Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of Aquifex aeolicus lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field.

(Scanning) transmission electron microscopy (TEM) images of samples in gas and liquid media are acquired with an environmental cell (EC) via silicon nitride membranes. The ratio of sample signal against the background is a significant factor for resolution. Depth-sectioning scanning TEM (STEM) is a promising technique that enhances the signal for a sample embedded in a matrix. It can increase the resolution to the atomic level, thereby enabling EC-STEM applications in important areas. This review introduces depth-sectioning STEM and its applications to high-resolution EC-STEM imaging of samples in gases and in liquids.

The manual identification and in situ correction of the state of the scanning probe tip is one of the most time-consuming and tedious processes in atomic-resolution scanning probe microscopy. This is due to the random nature of the probe tip on the atomic level, and the requirement for a human operator to compare the probe quality via manual inspection of the topographical images after any change in the probe. Previous attempts to automate the classification of the scanning probe state have focused on the use of machine learning techniques, but the training of these models relies on large, labeled data sets for each surface being studied. These data sets are extremely time-consuming to create and are not always available, especially when considering a new substrate or adsorbate system. In this paper, we show that the problem of tip classification from a topographical image can be solved by using only a single image of the surface along with a small amount of prior knowledge of the appearance of the system in question with a method utilizing template matching (TM). We find that by using these TM methods, comparable accuracy and precision can be achieved to values obtained with the use of machine learning. We demonstrate the efficacy of this technique by training a machine learning-based classifier and comparing the classifications with the TM classifier for two prototypical silicon-based surfaces. We also apply the TM classifier to a number of other systems where supervised machine learning-based training was not possible due to the nature of the training data sets. Finally, the applicability of the TM method to surfaces used in the literature, which have been classified using machine learning-based methods, is considered.

Wave function reconstruction from one or two defocus images is promising for live atomic resolution imaging in transmission electron microscopy. However, a robust and accurate reconstruction method we still need more attention. Here, we present a neural-network-based wave function reconstruction method, EWR-NN, that enables accurate wave function reconstruction from only two defocus images. Results from both simulated and two different experimental defocus series show that the EWR-NN method has better performance than the widely-used iterative wave function reconstruction (IWFR) method. Influence of image number, defocus deviation, residual image shifts and noise level were considered to validate the performance of EWR-NN under practical conditions. It is seen that these factors will not influence the arrangement of atom columns in the reconstructed phase images, while they can alter the absolute values of all-atom columns and degrade the contrast of the phase images.

Positron Emission Tomography (PET) ligands have advanced Alzheimer\'s disease (AD) diagnosis and treatment. Using autoradiography and cryo-EM, we identified AD brain tissue with elevated tau burden, purified filaments, and determined the structure of second-generation high avidity PET ligand MK-6240 at 2.31 Å resolution, which bound at a 1:1 ratio within the cleft of tau paired-helical filament (PHF), engaging with glutamine 351, lysine K353, and isoleucine 360. This information elucidates the basis of MK-6240 PET in quantifying PHF deposits in AD and may facilitate the structure-based design of superior ligands against tau amyloids.

Chemically resolved atomic resolution imaging can give fundamental information about material properties. However, even today, a technique capable of such achievement is still only an ambition. Here, we take further steps in developing the analytical field ion microscopy (aFIM), which combines the atomic spatial resolution of field ion microscopy (FIM) with the time-of-flight spectrometry of atom probe tomography (APT). To improve the performance of aFIM that are limited in part by a high level of background, we implement bespoke flight path time-of-flight corrections normalized by the ion flight distances traversed in electrostatic simulations modeled explicitly for an atom probe chamber. We demonstrate effective filtering in the field evaporation events upon spatially and temporally correlated multiples, increasing the mass spectrum\'s signal-to-background. In an analysis of pure tungsten, mass peaks pertaining to individual W isotopes can be distinguished and identified, with the signal-to-background improving by three orders of magnitude over the raw data. We also use these algorithms for the analysis of a CoTaB amorphous film to demonstrate application of aFIM beyond pure metals and binary alloys. These approaches facilitate elemental identification of the FIM-imaged surface atoms, making analytical FIM more precise and reliable.

The structural change in Pt networks composed of multiple chain connections among grains was observed in air at 1 atm using atomic-resolution environmental cell scanning transmission electron microscopy. An aberration-corrected incident electron probe with a wide convergence angle made it possible to increase the depth resolution that contributes to enhancing the signal-to-noise ratio of Pt network samples in air in an environmental cell, resulting in the achievement of atomic-resolution imaging. The exposure of the Pt networks to gas molecules under Brownian motion, stimulated by electron beams in the air, increases the collision probability between gas molecules and Pt networks, and the Pt networks are more intensely stressed from all directions than in a situation without electron irradiation. By increasing the electron beam dose rate, the structural change of the Pt networks became significant. Dynamic observation on an atomic scale suggested that the structural change of the networks was not attributed to the surface atomic-diffusion-induced step motion but mainly caused by the movement and deformation of unstable grains and grain boundaries. The oxidized surface layers may be one of the factors hindering the surface atomic step motion, mitigating the change in the size of the grains and grain boundaries.

Using in situ atomic-resolution scanning transmission electron microscopy, atomic movements and rearrangements associated with diffusive solid to solid phase transformations in the Pt-Sn system are captured to reveal details of the underlying atomistic mechanisms that drive these transformations. In the PtSn4 to PtSn2 phase transformation, a periodic superlattice substructure and a unique intermediate structure precede the nucleation and growth of the PtSn2 phase. At the atomic level, all stages of the transformation are templated by the anisotropic crystal structure of the parent PtSn4 phase. In the case of the PtSn2 to Pt2Sn3 transformation, the anisotropy in the structure of product Pt2Sn3 dictates the path of transformation. Analysis of atomic configurations at the transformation front elucidates the diffusion pathways and lattice distortions required for these phase transformations. Comparison of multiple Pt-Sn phase transformations reveals the structural parameters governing solid to solid phase transformations in this technologically interesting intermetallic system.

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

Charge density waves (CDWs) in 1T-TaS2 maintain 2D ordering by forming periodic in-plane star-of-David (SOD) patterns, while they also intertwined with orbital order in the c axis. Recent theoretical calculations and surface measurements have explored 3D CDW configurations, but interlayer intertwining of a 2D CDW order remains elusive. Here, we investigate the in- and out-of-plane ordering of the commensurate CDW superstructure in a 1T-TaS2 thin flake in real space, using aberration-corrected cryogenic transmission electronic microscopy (cryo-TEM) in low-dose mode, far below the threshold dose for an electron-induced CDW phase transition. By scrutinizing the phase intensity variation of modulated Ta atoms, we visualize the penetrative 3D CDW stacking structure, revealing an intertwining multidomain structure with three types of vertical CDW stacking configurations. Our results provide microstructural evidence for the coexistence of local Mott insulation and metal phases and offer a paradigm for studying the CDW structure and correlation order in condensed-matter physics using cryo-TEM.