Atomic Images Research Articles

Atomic resolution transmission electron microscopy visualisation of channel occupancy in beryl in different crystallographic directions

The causes of colour in beryl have been a research topic for decades. For some varieties, such as emerald (green, coloured by Cr3+ and/or V3+), the main cause of colour is substitutions by metal atoms within the framework. However, the causes for the yellow and blue colours in heliodor, golden beryl and aquamarine are still debated. It is generally agreed that Fe ions are responsible for the colour, but there are differing conclusions about the valence states of these ions, the occupied positions and the colour-inducing processes involved. The colour of aquamarine is commonly attributed to intervalence charge transfer (IVCT) between Fe3+ and Fe2+. Various combinations of sites have been proposed to host the Fe ions engaging in this IVCT. Here we present a new approach to address the topic of colour generation: atomic resolution scanning transmission electron microscopy (STEM). For the first time, atomic resolution images of a beryl (natural aquamarine) are presented in the three crystallographic directions [0001], [1-210] and [1-100]. Ions are clearly resolved in the channels. From the ratio of channel occupation and the correlation of the atoms per formula unit (apfu) calculations we conclude that Fe resides in the framework, not in the channels. The projections in the [1-210] direction directly show that the cavity channel site 2a is occupied, most likely by Cs, in agreement with recent results in the literature.

High-Fidelity Detection of Large-Scale Atom Arrays in an Optical Lattice.

Recent advances in quantum simulation based on neutral atoms have largely benefited from high-resolution, single-atom sensitive imaging techniques. A variety of approaches have been developed to achieve such local detection of atoms in optical lattices or optical tweezers. For alkaline-earth and alkaline-earth-like atoms, the presence of narrow optical transitions opens up the possibility of performing novel types of Sisyphus cooling, where the cooling mechanism originates from the capability to spatially resolve the differential optical level shifts in the trap potential. Up to now, it has been an open question whether high-fidelity imaging could be achieved in a "repulsive Sisyphus" configuration, where the trap depth of the ground state exceeds that of the excited state involved in cooling. Here, we demonstrate high-fidelity (99.971(1)%) and high-survival (99.80(5)%) imaging of strontium atoms using repulsive Sisyphus cooling. We use an optical lattice as a pinning potential for atoms in a large-scale tweezer array with up to 399 tweezers and show repeated, high-fidelity lattice-tweezer-lattice transfers. We furthermore demonstrate loading the lattice with approximately 10 000 atoms directly from the MOT and scalable imaging over >10 000 lattice sites with a combined survival probability and classification fidelity better than 99.2%. Our lattice thus serves as a locally addressable and sortable reservoir for continuous refilling of optical tweezer arrays in the future.

Magnetron carbon structures obtained by high-frequency magnetron sputtering in Argon and Nitrogen

Purpose of research. Creation and characterization of carbon nanostructures by high-frequency magnetron sputtering from a carbon target in argon on a silicon substrate and in a reactive nitrogen environment, obtained on a Ni catalyst buffer layer. Methods. High-frequency magnetron sputtering on a silicon substrate with changes in control parameters: sputtering time power and working gas pressure Ar and N. Research was carried out using X-ray phase analysis, atomic force microscopy and holographic microscopy, Raman scattering. Results. The formation of carbon nanotubes, including single-walled ones, was confirmed by the method of Raman scattering of light along the lines ID 1363 and IG 1564 cm-1, as well as ωRDМ 308 and 227 cm–1. Using atomic force microscopic images, the fractal dimension of the nanofilms was calculated, which indicated their 3D nature. Based on X-ray phase analysis of magnetron nanofilms, the dimensions of the coherence region, texture, microdeformations and interplanar deformation distortions were determined. Conclusion. In carbon magnetron nanofilms, deformations of both signs occur: both compressive (∆a < 0) and tensile (∆a > 0). Carbon magnetron nanofilms are represented, among other things, by single-walled carbon nanotubes, the chirality of which in an argon environment is (6, 6), and in a reactive mixture of nitrogen and argon on a Ni buffer layer (7, 7). It was discovered that in high-frequency magnetron mode, silicon carbide is formed in both inert and reactive environments.

Moiré fringe imaging of heterostructures by scanning transmission electron microscopy

A heterostructured crystalline bilayer specimen is known to produce moiré fringes (MFs) in the conventional transmission electron microscopy (TEM). However, the understanding of how these patterns form in scanning transmission electron microscopy (STEM) remains limited. Here, we extended the double-scattering model to establish the imaging theory of MFs in STEM for a bilayer sample and applied this theory to successfully explain both experimental and simulated STEM images of a perovskite PbZrO3/SrTiO3 system. Our findings demonstrated that the wave vectors of electrons exiting from Layer-1 and their relative positions with the atomic columns of Layer-2 should be taken into account. The atomic column misalignment leads to a faster reduction in the intensity of the secondary scattering beam compared to the single scattering beam as the scattering angle increases. Consequently, the intensity distribution of MFs in the bright field (BF)-STEM can be still described as the product of two single atomic images. However, in high angle annular dark field (HAADF)-STEM, it is approximately described as the superposition of the two images. Our work not only fills a knowledge gap of MFs in incoherent imaging, but also emphasizes the importance of the coherent scattering restricted by the real space when analyzing the HAADF-STEM imaging.

High-quality AFM image acquisition of living cells by modified residual encoder-decoder network

Atomic force microscope enables ultra-precision imaging of living cells. However, atomic force microscope imaging is a complex and time-consuming process. The obtained images of living cells usually have low resolution and are easily influenced by noise leading to unsatisfactory imaging quality, obstructing the research and analysis based on cell images. Herein, an adaptive attention image reconstruction network based on residual encoder-decoder was proposed, through the combination of deep learning technology and atomic force microscope imaging supporting high-quality cell image acquisition. Compared with other learning-based methods, the proposed network showed higher peak signal-to-noise ratio, higher structural similarity and better image reconstruction performances. In addition, the cell images reconstructed by each method were used for cell recognition, and the cell images reconstructed by the proposed network had the highest cell recognition rate. The proposed network has brought insights into the atomic force microscope-based imaging of living cells and cell image reconstruction, which is of great significance in biological and medical research.

Atomic imaging and optical properties of InAs/In0.5Ga0.5As0.5Sb0.5 type II superlattice

High-quality III–V quantum structures, advanced epitaxial technologies, and characterization methods are essential to drive the development of infrared optoelectronic materials and devices. As an important component of type II superlattices, InAs/InxGa1−xAsySb1−y would play an important role in the field of high-performance infrared detectors due to their excellent luminescence efficiency and high crystal quality. However, their interfacial characteristics and the associated minority carrier lifetime are still difficult to identify. In this paper, an atomic imaging technique was used to identify the arrangement and distribution of elements of the InAs/In0.5Ga0.5As0.5Sb0.5 superlattice. Our results confirm the epitaxy mechanism that the quaternary alloy consists of two kinds of ternary alloy in one monolayer. Moreover, by separating the cation and anion columns in the elementally resolved atomic images of the InAs/In0.5Ga0.5As0.5Sb0.5 superlattice, we demonstrate that the interfacial atomic intermixing is less than one molecular layer thickness. Therefore, benefiting from excellent interface quality, InAs/In0.5Ga0.5As0.5Sb0.5 superlattice exhibited high radiation recombination efficiency in the long-wave infrared band (∼8.5 μm), and longer minority carrier lifetime (∼810 ns at 90 K).

In-situ imaging of heat-induced phase transition in a two-dimensional conjugated metal-organic framework

Atomically-resolved in-situ high-resolution transmission electron microscopy (HRTEM) imaging of the structural dynamics in organic materials remains a major challenge. This difficulty persists even with aberration-corrected instruments, as HRTEM images necessitate a high electron dose that is generally intolerable for organic materials. In this study, we report the in-situ HRTEM imaging of heat-induced structural dynamics in a benzenehexathiol-based two-dimensional conjugated metal-organic framework (2D c-MOF, i.e., Cu3(BHT)). Leveraging its hydrogen-free structure and high electrical conductivity, Cu3(BHT) exhibits high electron beam resistance. We demonstrate atomic resolution imaging at an 80 kV electron accelerating voltage using our Cc/Cs-corrected SALVE instrument. However, continuous electron irradiation eventually leads to its amorphization. Intriguingly, under heating in a MEMS holder, the Cu3(BHT) undergoes a phase transition to a new crystalline phase and its phase transition, occurring within the temperature range of 480 °C to 620 °C in dependence on the electron beam illumination. Using HRTEM and energy-dispersive X-ray mapping, we identify this new phase as CuS. Our findings provide insights into the mechanisms governing structural transitions in purposefully engineered structures, potentially pivotal for future endeavours involving the production of metal oxide/sulfide nanoparticles from MOF precursors.

Differentiation Between Abscesses and Unnecessary Intervention Fluid After Pancreas Surgery Using Dual-Energy Computed Tomography.

This study aimed to evaluate the potential of dual-energy computed tomography (CT) to distinguish postoperative ascites, pancreatic fistula, and abscesses. Patients who underwent biliary and pancreatic surgery performed at our institution between June 2021 and February 2022 were included in the study. Postoperative body fluid samples were collected through a drain or percutaneous drainage. These samples were set in a phantom, and imaging data were obtained using dual-energy CT. Image analysis was performed to obtain CT values at each energy in virtual monoenergetic images (VMIs), effective atomic number, iodine map, and virtual non-contrast (VNC) images. VMIs were calculated from 80 and 140 kVp tube data at 10 kV each from 40-140 kV. Additionally, the effective atomic number, iodine map, and VNC images were reconstructed from the material decomposition process using water and iodine as the base material pair. In this study, 25 patients (eight with abscess and 17 with ascites) were included. No significant association was observed between the presence or absence of abscess and malignancy or surgical procedure. The intervention was performed in six of the eight patients with abscesses. In contrast, five of the 17 patients with postoperative ascites required intervention. A significant relationship was observed between the intervention and the presence of an abscess. Significant differences in C-reactive protein values and the incidence of fever were observed between the groups. Only VNC showed a significant difference between the groups. VNC using dual-energy CT could differentiate abscesses from postoperative fluid.

Background-free imaging of cold atoms in optical traps

Optical traps, including those used in atomic physics, cold chemistry, and quantum science, are widely used in the research on cold atoms and molecules. Owing to their microscopic structure and excellent operational capability, optical traps have been proposed for cold atom experiments involving complex physical systems, which generally induce violent background scattering. In this study, using a background-free imaging scheme in cavity quantum electrodynamics systems, a cold atomic ensemble was accurately prepared below a fiber cavity and loaded into an optical trap for transfer into the cavity. By satisfying the demanding requirements for the background-free imaging scheme in optical traps, cold atoms in an optical trap were detected with a high signal-to-noise ratio while maintaining atomic loading. The cold atoms were then transferred into the fiber cavity using an optical trap, and the vacuum Rabi splitting was measured, facilitating relevant research on cavity quantum electrodynamics. This method can be extended to related experiments involving cold atoms and molecules in complex physical systems using optical traps.

General Aqueous System Simulation through an AI-Embedded Metaverse Chemistry Laboratory.

Recent decades have witnessed the rapid development of autonomous laboratories and artificial intelligence, where experiments can be automatically run and optimized. Although human work is reduced, the total time of experimental optimization is still consuming due to limitations of the current ab metaverse framework, which accurately predicts the future state of the system by receiving and analyzing in situ experimental data. To substitute for traditional simulation methods, we designed a physically endorsed deep learning model to predict the future system picture ranging from atomic image to bulk appearance, intensively using the correlations between properties of the system. Through this framework, we studied the general aqueous system, covering 100+ common ionic solutions. We can accurately simulate properties for a general aqueous system as well as predict the time of solvation of ionic compounds ahead of real experiments. In this way, the experiments can be optimized more efficiently without waiting for the end of a bad iteration. We hope our work offers a fresh direction for the digitization of chemical information, enhancing access to and use of experimental data in advancing the field of physical chemistry.

Direct Fabrication of Atomically Defined Pores in MXenes Using Feedback-Driven STEM.

Controlled fabrication of nanopores in 2D materials offer the means to create robust membranes needed for ion transport and nanofiltration. Techniques for creating nanopores have relied upon either plasma etching or direct irradiation; however, aberration-corrected scanning transmission electron microscopy (STEM) offers the advantage of combining a sub-Å sized electron beam for atomic manipulation along with atomic resolution imaging. Here, a method for automated nanopore fabrication is utilized with real-time atomic visualization to enhance the mechanistic understanding of beam-induced transformations. Additionally, an electron beam simulation technique, Electron-Beam Simulator (E-BeamSim) is developed to observe the atomic movements and interactions resulting from electron beam irradiation. Using the MXene Ti3C2Tx, the influence of temperature on nanopore fabrication is explored by tracking atomic transformations and find that at room temperature the electron beam irradiation induces random displacement and results in titanium pileups at the nanopore edge, which is confirmed by E-BeamSim. At elevated temperatures, after removal of the surface functional groups and with the increased mobility of atoms results in atomic transformations that lead to the selective removal of atoms layer by layer. This work can lead to the development of defect engineering techniques within functionalized MXene layers and other 2D materials.

Application of the polyhedral template matching method for characterization of 2D atomic resolution electron microscopy images

High-throughput image segmentation of atomic resolution electron microscopy data poses an ongoing challenge for materials characterization. In this paper, we investigate the application of the polyhedral template matching (PTM) method, a technique widely employed for visualizing three-dimensional (3D) atomistic simulations, to the analysis of two-dimensional (2D) atomic resolution electron microscopy images. This technique is complementary with other atomic resolution data reduction techniques, such as the centrosymmetry parameter, that use the measured atomic peak positions as the starting input. Furthermore, since the template matching process also gives a measure of the local rotation, the method can be used to segment images based on local orientation. We begin by presenting a 2D implementation of the PTM method, suitable for atomic resolution images. We then demonstrate the technique's application to atomic resolution scanning transmission electron microscopy images from close-packed metals, providing examples of the analysis of twins and other grain boundaries in FCC gold and martensite phases in 304 L austenitic stainless steel. Finally, we discuss factors, such as positional errors in the image peak locations, that can affect the accuracy and sensitivity of the structural determinations.

An atomic boson sampler.

A boson sampler implements a restricted model of quantum computing. It is defined by the ability to sample from the distribution resulting from the interference of identical bosons propagating according to programmable, non-interacting dynamics1. An efficient exact classical simulation of boson sampling is not believed to exist, which has motivated ground-breaking boson sampling experiments in photonics with increasingly many photons2-12. However, it is difficult to generate and reliably evolve specific numbers of photons with low loss, and thus probabilistic techniques for postselection7 or marked changes to standard boson sampling10-12 are generally used. Here, we address the above challenges by implementing boson sampling using ultracold atoms13,14 in a two-dimensional, tunnel-coupled optical lattice. This demonstration is enabled by a previously unrealized combination of tools involving high-fidelity optical cooling and imaging of atoms in a lattice, as well as programmable control of those atoms using optical tweezers. When extended to interacting systems, our work demonstrates the core abilities required to directly assemble ground and excited states in simulations of various Hubbard models15,16.

Crystal structures of two new high-pressure oxynitrides with composition SnGe4N4O4, from single-crystal electron diffraction.

SnGe4N4O4 was synthesized at high pressure (16 and 20 GPa) and high temperature (1200 and 1500°C) in a large-volume press. Powder X-ray diffraction experiments using synchrotron radiation indicate that the derived samples are mixtures of known and unknown phases. However, the powder X-ray diffraction patterns are not sufficient for structural characterization. Transmission electron microscopy studies reveal crystals of several hundreds of nanometres in size with different chemical composition. Among them, crystals of a previously unknown phase with stoichiometry SnGe4N4O4 were detected and investigated using automated diffraction tomography (ADT), a three-dimensional electron diffraction method. Via ADT, the crystal structure could be determined from single nanocrystals in space group P63mc, exhibiting a nolanite-type structure. This was confirmed by density functional theory calculations and atomic resolution scanning transmission electron microscopy images. In one of the syntheses runs a rhombohedral 6R polytype of SnGe4N4O4 could be found together with the nolanite-type SnGe4N4O4. The structure of this polymorph was solved as well using ADT.

A novel STM for quality atomic resolution with piezoelectric motor of high compactness and simplicity

Scanning tunneling microscope (STM) is a renowned scientific tool for obtaining high-resolution atomic images of materials. Herein, we present an innovative design of the scanning unit with a compact yet powerful inertial piezoelectric motor inspired by the Spider Drive motor principle. The scanning unit mainly consists of a small 9 mm long piezoelectric tube scanner (PTS), one end of which is coaxially connected to the main sapphire body of the STM. Of particular emphasis in this design is the piezoelectric shaft (PS), constructed from piezoelectric material instead of conventional metallic or zirconium materials. The PS is a rectangular piezoelectric stack composed of two piezoelectric plates, which are elastically clamped on the inner wall of the PTS via a spring strip. The PTS and PS expand and contract independently with each other to improve the inertial force and reduce the threshold voltage. To ensure the stability of the PS and balance the stepping performance of the inertial motor, a counterweight, and a matching conical spring are fixed at the tail of the PS. This innovative design allows for the assessment of scanning unit performance by applying a driving signal, threshold voltage is 50 V at room temperature. Step sizes vary from 0.1 to 1 µm by changing the driving signal at room temperature. Furthermore, we successfully obtained atomic-resolution images of a highly oriented pyrolytic graphite (HOPG) sample and low drift rates of 23.4 pm/min and 34.6 pm/min in X-Y plane and Z direction, respectively, under ambient conditions. This small, compact STM unit has the potential for the development of a rotatable STM for use in cryogen-free magnets, and superconducting magnets.

Superstructure of Fe5-xGeTe2 Determined by Te K-Edge Extended X-ray Absorption Fine Structure and Te Kα X-ray Fluorescence Holography.

The local structure of the two-dimensional van der Waals material, Fe5-xGeTe2, which exhibits unique structural/magnetic phase transitions, was investigated by Te K-edge extended X-ray absorption fine structure (EXAFS) and Te Kα X-ray fluorescence holography (XFH) over a wide temperature range. The formation of a trimer of Te atoms at low temperatures has been fully explored using these methods. An increase in the Te-Fe distance at approximately 150 K was suggested by EXAFS and presumably indicates the formation of a Te trimer. Moreover, XFH displayed clear atomic images of Te atoms. Additionally, the distance between the Te atoms shortened, as confirmed from the atomic images reconstructed from XFH, indicating the formation of a trimer of Te atoms, i.e., a charge-ordered superstructure. Furthermore, Te Kα XFH provided unambiguous atomic images of Fe atoms occupying the Fe1 site; the images were not clearly observed in the Ge Kα XFH that was previously reported because of the low occupancy of Fe and Ge atoms. In this study, EXAFS and XFH clearly showed the local structure around the Te atom; in particular, the formation of Te trimers caused by charge-ordered phase transitions was clearly confirmed. The charge-ordered phase transition is fully discussed based on the structural variation at low temperatures, as established from EXAFS and XFH.

Wavefront distortion correction in scanning tunneling microscope image.

We report an algorithm to identify and correct distorted wavefronts in atomic resolution scanning tunneling microscope images. This algorithm can be used to correct nonlinear in-plane distortions without prior knowledge of the physical scanning parameters, the characteristics of the piezoelectric actuator, or individual atom positions. The 2D image is first defined as a sum of sinusoidal plane waves, where a nonlinear distortion renders a curve for an otherwise ideal linear wavefront. Using the Fourier transforms of local areas of the image, the algorithm generates a wavefront vector field. The identified wavefronts are subsequently linearized for each plane wave without changing lattice orders, giving rise to distortion corrections. Our algorithm is complementary to conventional post-processing algorithms that require prior detection of real space features, which can also be used to correct nonlinear distortions in 2D images acquired by other microscopy techniques.

Nanotubes from Lanthanide-Based Misfit-Layered Compounds: Understanding the Growth, Thermodynamic, and Kinetic Stability Limits.

Gaining insights into the kinetics and the thermodynamic limits of nanostructures in high-temperature reactions is crucial for controlling their unique morphology, phase, and structure. Nanotubes from lanthanide-based misfit-layered compounds (MLCs) have been known for more than a decade and were successfully produced mostly via a chemical vapor transport protocol. The MLC nanotubes show diverse structural arrangements and lattice disorders, which could have a salient impact on their properties. Though their structure and charge transfer properties are reasonably well understood, a lack of information on their thermodynamic and kinetic stability limits their scalable synthesis and their applicability in modern technologies. In this study, the growth, thermodynamic stability, and decomposition kinetics of lanthanide-based misfit nanotubes of two model compounds, i.e., (LaS)1.14TaS2 and (SmS)1.19TaS2 are elucidated in detail. The nanotubes were carefully analyzed via atomic resolution electron microscopy imaging and synchrotron-based X-ray and electron diffraction techniques, and the information on their morphology, phase, and structures was deduced. The key insights gained would help to establish the parameters to explore their physio-chemical properties further. Furthermore, this study sheds light on the complex issue of the high-temperature stability of nanotubes and nanostructures in general.

Determination of Crack Resistance of the Cover and Slide Glass by Indentation Method with the Visualization Using Atomic Force Microscopy

Crack resistance of two types of glass was studied – cover glass (0.17 mm thick) and slide glass (2 mm thick) using an improved technique through the use of the probe methods, which makes it possible to increase the accuracy of determining the crack resistance of glass. Colorless silicate glass was used. Crack resistance was determined by the Vickers pyramid indentation method. Microstructure of glasses surface and deformation region after indentation were studied using an atomic force microscope. Mechanical properties of glasses were determined by nanoindentation. Surface relief of a glass slide is rougher than that one of a cover glass. Roughness Rz for a cover glass is less than for a slide glass. Specific surface energy value of 0.26 N/m is higher for the slide glass compared to the coverslip. One elastic modulus value E of the cover glass is 48 GPa, and that one of the slide glass is 58 GPa. The microhardness value H is almost the same for by the glasses and amounts to 6.7 GPa for a slide glass and 6.4 GPa for a cover glass. Atomic force microscope images of deformation region after indentation with a Vickers pyramid show that the first cracks appear at a load of 1 N on the slide glass, and at 2 N on the cover glass. At a load of 3 N, the cover glass is destroyed. Based on the results of crack resistance calculations it was found that critical stress intensity coefficient KIC values are 1.42 MPa∙m1/2 for a glass slide, and 1.10 MPa∙m1/2 for a cover glass.

Seeing is believing: Correlating optoelectronic functionality with atomic scale imaging of single semiconductor nanocrystals.

A unique on-chip method for the direct correlation of optical properties, with atomic-scale chemical-structural characteristics for a single quantum dot (QD), is developed and utilized in various examples. This is based on performing single QD optical characterization on a modified glass substrate, followed by the extraction of the relevant region of interest by focused-ion-beam-scanning electron microscope processing into a lamella for high resolution scanning transmission electron microscopy (STEM) characterization with atomic scale resolution. The direct correlation of the optical response under an electric field with STEM analysis of the same particle allows addressing several single particle phenomena: first, the direct correlation of single QD photoluminescence (PL) polarization and its response to the external field with the QD crystal lattice alignment, so far inferred indirectly; second, the identification of unique yet rare few-QD assemblies, correlated directly with their special spectroscopic optical characteristics, serving as a guide for future designed assemblies; and third, the study on the effect of metal island growth on the PL behavior of hybrid semiconductor-metal nanoparticles, with relevance for their possible functionality in photocatalysis. This work, therefore, establishes the use of the direct on-chip optical-structural correlation method for numerous scenarios and timely questions in the field of QD research.