Liquid Phase Electron Microscopy of Bacterial Ultrastructure.

Recent advances in liquid phase scanning transmission electron microscopy (LP-STEM) have enabled the study of dynamic biological processes at nanometer resolutions, paving the way for live-cell imaging using electron microscopy. However, this technique is often hampered by the inherent thickness of whole cell samples and damage from electron beam irradiation. These restrictions degrade image quality and resolution, impeding biological interpretation. Using graphene encapsulation, scanning transmission electron microscopy (STEM), and energy-dispersive X-ray (EDX) spectroscopy to mitigate these issues provides unprecedented levels of intracellular detail in aqueous specimens. This study demonstrates the potential of LP-STEM to examine and identify internal cellular structures in thick biological samples. Specifically, it highlights the use of LP-STEM to investigate the radiation resistant, gram-positive bacterium, Deinococcus radiodurans using various imaging techniques.

Observation of Antiferroelectric Domain Walls in a Uniaxial Hyperferroelectric.

Ferroelectric domain walls are a rich source of emergent electronic properties and unusual polar order. Recent studies show that the configuration of ferroelectric walls can go well beyond the conventional Ising-type structure. Néel-, Bloch-, and vortex-like polar patterns have been observed, displaying strong similarities with the spin textures at magnetic domain walls. Here, the discovery of antiferroelectric domain walls in the uniaxial ferroelectric Pb5Ge3O11 is reported. Highly mobile domain walls with an alternating displacement of Pb atoms are resolved, resulting in a cyclic 180° flip of dipole direction within the wall. Density functional theory calculations show that Pb5Ge3O11 is hyperferroelectric, allowing the system to overcome the depolarization fields that usually suppress the antiparallel ordering of dipoles along the longitudinal direction. Interestingly, the antiferroelectric walls observed under the electron beam are energetically more costly than basic head-to-head or tail-to-tail walls. The results suggest a new type of excited domain-wall state, expanding previous studies on ferroelectric domain walls into the realm of antiferroic phenomena.

Diffusion distribution model for damage mitigation in scanning transmission electron microscopy.

Despite the widespread use of Scanning Transmission Electron Microscopy (STEM) for observing the structure of materials at the atomic scale, a detailed understanding of some relevant electron beam damage mechanisms is limited. Recent reports suggest that certain types of damage can be modelled as a diffusion process and that the accumulation effects of this process must be kept low in order to reduce damage. We therefore develop an explicit mathematical formulation of spatiotemporal diffusion processes in STEM that take into account both instrument and sample parameters. Furthermore, our framework can aid the design of Diffusion Controlled Sampling (DCS) strategies using optimally selected probe positions in STEM, that constrain the cumulative diffusion distribution. Numerical simulations highlight the variability of the cumulative diffusion distribution for different experimental STEM configurations. These analytical and numerical frameworks can subsequently be used for careful design of 2- and 4-dimensional STEM experiments where beam damage is minimised.

Characterization of structure and mixing in nanoparticle hetero-aggregates using convolutional neural networks: 3D-reconstruction versus 2D-projection.

Structural and chemical characterization of nanomaterials provides important information for understanding their functional properties. Nanomaterials with characteristic structure sizes in the nanometer range can be characterized by scanning transmission electron microscopy (STEM). In conventional STEM, two-dimensional (2D) projection images of the samples are acquired, information about the third dimension is lost. This drawback can be overcome by STEM tomography, where the three-dimensional (3D) structure is reconstructed from a series of projection images acquired using various projection directions. However, 3D measurements are expensive with respect to acquisition and evaluation time. Furthermore, the method is hardly applicable to beam-sensitive materials, i.e. samples that degrade under the electron beam. For this reason, it is desirable to know whether sufficient information on structural and chemical information can be extracted from 2D-projection measurements. In the present work, a comparison between 3D-reconstruction and 2D-projection characterization of structure and mixing in nanoparticle hetero-aggregates is provided. To this end, convolutional neural networks are trained in 2D and 3D to extract particle positions and material types from the simulated or experimental measurement. Results are used to evaluate structure, particle size distributions, hetero-aggregate compositions and mixing of particles quantitatively and to find an answer to the question, whether an expensive 3D characterization is required for this material system for future characterizations.

Single-Image-Based Deep Learning for Precise Atomic Defect Identification.

Defect engineering is widely used to impart the desired functionalities on materials. Despite the widespread application of atomic-resolution scanning transmission electron microscopy (STEM), traditional methods for defect analysis are highly sensitive to random noise and human bias. While deep learning (DL) presents a viable alternative, it requires extensive amounts of training data with labeled ground truth. Herein, employing cycle generative adversarial networks (CycleGAN) and U-Nets, we propose a method based on a single experimental STEM image to tackle high annotation costs and image noise for defect detection. Not only atomic defects but also oxygen dopants in monolayer MoS2 are visualized. The method can be readily extended to other two-dimensional systems, as the training is based on unit-cell-level images. Therefore, our results outline novel ways to train the model with minimal data sets, offering great opportunities to fully exploit the power of DL in the materials science community.

Atomic-Scale Characterization of Dilute Dopants in Topological Insulators via STEM-EDS Using Registration and Cell Averaging Techniques.

Magnetic dopants in three-dimensional topological insulators (TIs) offer a promising avenue for realizing the quantum anomalous Hall effect (QAHE) without the necessity for an external magnetic field. Understanding the relationship between site occupancy of magnetic dopant elements and their effect on macroscopic property is crucial for controlling the QAHE. By combining atomic-scale energy-dispersive X-ray spectroscopy (EDS) maps obtained by aberration-corrected scanning transmission electron microscopy (AC-STEM) and novel data processing methodologies, including semi-automatic lattice averaging and frame registration, we have determined the substitutional sites of Mn atoms within the 1.2% Mn-doped Sb2Te3 crystal. More importantly, the methodology developed in this study extends beyond Mn-doped Sb2Te3 to other quantum materials, traditional semiconductors, and even electron irradiation sensitive materials.

Ultraclean Suspended Graphene by Radiolysis of Adsorbed Water.

Access to intrinsic properties of a 2D material is challenging due to the absence of a bulk that would dominate over surface contamination, and this lack of bulk also precludes effective conventional cleaning methods that are almost always sacrificial. Suspended graphene and carbon contaminants represent the most salient challenge. This work has achieved ultraclean graphene, attested by electron energy loss (EEL) spectra unprecedentedly exhibiting fine-structure features expected from bonding and band structure. In the cleaning process in a transmission electron microscope, radicals generated by radiolysis of intentionally adsorbed water remove organic contaminants, which would otherwise be feedstock of the notorious electron irradiation induced carbon deposition. This method can be readily adapted to other experimental settings and other materials to enable previously inhibited undertakings that rely on the intrinsic properties or ultimate thinness of 2D materials. Importantly, the method is surprisingly simple and robust, easily implementable with common lab equipment.

The Combined ICP-MS, ESEM-EDX, and HAADF-STEM-EDX Approach for the Assessment of Metal Sub-Micro- and Nanoparticles in Wheat Grain.

Metal sub-microparticles (SMPs) and nanoparticles (NPs) presence in food is attributable to increasing pollution from the environment in raw materials and finished products. In the present study, a multifaceted analytical strategy based on Environmental Scanning Electron Microscopy and High-Angle Annular Dark-Field-Scanning Transmission Electron Microscopy coupled with Energy-Dispersive X-ray Spectroscopy (ESEM-EDX, HAADF-STEM-EDX) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was proposed for the detection and characterization of metal and metal-containing SMPs and NPs in durum wheat samples, covering a size measurement range from 1 nm to multiple µm. ESEM-EDX and ICP-MS techniques were applied for the assessment of SMP and NP contamination on the surface of wheat grains collected from seven geographical areas characterized by different natural and anthropic conditions, namely Italy, the USA, Australia, Slovakia, Mexico, Austria, and Russia. ICP-MS showed significant differences among the mean concentration levels of metals, with the USA and Italy having the highest level. ESEM-EDX analysis confirmed ICP-MS concentration measurements and measured the highest presence of particles < 0.8 µm in size in samples from Italy, followed by the USA. Less marked differences were observed when particles < 0.15 µm were considered. HAADF-STEM-EDX was applied to a selected number of samples for a preliminary assessment of internal contamination by metal SMPs and NPs, and to expand the measurable particle size range. The multifaceted approach provided similar results for Fe-containing SMPs and NPs. ICP-MS and ESEM-EDX also highlighted the presence of a significant abundance of Ti- and Al-containing particles, while for STEM-EDX, sample preparation artifacts complicated the interpretation. Finally, HAADF-STEM-EDX results provided relevant information about particles in the low nm range, since, by applying this technique, no particles smaller than 50 nm were observed in accordance with ESEM-EDX.

The Development and Atomic Structure of Zinc Oxide Crystals Grown within Polymers from Vapor Phase Precursors.

Sequential infiltration synthesis (SIS), also known as vapor phase infiltration (VPI), is a quickly expanding technique that allows growth of inorganic materials within polymers from vapor phase precursors. With an increasing materials library, which encompasses numerous organometallic precursors and polymer chemistries, and an expanding application space, the importance of understanding the mechanisms that govern SIS growth is ever increasing. In this work, we studied the growth of polycrystalline ZnO clusters and particles in three representative polymers: poly(methyl methacrylate), SU-8, and polymethacrolein using vapor phase diethyl zinc and water. Utilizing two atomic resolution methods, high-resolution scanning transmission electron microscopy and synchrotron X-ray absorption spectroscopy, we probed the evolution of ZnO nanocrystals size and crystallinity level inside the polymers with advancing cycles─from early nucleation and growth after a single cycle, through the formation of nanometric particles within the films, and to the coalescence of the particles upon polymer removal and thermal treatment. Through in situ Fourier transform infrared spectroscopy and microgravimetry, we highlight the important role of water molecules throughout the process and the polymers' hygroscopic level that leads to the observed differences in growth patterns between the polymers, in terms of particle size, dispersity, and the evolution of crystalline order. These insights expand our understanding of crystalline materials growth within polymers and enable rational design of hybrid materials and polymer-templated inorganic nanostructures.

Mesoscale characterization of osseointegration around an additively manufactured genistein-coated implant.

Given the hierarchical nature of bone and bone interfaces, osseointegration, namely the formation of a direct bone-implant contact, is best evaluated using a multiscale approach. However, a trade-off exists between field of view and spatial resolution, making it challenging to image large volumes with high resolution. In this study, we combine established electron microscopy techniques to probe bone-implant interfaces at the microscale and nanoscale with plasma focused ion beam-scanning electron microscopy (PFIB-SEM) tomography to evaluate osseointegration at the mesoscale. This characterization workflow is demonstrated for bone response to an additively manufactured Ti-6Al-4V implant which combines engineered porosity to facilitate bone ingrowth and surface functionalization via genistein, a phytoestrogen, to counteract bone loss in osteoporosis. SEM demonstrated new bone formation at the implant site, including in the internal implant pores. At the nanoscale, scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy confirmed the gradual nature of the bone-implant interface. By leveraging mesoscale analysis with PFIB-SEM tomography that captures large volumes of bone-implant interface with nearly nanoscale resolution, the presence of mineral ellipsoids varying in size and orientation was revealed. In addition, a well-developed lacuno-canalicular network and mineralization fronts directed both towards the implant and away from it were highlighted.

Crystallographic Pathways to Tailoring Metal-Insulator Transition through Oxygen Transport in VO2.

The metal-insulator (MI) transition of vanadium dioxide (VO2) is effectively modulated by oxygen vacancies, which decrease the transition temperature and insulating resistance. Oxygen vacancies in thin films can be driven by oxygen transport using electrochemical potential. This study delves into the role of crystallographic channels in VO2 in facilitating oxygen transport and the subsequent tuning of electrical properties. A model system is designed with two types of VO2 thin films: (100)- and (001)-oriented, where channels align parallel and perpendicular to the surface, respectively. Growing an oxygen-deficient TiO2 layer on these VO2 films prompted oxygen transport from VO2 to TiO2. Notably, in (001)-VO2 film, where oxygen ions move along the open channels, the oxygen migration deepens the depleted region beyond that in (100)-VO2, leading to more pronounced changes in metal-insulator transition behaviors. The findings emphasize the importance of understanding the intrinsic crystal structure, such as channel pathways, in controlling ionic defects and customizing electrical properties for applications.

Cell Wall Microdomains in the External Glands of Utricularia dichotoma Traps.

The genus Utricularia (bladderworts) species are carnivorous plants that prey on invertebrates using traps with a high-speed suction mechanism. The outer trap surface is lined by dome-shaped glands responsible for secreting water in active traps. In terminal cells of these glands, the outer wall is differentiated into several layers, and even cell wall ingrowths are covered by new cell wall layers. Due to changes in the cell wall, these glands are excellent models for studying the specialization of cell walls (microdomains). The main aim of this study was to check if different cell wall layers have a different composition. Antibodies against arabinogalactan proteins (AGPs) were used, including JIM8, JIM13, JIM14, MAC207, and JIM4. The localization of the examined compounds was determined using immunohistochemistry techniques and immunogold labeling. Differences in composition were found between the primary cell wall and the cell secondary wall in terminal gland cells. The outermost layer of the cell wall of the terminal cell, which was cuticularized, was devoid of AGPs (JIM8, JIM14). In contrast, the secondary cell wall in terminal cells was rich in AGPs. AGPs localized with the JIM13, JIM8, and JIM14 epitopes occurred in wall ingrowths of pedestal cells. Our research supports the hypothesis of water secretion by the external glands.

Separation of Damage Mechanisms in Full Forward Rod Extruded Case-Hardening Steel 16MnCrS5 Using 3D Image Segmentation.

In general, formed components are lightweight as well as highly economic and resource efficient. However, forming-induced ductile damage, which particularly affects the formation and growth of pores, has not been considered in the design of components so far. Therefore, an evaluation of forming-induced ductile damage would enable an improved design and take better advantage of the lightweight nature as it affects the static and dynamic mechanical material properties. To quantify the amount, morphology and distribution of the pores, advanced scanning electron microscopy (SEM) methods such as scanning transmission electron microscopy (STEM) and electron channeling contrast imaging (ECCI) were used. Image segmentation using a deep learning algorithm was applied to reproducibly separate the pores from inclusions such as manganese sulfide inclusions. This was achieved via layer-by-layer ablation of the case-hardened steel 16MnCrS5 (DIN 1.7139, AISI/SAE 5115) with a focused ion beam (FIB). The resulting images were reconstructed in a 3D model to gain a mechanism-based understanding beyond the previous 2D investigations.

New Poisson denoising method for pulse-count STEM imaging.

With the recent progress in the development of detectors in electron microscopy, it has become possible to directly count the number of electrons per pixel, even with a scintillator-type detector, by incorporating a pulse-counting module. To optimize a denoising method for electron counting imaging, in this study, we propose a Poisson denoising method for atomic-resolution scanning transmission electron microscopy images. Our method is based on the Markov random field model and Bayesian inference, and we can reduce the electron dose by a factor of about 15 times or further below. Moreover, we showed that the method of reconstruction from multiple images without integrating them performs better than that from an integrated image.

Do Arabinogalactan Proteins Occur in the Transfer Cells of Utricularia dichotoma?

Species in the genus Utricularia are carnivorous plants that prey on invertebrates using traps of leaf origin. The traps are equipped with numerous different glandular trichomes. Trichomes (quadrifids) produce digestive enzymes and absorb the products of prey digestion. The main aim of this study was to determine whether arabinogalactan proteins (AGPs) occur in the cell wall ingrowths in the quadrifid cells. Antibodies (JIM8, JIM13, JIM14, MAC207, and JIM4) that act against various groups of AGPs were used. AGP localization was determined using immunohistochemistry techniques and immunogold labeling. AGPs localized with the JIM13, JIM8, and JIM14 epitopes occurred in wall ingrowths of the pedestal cell, which may be related to the fact that AGPs regulate the formation of wall ingrowths but also, due to the patterning of the cell wall structure, affect symplastic transport. The presence of AGPs in the cell wall of terminal cells may be related to the presence of wall ingrowths, but processes also involve vesicle trafficking and membrane recycling, in which these proteins participate.

Interface Design beyond Epitaxy: Oxide Heterostructures Comprising Symmetry-Forbidden Interfaces.

Epitaxial growth of thin-film heterostructures is generally considered the most successful procedure to obtain interfaces of excellent structural and electronic quality between 3D materials. However, these interfaces can only join material systems with crystal lattices of matching symmetries and lattice constants. This article presents a novel category of interfaces, the fabrication of which is membrane-based and does not require epitaxial growth. These interfaces therefore overcome the limitations imposed by epitaxy. Leveraging the additional degrees of freedom gained, atomically clean interfaces are demonstrated between threefold symmetric sapphire and fourfold symmetric SrTiO3. Atomic-resolution imaging reveals structurally well-defined interfaces with a novel moiré-type reconstruction.

High-Entropy Transition Metal Phosphorus Trichalcogenides for Rapid Sodium Ion Diffusion.

High-entropy strategies are regarded as a powerful means to enhance performance in energy storage fields. The improved properties are invariably ascribed to entropy stabilization or synergistic cocktail effect. Therefore, the manifested properties in such multicomponent materials are usually unpredictable. Elucidating the precise correlations between atomic structures and properties remains a challenge in high-entropy materials (HEMs). Herein, atomic-resolution scanning transmission electron microscopy annular dark field (STEM-ADF) imaging and four dimensions (4D)-STEM are combined to directly visualize atomic-scale structural and electric information in high-entropy FeMnNiVZnPS3. Aperiodic stacking is found in FeMnNiVZnPS3 accompanied by high-density strain soliton boundaries (SSBs). Theoretical calculation suggests that the formation of such structures is attributed to the imbalanced stress of distinct metal-sulfur bonds in FeMnNiVZnPS3. Interestingly, the electric field concentrates along the two sides of SSBs and gradually diminishes toward the two-dimensional (2D) plane to generate a unique electric field gradient, strongly promoting the ion-diffusion rate. Accordingly, high-entropy FeMnNiVZnPS3 demonstrates superior ion-diffusion coefficients of 10-9.7-10-8.3 cm2 s-1 and high-rate performance (311.5 mAh g-1 at 30 A g-1). This work provides an alternative way for the atomic-scale understanding and design of sophisticated HEMs, paving the way for property engineering in multi-component materials.

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.

Engineering Oxide Epitaxy beyond Substrate Constraint.

Orientation engineering is a crucial aspect of thin film growth, and it is rather challenging to engineer film epitaxy beyond the substrate constraint. Guided by density functional theory calculations, we use SrRuO3 (SRO) as a buffer layer and successfully deposit [111]-oriented CoFe2O4 (CFO) on [001]-, [110]-, and [111]-oriented SrTiO3 (STO) substrates. This enables subsequent growth of [111]-oriented functional oxides, such as PbTiO3 (PTO), overcoming the constraint of the substrate. This strategy is quite general and applicable to lanthanum aluminate and yttria-stabilized zirconia substrates as well. X-ray Φ scans and atomic resolution aberration-corrected scanning transmission electron microscopy (AC-STEM) reveal detailed epitaxial relations in each of the cases, with four variants of [111]-CFO found on [001]-STO and two variants found on [110]-STO, formed to mitigate the large lattice misfit strain between the film and substrate. Our strategy thus provides a general pathway for orientation engineering of oxide epitaxy beyond substrate constraint.

Density and porosity analyses of porous hybrid microparticles containing gas in closed pores using centrifugal liquid sedimentation-dynamic light scattering combined analytical method.

Porous hybrid microparticles are characterized by their densities and porosities. Consequently, the evaluation for density and porosity of porous hybrid microparticles in liquids is crucial for predicting the transport of particles in the atmosphere, human body, and industrial processes. However, direct measurement of the density and porosity of porous hybrid microparticles in liquids remains a challenge. In this study, we investigated the centrifugal sedimentation of polystyrene-silica hybrid microparticles with and without gas-containing closed pores. A centrifugal liquid sedimentation-dynamic light scattering combined analytical method was employed to determine the apparent densities of hybrid microparticles with and without gas-containing closed pores. The porosity of the hybrid microparticles with gas-containing closed pores was elucidated based on the inner buoyancy, which is a centrifugal force generated by the presence of low-density gas inside numerous closed pores. Further, the inner gas buoyancy was analyzed to estimate the particle porosity in liquids. The results obtained in this study confirmed the feasibility of utilizing the proposed method to determine the apparent density and porosity of porous hybrid microparticles in liquids.