical tungsten micromanipulator inside the FIB. The main advantages of this approach are the significantly reduced stress-induced bending during transfer and attachment of the TEM sample, the very short time required to attach and cut the nanowire, the operation at very low dose and ion current, and only using the e-beam for Pt deposition during the transfer of sensitive TEM samples. This results in a reduced sample preparation time and reduced exposure to the ion beam or e-beam for Pt deposition during the sample preparation and thus also reduced contamination and beam damage. The method was applied to a number of thin films and different TEM samples in order to illustrate the advantageous benefits of the concept. In particular, the technique has been successfully tested for the transfer of a thin film onto a MEMS heating chip for in situ TEM experiments.

Abstract: In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific zeolite sample. We make use of a 2D diffusion model that describes the dissipation of the deposited beam energy in the sequence of probe positions that are visited during the scan pattern. The diffusion process allows for the concept of trying to ‘outrun’ the beam damage by carefully tuning the dwell time and distance between consecutively visited probe positions. We add a non linear function to include a threshold effect and evaluate the accumulated damage in each part of the image as a function of scan pattern details. Together, these ingredients are able to describe qualitatively all aspects of the experimental data and provide us with a model that could guide a further optimisation towards even lower beam damage without lowering the applied electron dose. We deliberately remain vague on what is diffusing here which avoids introducing too many sample specific details. This provides hope that the model can be applied also in sample classes that were not yet studied in such great detail by adjusting higher level parameters: a sample dependent diffusion constant and damage threshold.

Abstract: This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In
addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.

Abstract: Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements.

Abstract: Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15–30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.

Abstract: In this paper convexity constraints are derived for a background model of electron energy loss spectra (EELS) that is linear in the fitting parameters. The model outperforms a power-law both on experimental and simulated backgrounds, especially for wide energy ranges, and thus improves elemental quantification results. Owing to the model’s linearity, the constraints can be imposed through fitting by quadratic programming. This has important advantages over conventional nonlinear power-law fitting such as high speed and a guaranteed unique solution without need for initial parameters. As such, the need for user input is significantly reduced, which is essential for unsupervised treatment of large datasets. This is demonstrated on a demanding spectrum image of a semiconductor device sample with a high number of elements over a wide energy range.

Abstract: Ptychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often found with the probe focused to the middle of the sample. The phase contribution due to defocus at each sample slice above and below the central plane in this configuration effectively cancels out, which can prevent contrast reversals when dynamical scattering effects are not overly strong. In addition we show that the convergence angle can be an important consideration for removal of contrast reversals in relatively thin samples.

Abstract: Mesoporous MIL-101(Cr) is used as host for a ship-in-a-bottle type adsorbent for selective U(VI) recovery from aqueous environments. The acid-resistant cage-type MOF is built in-situ around N,N-Diisobutyl-2-(octylphenylphosphoryl)acetamide (CMPO), a sterically demanding ligand with high U(VI) affinity. This one-step procedure yields an adsorbent which is an ideal compromise between homogeneous and heterogeneous systems, where the ligand can act freely within the pores of MIL-101, without leaching, while the adsorbent is easy separable and reusable. The adsorbent was characterized by XRD, FTIR spectroscopy, nitrogen adsorption, XRF, ADF-STEM and EDX, to confirm and quantify the successful encapsulation of the CMPO in MIL-101, and the preservation of the host. Adsorption experiments with a central focus on U(VI) recovery were performed. Very high selectivity for U(VI) was observed, while competitive metal adsorption (rare earths, transition metals...) was almost negligible. The adsorption capacity was calculated at 5.32 mg U/g (pH 3) and 27.99 mg U/g (pH 4), by fitting equilibrium data to the Langmuir model. Adsorption kinetics correlated to the pseudo-second-order model, where more than 95% of maximum uptake is achieved within 375 min. The adsorbed U(VI) is easily recovered by desorption in 0.1 M HNO3. Three adsorption/desorption cycles were performed. (C) 2017 Elsevier B.V. All rights reserved.

Abstract: The covalent triazine framework, CTF-1, served as host material for the in situ synthesis of Fe2O3 nanoparticles. The composite material consisted of 20 +/- 2 m% iron, mainly in gamma-Fe2O3 phase. The resulting gamma-Fe2O3@CTF-1 was examined for the adsorption of As-III, As-V and H-II from synthetic solutions and real surface-, ground- and wastewater. The material shows excellent removal efficiencies, independent from the presence of Ca2+, Mg2+ or natural organic matter and only limited dependency on the presence of phosphate ions. Its adsorption capacity towards arsenite (198.0 mg g(-1)), arsenate (102.3 mg g(-1)) and divalent mercury (165.8 mg g(-1)) belongs amongst the best-known adsorbents, including many other iron-based materials. Regeneration of the adsorbent can be achieved for use over multiple cycles without a decrease in performance by elution at 70 degrees C with 0.1 M NaOH, followed by a stirring step in a 5 m% H2O2 solution for As or 0.1 M thiourea and 0.001 M HCl for Hg. In highly contaminated water (100 mu gL(-1)), the adsorbent polishes the water quality to well below the current WHO limits.

Abstract: The aqueous phase electrochemical degradation of nalidixic acid (NAL) is studied in this work, using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) as instrumental techniques. The promotional effect of multi-walled carbon nanotubes (MWCNT) on the the performance of glassy carbon electrodes is demonstrated, being observed that these materials catalyze the NAL reduction. The effect of surface functional groups on MWCNT −MWCNT-COOH and MWCNT-NH2was also studied. The modification of glassy carbon electrode (GCE) with MWCNT leads to an improved performance for NAL reduction following the order of MWCNT > MWCNT-NH2 > MWCNT-COOH. The best behavior at MWCNT-GCE is mainly due to both the increased electrode active area and the enhanced MWCNT adsorption properties. The NAL degradation was carried out under optimal conditions (pH = 5.0, deposition time = 20 s and volume of MWCNT = 10 μL) using MWCNT-GCE obtaining an irreversible reduction of NAL to less toxic products. Paramaters as the number of DPV cycles and the volume/area (V/A) ratio were optimized for maximize pollutant degradation. It was observed that after 15 DPV scans and V/A = 8, a complete reduction was obtained, obtaining two sub-products identified by liquid chromatography-mass spectrometry (LCMS).

Abstract: The activity concentration of 226Ra, 232Th and 40K in gas concrete samples collected from different suppliers and some provinces in Turkey were measured using gamma-ray spectrometry. Knowledge of radioactivity in gas concrete used in building materials enables one to assess any possible radiological risks to human health. The mean activity concentrations observed in the gas concrete samples were 82.0, 28.2 and 383.9 Bq kg−1 for 226Ra, 232Th and 40K, respectively. The radium equivalent activity, external and internal hazard indices as well as terrestrial absorbed dose and annual effective dose rate was calculated. The results indicate that the radium equivalent activity values of gas concrete samples are lower than the limit of 370 Bq kg−1, equivalent to a gamma-dose of 1.5 mSv y−1. Moreover, mass attenuation coefficients were measured in some gas concrete samples. It was found that the mass attenuation coefficients decreased with increasing photon energies. Also, chemical compositions and structural analysis (XRD and SEM) of the gas concrete samples were investigated.