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.

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.

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.

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.

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.

Misfit dislocations at a heteroepitaxial interface produce huge strain and, thus, have a significant impact on the properties of the interface. Here, we use scanning transmission electron microscopy to demonstrate a quantitative unit-cell-by-unit-cell mapping of the lattice parameters and octahedral rotations around misfit dislocations at the BiFeO3/SrRuO3 interface. We find that huge strain field is achieved near dislocations, i.e., above 5% within the first three unit cells of the core, which is typically larger than that achieved from the regular epitaxy thin-film approach, thus significantly altering the magnitude and direction of the local ferroelectric dipole in BiFeO3 and magnetic moments in SrRuO3 near the interface. The strain field and, thus, the structural distortion can be further tuned by the dislocation type. Our atomic-scale study helps us to understand the effects of dislocations in this ferroelectricity/ferromagnetism heterostructure. Such defect engineering allows us to tune the local ferroelectric and ferromagnetic order parameters and the interface electromagnetic coupling, providing new opportunities to design nanosized electronic and spintronic devices.

Cantilever-based atomic force microscopy (AFM) performed under ambient conditions has become an important tool to characterize new material systems as well as devices. Current instruments permit robust scanning over large areas, atomic-scale lateral resolution, and the characterization of various sample properties using multifrequency and multimodal AFM operation modes. Research of new quantum materials and devices, however, often requires low temperatures and ultrahigh vacuum (UHV) conditions and, more specifically, AFM instrumentation providing atomic resolution. For this, AFM instrumentation based on a tuning fork force sensor became increasingly popular. In comparison to microfabricated cantilevers, the more macroscopic tuning forks, however, lack sensitivity, which limits the measurement bandwidth. Moreover, multimodal and multifrequency techniques, such as those available in cantilever-based AFM carried out under ambient conditions, are challenging to implement. In this article, we describe a cantilever-based low-temperature UHV AFM setup that allows one to transfer the versatile AFM techniques developed for ambient conditions to UHV and low-temperature conditions. We demonstrate that such a cantilever-based AFM offers experimental flexibility by permitting multimodal or multifrequency operations with superior force derivative sensitivities and bandwidths. Our instrument has a sub-picometer gap stability and can simultaneously map not only vertical and lateral forces with atomic-scale resolution, but also perform rapid overview scans with the tip kept at larger tip-sample distances for robust imaging.

Nanoscale positioning has numerous applications in both academia and industry. A growing number of applications require devices with long working distances and nanoscale resolutions. Friction-inertia piezoelectric positioners, which are based on the stick-slip mechanism, achieve both nanometer resolution and centimeter-scale travel. However, the requirements of complex preload mechanism, precision machining, and precise assembly increase the cost of conventional friction-inertia nanopositioners. Herein we present the design of an open-source XYZ-axis nanopositioning system. Utilizing a magnet-based stick-slip driving mechanism, the proposed XYZ nanopositioner provides several advantages, including sub-nanometer resolution, a payload capacity of up to 12 kg (horizontal), compact size, low cost, and easy assembly; furthermore, the system is adjustment-free. The performance tests validate the precision of the system in both scanning and stepping operation modes. Moreover, the resonant spectra affirm the rigidity and dynamic response of the mechanism. In addition, we demonstrate the practical applications of this nanopositioner in various measurement techniques, including scanning electron microscopy, vibrometry, and atomic force microscopy. Furthermore, we present 11 variations of the nanopositioner designs that are either compatible with ultra-high-vacuum systems and other existing systems, 3D printable, or hacking commercial linear slides.

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

Transition metal oxides constitute one of the most fruitful sources of materials with continuously increasing potential applications prompted by the expectations derived from the reduction of the particle size. The recent advances in transmission electron microscopy, because of the development of lenses, have made it possible to reach atomic resolution, which can provide answers regarding the performance of the transition metal nano-oxides. This critical information is related not only to the ability to study their microstructural characteristics but also their local composition and the oxidation state of the transition metal. Exploring these features is a well-known task in nano-oxides for energy and electronic technologies, but they are not so commonly used for elucidating the activity of these oxides for biomedical applications. Nevertheless, the identification at the atomic level of a certain dopant or the unambiguous determination of the oxidation state of a transition metal in a nano-oxide can be important questions to be answered in a certain biomedical application. In this work, we provide several examples in transition metal nano-oxides to show how atomic-resolution electron microscopy can be a key tool for its understanding.