Three-dimensional Atomic Images Research Articles

Near-isotropic sub-Ångstrom 3d resolution phase contrast imaging achieved by end-to-end ptychographic electron tomography

Abstract Three-dimensional atomic resolution imaging using transmission electron microscopes is a unique capability that requires challenging experiments. Linear electron tomography methods are limited by the missing wedge effect, requiring a high tilt range. Multislice ptychography can achieve deep sub-Ångstrom resolution in the transverse direction, but depth resolution is limited to 2 to 3 nanometers. In this paper, we propose and demonstrate an end-to-end approach to reconstructing the electrostatic potential volume of the sample directly from the 4D-STEM datasets. End-to-end multislice ptychographic tomography recovers several slices at each tomography tilt angle and compensates for the missing wedge effect. The algorithm is initially tested in simulation with a Pt@Al2O3 core–shell nanoparticle, where both heavy and light atoms are recovered in 3D from an unaligned 4D-STEM tilt series with a restricted tilt range of 90 degrees. We also demonstrate the algorithm experimentally, recovering a Te nanoparticle with sub-Ångstrom resolution.

Anomalous atomic fluctuations in the local structure around Mn of (Zn,Sn,Mn)As2 thin films

Local atomic structures around Mn in $(\mathrm{Zn},\mathrm{Sn},\mathrm{Mn}){\mathrm{As}}_{2}$ thin films grown on InP (001) substrates were studied using x-ray fluorescence holography. The reconstructed three-dimensional atomic images showed that the addition of Mn resulted in further distortions of the As sublattice from the pure sphalerite ${\mathrm{ZnSnAs}}_{2}$. The first-principles calculations showed that the further distortion could be attributed to the shortening of the Mn-As bond length induced by the p-d exchange mechanism, which mediates the ferromagnetism in this material. In addition, we found that the positional fluctuation of the cations was maximized at the second nearest neighbor cation shell from detailed analysis of the atomic images. This anomaly in the fluctuation could be explained by the calculated forces acting on the cations.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality.

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid–liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.

Determination of site occupancy of boron in 6H–SiC by multiple-wavelength neutron holography

The local structure around boron doped in 6H-type silicon carbide (SiC) was investigated using neutron holography. Three-dimensional atomic images reconstructed from multiple-wavelength holograms revealed the boron substitution for both silicon and carbon. To determine boron locations accurately, we calculated holograms with varying occupancies of six different sites and fit image intensities with those obtained from experimental holograms by the steepest descent method. As a result, it was found that boron atoms were selectively located at the Si–C-cubic site layer. Furthermore, boundaries right above the boron locations were suggested from the absence of atomic images in the upper region of reconstruction.

High-precision atomic image reconstruction from photoelectron hologram of O on W(110) by SPEA-L1

In recent years, the analysis of atomic arrangements of dopants using photoelectron holography has attracted much attention. A three-dimensional atomic image around the photoelectron-emitting atoms can be reconstructed from the photoelectron hologram. In this method, the theory of reconstructing an atomic arrangement from a photoelectron hologram is important. The recently developed Scattering Pattern Extraction Algorithm using L1 regularization (SPEA-L1) is capable of precisely reconstructing atomic images. We evaluated the accuracy of SPEA-L1 by comparing it with the Barton method using photoelectron holograms of W(110)-O. As a result, it was observed that SPEA-L1 could accurately reproduce an atomic image with a width as small as a fraction of the width of the reconstructed atomic positions compared to the Barton method. The obtained W(110)-O structure agreed well with the structure obtained by Low Energy Electron Diffraction(LEED) and calculations with an accuracy of 0.1 Å. • Local structure analysis of W(110)-O using photoelectron holography. • The analytical results are in good agreement with theoretical calculations. • Accuracy of Atomic Image Reconstruction Theory Revealed. • The accuracy of SPEA-L1 is evaluated using photoelectron holograms of W(110)-O. • The obtained structure agreed with the structure obtained by LEED and calculations with an accuracy of 0.1 Å.

Three-dimensional Atomic Image of FeSe High-temperature Superconductor by X-ray Fluorescence Holography

Fe Kα X-ray fluorescence holography measurements were carried out at room temperature on an FeSe high-temperature superconductor to clarify the relationship between the local structures around the Fe atoms and the superconducting nature. The obtained three-dimensional atomic arrangements strongly reveal a formation of strong FeSe4 clusters. On the other hand, the Se—Fe—Se bond angle largely spreads, causing a large ambiguity in the chalcogen height and large displacements of the Fe sublattice. Thus, it is reasonable that the tetragonal-to-orthorhombic structural (nematic) transition does not affect the magnetic ordering in the Fe layer.

Extreme dislocation-mediated plasticity of yttria-stabilized zirconia

Ceramics constitute a major class of engineering materials, but their applications are severely undercut by the propensity to catastrophic brittle fracture. Due to the brittleness and sensitivity to flaws, dislocation-mediated plasticity is rarely achieved in ceramics at room temperature. Here, we report in-situ mechanical testing on oriented submicron single-crystal pillars of cubic yttria-stabilized zirconia (YSZ) in the transmission electron microscope, to show that ultra-large plastic deformation mediated by dislocations can be achieved at room temperature. By employing three-dimensional tomography and atomic imaging, unprecedented details of spatial features of the generated dislocations are demonstrated. While deformation in pillars compressed along <111> directions is achieved by dislocation slip on the non-close-packed {001} planes, strains in those compressed along <001> are by slip on the close-packed {111} planes. Different dislocation slips cause obvious anisotropy in mechanical properties of YSZ crystal. The <111> pillars exhibit much greater plastic deformability than the <001> pillars, with observed strains as high as 61.6%. These results may lead to potentially new applications of YSZ at submicron scales and provide important insights into deformation mechanisms of ionic ceramics in general.

In Situ Spectroscopic Study of the Optomechanical Properties of Evaporating Field Ion Emitters

The possibility of measuring in situ operando photoluminescence spectroscopy within a photonic atom probe allows for the real-time study of the mechanical stress state within a field emitter either statically, as a function of the field-induced tensile stress, or dynamically, as a result of the evolution of the shape of the emitter upon its evaporation. Dynamic evolution results from the relaxation of strain induced by lattice mismatch and by the propagation of stress from the apex, while the morphology of the field emitter changes. Optomechanical information can be interpreted through the three-dimensional atomic scale images of the chemical composition of the emitter obtained through standard atom probe analysis. Here, the photoluminescence signal of a $\mathrm{Zn}\mathrm{O}/(\mathrm{Mg},\mathrm{Zn})\mathrm{O}$ quantum well allows for the local measurement of strain within the well and of the electrostatic field applied to the apex of the nanoscale field emitter.

Three-Dimensional Atomic Structure of Grain Boundaries Resolved by Atomic-Resolution Electron Tomography

Summary Grain boundaries (GBs) determine the properties of polycrystals, and tailoring the GB structure offers a promising method for the discovery and engineering of new materials. However, GB structures are far from well understood because of their structural complexity and limitations of conventional projection imaging methods. Here, we decipher three-dimensional atomic structure and crystallography of GBs in nanometals using atomic-resolution electron tomography. Unlike conventional descriptions, whereby they are either straight or curved planar planes with one-dimensional translational symmetry, we show that the high-angle GBs completely lose translational symmetry due to undulated curvature related to configurations of structural units. Moreover, we directly visualize kinks and jogs at the single-atom scale in dislocation-type GBs and investigate their mobilities. Our findings bring new insights to the conventional wisdom of GBs and show the importance of developing methods to include the non-planar nature of GBs to statistically evaluate the behavior of GBs in modeling studies.

Progress of Three-Dimensional Atomic Image Investigations by X-Ray Fluorescence Holography

Progress of Three-Dimensional Atomic Image Investigations by X-Ray Fluorescence Holography

Impurity position and lattice distortion in a Mn-doped Bi2Te3 topological insulator investigated by x-ray fluorescence holography and x-ray absorption fine structure

Mn $K\ensuremath{\alpha}$ x-ray fluorescence holography (XFH) measurements were performed on a single crystal of a ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}{\mathrm{Mn}}_{0.1}$ topological insulator at 100 and 300 K to search for the impurity sites of the Mn atoms in this functional crystal. The three-dimensional atomic images were reconstructed using an ${L}_{1}$-regularized linear regression. X-ray absorption fine-structure (XAFS) experiments were also carried out at 30--300 K to obtain additional structural information. The local structural information was obtained from these data, such as the positions of the Mn impurity sites, the Mn-Te interatomic distances, the lattice distortions, and the positional fluctuations around the impurity Mn atoms. The possible Mn impurity sites are twofold, i.e., an interlayer site with an octahedral symmetry and a substitutional site of Te on the layer surface. A distinct temperature dependence is seen in the positional fluctuations of the impurity Mn atoms in the substitutional site. These findings for the impurity sites cannot be easily obtained by diffraction or XAFS experiment in the usual way, but only using a combination of the XFH and XAFS measurements.

Large As sublattice distortion in sphalerite ZnSnAs2 thin films revealed by x-ray fluorescence holography

The structure of a ZnSnAs2 thin film epitaxially grown on an InP substrate was evaluated using x-ray fluorescence holography. The reconstructed three-dimensional atomic images clearly show that the crystal structure of the ZnSnAs2 thin film is mainly of the sphalerite type, in contrast to the bulk form. A large disordering of the As layers is observed, whereas the positions of the Zn/Sn atoms are relatively stable. The analysis of the data indicates that the As layers serve as a buffer and relax the strain caused by the random occupation of Zn and Sn atoms. These results provide further understanding and a means of controlling the growth of Mn-doped ZnSnAs2, a high-Tc diluted magnetic semiconductor.

Atomic Image Reconstruction from Atomic Resolution Holography Using &lt;i&gt;L&lt;/i&gt;&lt;sub&gt;1&lt;/sub&gt;-Regularized Linear Regression

Inverse x-ray fluorescence holography provides new knowledge about the local atomic structure around dopants in crystals. The three-dimensional atomic image is reconstructed from the inverse x-ray fluorescence hologram using a calculation. The performance of the algorithm used for this calculation is important. The Barton method, which is based on the Fourier transform, is typically used. However, images reconstructed by this method sometimes contain artifacts. I developed an algorithm (SPEA-L1) using an iterative method with L1 regularization and report its performance. [DOI: 10.1380/ejssnt.2016.158]

Fast Calculation Algorithm Using Barton's Method for Reconstructing Three-Dimensional Atomic Images from X-ray Fluorescence Holograms

Abstract A fast calculation algorithm for three-dimensional atomic image reconstruction from X-ray fluorescence holography (Barton's method) is described. This method employs HEALPix, an algorithm that is used to subdivide a spherical surface in which each pixel covers an identical surface area. Using this algorithm, the computing time for atomic image reconstruction is reduced by a factor of 14.5. The time can be reduced further by parallel processing and an optimization of the resolution parameter of HEALPix.

Local Clusters in a Distorted Rocksalt GeTe Crystal Found by X-ray Fluorescence Holography

A Ge Kα X-ray fluorescence holography (XFH) measurement was performed on a single-crystal GeTe film with a deformed rocksalt (rhombohedral) lattice, for which careful analyses and observations of the reconstructed atomic images were needed. The three-dimensional atomic images obtained around the central Ge atom were compared with the theoretical images obtained from a simulated hologram in the full sphere range and in the limited θ range (0 < θ < 74°), as in the experiment. It was found that reliable atomic images were realized only when neighboring atoms are located on the surface side of the central Ge atom. GeTe3 clusters were found by XFH, which cannot be easily detected by diffraction, and confirmed by ab initio molecular dynamics simulation.

Distorted and Undistorted Atomic Sites in a Ferromagnetic Semiconductor Ge0.6Mn0.4Te Film Determined by X-ray Fluorescence Holography

Local atomic structures around Ge and Mn atoms in a ferromagnetic semiconductor Ge0.6Mn0.4Te thin film were investigated by performing Ge and Mn Kα X-ray fluorescence holographic experiments. The obtained three-dimensional atomic images revealed that the local structure around Mn formed a rock salt lattice, whereas the lattice around Ge was strongly distorted, which is reflected by a rhombohedral structure of GeTe. The undistorted rock salt environment around the Mn atoms is considered to be a key factor allowing for this alloy to exhibit high-temperature ferromagnetism.

Features of atomic images reconstructed from photoelectron, Auger electron, and internal detector electron holography using SPEA-MEM

Three-dimensional atomic images can be reconstructed from photoelectron, Auger electron, and internal detector electron holograms using a scattering pattern extraction algorithm using the maximum entropy method (SPEA-MEM) that utilizes an integral transform. An integral kernel function for the integral transform is the key to clear atomic image reconstruction. We composed the kernel function using a scattering pattern function and estimated its ability. Image distortion caused by multiple scattering was also evaluated. Four types of Auger electron wave functions were investigated, and the effect of these wave function types was estimated. In addition, we addressed refraction at the surface, the effects of data limitation, and energy and angular resolutions.

Correlations between 1/f noise and thermal treatment of Al-doped ZnO thin films deposited by direct current sputtering

Al-doped ZnO thin films (AZO) have been deposited on amorphous glass substrates by DC sputtering at different substrate temperatures Ts. X-Ray diffraction results reveal that AZO thin films have a hexagonal wurtzite structure with (002) preferred orientation. (002) peaks indicate that the crystalline structure of the films is oriented with c-axis perpendicular to the substrate. Three-dimensional (3D) atomic force microscopy images of AZO thin films deposited on glass substrate at 200 °C, 300 °C, and 400 °C, respectively, shows the improvement of the crystallinity and the homogeneity of AZO thin films with Ts which is in agreement with the noise measurements. The noise was characterized between 1 Hz and 100 kHz and we have obtained 1/f spectra. The noise is very sensitive to the crystal structure especially to the orientation of the crystallites which is perpendicular to the substrate and to the grain boundaries which generate a high current flow and a sharp increase in noise. Through time, Rsh and [αμ]eff increase with the modification of the crystallinity of AZO thin films. Study of noise aging shows that the noise is more sensitive than resistivity for all AZO thin films.

Element Assignment for Three-Dimensional Atomic Imaging by Photoelectron Holography

Photoelectron holography has been expected to be a powerful tool for visualizing three-dimensional (3D) local atomic structures around a photoelectron emitter atom. Photoelectron emitter atom sites with different elements can be distinguished by photoelectron kinetic energy. The elements of atoms reconstructed in atomic images, however, could not be assigned. We developed a method for the elemental characterization of the reconstructed atoms using a small difference of the scattered electron waves and demonstrated it using a measured InP(001) photoelectron hologram. Element assignment for both the emitter atom and the reconstructed atoms in 3D atomic images became possible.

Direct three-dimensional atomic imaging by means of electron diffraction patterns

Direct three-dimensional atomic imaging by means of electron diffraction patterns