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.

DFT-Assisted Investigation of the Electric Field and Charge Density Distribution of Pristine and Defective 2D WSe2 by Differential Phase Contrast Imaging.

Most properties of solid materials are defined by their internal electric field and charge density distributions which so far are difficult to measure with high spatial resolution. Especially for 2D materials, the atomic electric fields influence the optoelectronic properties. In this study, the atomic-scale electric field and charge density distribution of WSe2 bi- and trilayers are revealed using an emerging microscopy technique, differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). For pristine material, a higher positive charge density located at the selenium atomic columns compared to the tungsten atomic columns is obtained and tentatively explained by a coherent scattering effect. Furthermore, the change in the electric field distribution induced by a missing selenium atomic column is investigated. A characteristic electric field distribution in the vicinity of the defect with locally reduced magnitudes compared to the pristine lattice is observed. This effect is accompanied by a considerable inward relaxation of the surrounding lattice, which according to first principles DFT calculation is fully compatible with a missing column of Se atoms. This shows that DPC imaging, as an electric field sensitive technique, provides additional and remarkable information to the otherwise only structural analysis obtained with conventional STEM imaging.

Preparation and Synergy of Supported Ru0 and Pd0 for Rapid Chlorate Reduction at pH 7.

Chlorate (ClO3-) is a common water pollutant due to its gigantic scale of production, wide applications in agriculture and industry, and formation as a toxic byproduct in various water treatment processes. This work reports on the facile preparation, mechanistic elucidation, and kinetic evaluation of a bimetallic catalyst for highly active ClO3- reduction into Cl-. Under 1 atm H2 and 20 °C, PdII and RuIII were sequentially adsorbed and reduced on a powdered activated carbon support, affording Ru0-Pd0/C from scratch within only 20 min. The Pd0 particles significantly accelerated the reductive immobilization of RuIII as >55% dispersed Ru0 outside Pd0. At pH 7, Ru-Pd/C shows a substantially higher activity of ClO3- reduction (initial turnover frequency >13.9 min-1 on Ru0; rate constant at 4050 L h-1 gmetal-1) than reported catalysts (e.g., Rh/C, Ir/C, Mo-Pd/C) and the monometallic Ru/C. In particular, Ru-Pd/C accomplished the reduction of concentrated 100 mM ClO3- (turnover number > 11,970), whereas Ru/C was quickly deactivated. In the bimetallic synergy, Ru0 rapidly reduces ClO3- while Pd0 scavenges the Ru-passivating ClO2- and restores Ru0. This work demonstrates a simple and effective design for heterogeneous catalysts tailored for emerging water treatment needs.

Accelerating Catalytic Oxyanion Reduction with Inert Metal Hydroxides.

Adding CrIII or AlIII salts into the water suspension of platinum group metal (PGM) catalysts accelerated oxyanion pollutant reduction by up to 600%. Our initial attempts of adding K2CrVIO4, K2CrVI2O7, or KCrIII(SO4)2 into Pd/C enhanced BrO3- reduction with 1 atm H2 by 6-fold. Instrument characterizations and kinetic explorations collectively confirmed the immobilization of reduced CrVI as CrIII(OH)3 on the catalyst surface. This process altered the ζ-potentials from negative to positive, thus substantially enhancing the Langmuir-Hinshelwood adsorption equilibrium constant for BrO3- onto Pd/C by 37-fold. Adding AlIII(OH)3 from alum at pH 7 achieved similar enhancements. The Cr-Pd/C and Al-Pd/C showed top-tier efficiency of catalytic performance (normalized with Pd dosage) among all the reported Pd catalysts on conventional and nanostructured support materials. The strategy of adding inert metal hydroxides works for diverse PGMs (palladium and rhodium), substrates (BrO3- and ClO3-), and support materials (carbon, alumina, and silica). This work shows a simple, inexpensive, and effective example of enhancing catalyst activity and saving PGMs for environmental applications.

Benchmark Tests of Atom Segmentation Deep Learning Models with a Consistent Dataset.

The information content of atomic-resolution scanning transmission electron microscopy (STEM) images can often be reduced to a handful of parameters describing each atomic column, chief among which is the column position. Neural networks (NNs) are high performance, computationally efficient methods to automatically locate atomic columns in images, which has led to a profusion of NN models and associated training datasets. We have developed a benchmark dataset of simulated and experimental STEM images and used it to evaluate the performance of two sets of recent NN models for atom location in STEM images. Both models exhibit high performance for images of varying quality from several different crystal lattices. However, there are important differences in performance as a function of image quality, and both models perform poorly for images outside the training data, such as interfaces with large difference in background intensity. Both the benchmark dataset and the models are available using the Foundry service for dissemination, discovery, and reuse of machine learning models.

How Fast is Your Detector? The Effect of Temporal Response on Image Quality.

With increasing interest in high-speed imaging, there should be an increased interest in the response times of our scanning transmission electron microscope detectors. Previous works have highlighted and contrasted the performance of various detectors for quantitative compositional or structural studies, but here, we shift the focus to detector temporal response, and the effect this has on captured images. The rise and decay times of eight detectors' single-electron response are reported, as well as measurements of their flatness, roundness, smoothness, and ellipticity. We develop and apply a methodology for incorporating the temporal detector response into simulations, showing that a loss of resolution is apparent in both the images and their Fourier transforms. We conclude that the solid-state detector outperforms the photomultiplier tube-based detectors in all areas bar a slightly less elliptical central hole and is likely the best detector to use for the majority of applications. However, using the tools introduced here, we encourage users to effectively evaluate which detector is most suitable for their experimental needs.

Atomic-Scale Mapping and Quantification of Local Ruddlesden-Popper Phase Variations.

The Ruddlesden-Popper (An+1BnO3n+1) compounds are highly tunable materials whose functional properties can be dramatically impacted by their structural phase n. The negligible differences in formation energies for different n can produce local structural variations arising from small stoichiometric deviations. Here, we present a Python analysis platform to detect, measure, and quantify the presence of different n-phases based on atomic-resolution scanning transmission electron microscopy (STEM) images. We employ image phase analysis to identify horizontal Ruddlesden-Popper faults within the lattice images and quantify the local structure. Our semiautomated technique considers effects of finite projection thickness, limited fields of view, and lateral sampling rates. This method retains real-space distribution of layer variations allowing for spatial mapping of local n-phases to enable quantification of intergrowth occurrence and qualitative description of their distribution suitable for a wide range of layered materials.

Revealing momentum-dependent electron-phonon and phonon-phonon coupling in complex materials with ultrafast electron diffuse scattering.

ABSTRACT: Despite their fundamental role in determining many important properties of materials, detailed momentum-dependent information on the strength of electron-phonon and phonon-phonon coupling across the entire Brillouin zone has remained elusive. Ultrafast electron diffuse scattering (UEDS) is a recently developed technique that is making a significant contribution to these questions. Here, we describe both the UEDS methodology and the information content of ultrafast, photoinduced changes in phonon-diffuse scattering from single-crystal materials. We present results obtained from Ni, WSe2, and TiSe2, materials that are characterized by a complex interplay between electronic (charge, spin) and lattice degrees of freedom. We demonstrate the power of this technique by unraveling carrier-phonon and phonon-phonon interactions in both momentum and time and following nonequilibrium phonon dynamics in detail on ultrafast time scales. By combining ab initio calculations with ultrafast diffuse electron scattering, insights into electronic and magnetic dynamics that impact UEDS indirectly can also be obtained.

Biological Reduction of a U(V)-Organic Ligand Complex.

Metal-reducing microorganisms such as Shewanella oneidensis MR-1 reduce highly soluble species of hexavalent uranyl (U(VI)) to less mobile tetravalent uranium (U(IV)) compounds. The biologically mediated immobilization of U(VI) is being considered for the remediation of U contamination. However, the mechanistic underpinnings of biological U(VI) reduction remain unresolved. It has become clear that a first electron transfer occurs to form pentavalent (U(V)) intermediates, but it has not been definitively established whether a second one-electron transfer can occur or if disproportionation of U(V) is required. Here, we utilize the unusual properties of dpaea2- ((dpaeaH2═bis(pyridyl-6-methyl-2-carboxylate)-ethylamine)), a ligand forming a stable soluble aqueous complex with U(V), and investigate the reduction of U(VI)-dpaea and U(V)-dpaea by S. oneidensis MR-1. We establish U speciation through time by separating U(VI) from U(IV) by ion exchange chromatography and characterize the reaction end-products using U M4-edge high resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy. We document the reduction of solid phase U(VI)-dpaea to aqueous U(V)-dpaea but, most importantly, demonstrate that of U(V)-dpaea to U(IV). This work establishes the potential for biological reduction of U(V) bound to a stabilizing ligand. Thus, further work is warranted to investigate the possible persistence of U(V)-organic complexes followed by their bioreduction in environmental systems.

Atomic-Scale Fabrication of In-Plane Heterojunctions of Few-Layer MoS2 via In Situ Scanning Transmission Electron Microscopy.

Layered MoS2 is a prospective candidate for use in energy harvesting, valleytronics, and nanoelectronics. Its properties strongly related to its stacking configuration and the number of layers. Due to its atomically thin nature, understanding the atomic-level and structural modifications of 2D transition metal dichalcogenides is still underdeveloped, particularly the spatial control and selective precision. Therefore, the development of nanofabrication techniques is essential. Here, an atomic-scale approach used to sculpt 2D few-layer MoS2 into lateral heterojunctions via in situ scanning/transmission electron microscopy (STEM/TEM) is developed. The dynamic evolution is tracked using ultrafast and high-resolution filming equipment. The assembly behaviors inherent to few-layer 2D-materials are observed during the process and included the following: scrolling, folding, etching, and restructuring. Atomic resolution STEM is employed to identify the layer variation and stacking sequence for this new 2D-architecture. Subsequent energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy analyses are performed to corroborate the elemental distribution. This sculpting technique that is established allows for the formation of sub-10 nm features, produces diverse nanostructures, and preserves the crystallinity of the material. The lateral heterointerfaces created in this study also pave the way for the design of quantum-relevant geometries, flexible optoelectronics, and energy storage devices.

STEM tomography analysis of the trypanosome transition zone.

The protist Trypanosoma brucei is an emerging model for the study of cilia and flagella. Here, we used scanning transmission electron microscopy (STEM) tomography to describe the structure of the trypanosome transition zone (TZ). At the base of the TZ, nine transition fibres irradiate from the B microtubule of each doublet towards the membrane. The TZ adopts a 9 + 0 structure throughout its length of ∼300 nm and its lumen contains an electron-dense structure. The proximal portion of the TZ has an invariant length of 150 nm and is characterised by a collarette surrounding the membrane and the presence of electron-dense material between the membrane and the doublets. The distal portion exhibits more length variation (from 55 to 235 nm) and contains typical Y-links. STEM analysis revealed a more complex organisation of the Y-links compared to what was reported by conventional transmission electron microscopy. Observation of the very early phase of flagellum assembly demonstrated that the proximal portion and the collarette are assembled early during construction. The presence of the flagella connector that maintains the tip of the new flagellum to the side of the old was confirmed and additional filamentous structures making contact with the membrane of the flagellar pocket were also detected. The structure and potential functions of the TZ in trypanosomes are discussed, as well as its mode of assembly.

Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography.

Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach.

Direct Observation of Impurity Segregation at Dislocation Cores in an Ionic Crystal.

Dislocations, one-dimensional lattice defects, are known to strongly interact with impurity atoms in a crystal. This interaction is generally explained on the basis of the long-range strain field of the dislocation. In ionic crystals, the impurity-dislocation interactions must be influenced by the electrostatic effect in addition to the strain effect. However, such interactions have not been verified yet. Here, we show a direct evidence of the electrostatic impurity-dislocation interaction in α-Al2O3 by visualizing the dopant atom distributions at dislocation cores using atomic-resolution scanning transmission electron microscopy (STEM). It was found that the dopant segregation behaviors strongly depend on the kind of elements, and their valence states are considered to be a critical factor. The observed segregation behaviors cannot be explained by the elastic interactions only, but can be successfully understood if the electrostatic interactions are taken into account. The present findings will lead to the precise and quantitative understanding of impurity induced dislocation properties in many materials and devices.

Catalytic Partial Oxidation of Cyclohexane by Bimetallic Ag/Pd Nanoparticles on Magnesium Oxide.

The liquid-phase oxidation of cyclohexane to cyclohexanol and cyclohexanone was investigated by synthesizing and testing an array of heterogeneous catalysts comprising: monometallic Ag/MgO, monometallic Pd/MgO and a set of bimetallic AgPd/MgO catalysts. Interestingly, Ag/MgO was capable of a conversion comparable to current industrial routes of approximately 5 %, and with a high selectivity (up to 60 %) to cyclohexanol, thus making Ag/MgO an attractive system for the synthesis of intermediates for the manufacture of nylon fibres. Furthermore, following the doping of Ag nanoparticles with Pd, the conversion increased up to 10 % whilst simultaneously preserving a high selectivity to the alcohol. Scanning transmission electron microscopy and energy dispersive spectroscopy of the catalysts showed a systematic particle-size-composition variation with the smaller Ag-Pd nanoparticles being statistically richer in Pd. Analysis of the reaction mixture by electron paramagnetic resonance (EPR) spectroscopy coupled with the spin-trapping technique showed the presence of large amounts of alkoxy radicals, thus providing insights for a possible reaction mechanism.

On the origin of extraordinary cyclic strengthening of the austenitic stainless steel Sanicro 25 during fatigue at 700°C.

The origin of the extraordinary strengthening of the highly-alloyed austenitic stainless steel Sanicro 25 during cyclic loading at 700°C was investigated by use of advanced scanning transmission electron microscopy (STEM). Along with substantial change of dislocation structure, nucleation of two distinct populations of nanoparticles was revealed. Fully coherent Cu-rich nanoparticles were observed homogeneously dispersed with high density along with nanometer-sized incoherent NbC carbides precipitating on dislocations during cyclic loading. Probe-corrected HAADF STEM imaging was used to characterize the atomic structure of nanoparticles. Compositional analysis was conducted using both EELS and high spatial resolution EDS. High temperature exposure induced precipitation of a high density of coherent Cu-rich nanoparticles while strain-induced nucleation of incoherent NbC nanoparticles leads to retardation of dislocation movement. The pinning effects and associated obstacles to dislocation motion prevent recovery and formation of the localized low-energy cellular structures. As a consequence, the alloy exhibits remarkable cyclic hardening at elevated temperature.

Atomic Ordering in InGaN Alloys within Nanowire Heterostructures.

Ternary III-nitride based nanowires (NWs) are promising for optoelectronic applications by offering advantageous design and control over composition, structure, and strain. Atomic-level chemical ordering in wurtzite InGaN alloys along the c-plane direction with a 1:1 periodicity within InGaN/GaN NW heterostructures was investigated by scanning transmission electron microscopy. Atomic-number-sensitive imaging contrast was used to simultaneously assign the In-rich and Ga-rich planes and determine the crystal polarity to differentiate unique sublattice sites. The nonrandom occupation of the c-planes in the InGaN alloys is confirmed by the occurrence of additional superlattice spots in the diffraction pattern within the ternary alloy. Compositional modulations in the ordered InGaN was further studied using atomic-resolution elemental mapping, outlining the substantial In-enrichment. Confirming the preferential site occupation of In-atoms provides experimental validation for the previous theoretical model of ordered InGaN alloys in bulk epilayers based on differences in surface site energy. Therefore, this study strongly suggests that atomic ordering in InGaN has a surface energetics-induced origin. Optimization of atomic ordering, in particular in III-nitride NW heterostructures, could be an alternative design tool toward desirable structural and compositional properties for various device applications operating at longer visible wavelengths.

Analysis of acute brain slices by electron microscopy: a correlative light-electron microscopy workflow based on Tokuyasu cryo-sectioning.

Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu's protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of antigenicity. Finally, an important feature of this approach is that the fluorescence of the GFP signal is preserved throughout the entire preparation process until the last step before electron microscopy.

Aberration-corrected STEM for atomic-resolution imaging and analysis.

Aberration-corrected scanning transmission electron microscopes are able to form electron beams smaller than 100 pm, which is about half the size of an average atom. Probing materials with such beams leads to atomic-resolution images, electron energy loss and energy-dispersive X-ray spectra obtained from single atomic columns and even single atoms, and atomic-resolution elemental maps. We review briefly how such electron beams came about, and show examples of applications. We also summarize recent developments that are propelling aberration-corrected scanning transmission electron microscopes in new directions, such as complete control of geometric aberration up to fifth order, and ultra-high-energy resolution EELS that is allowing vibrational spectroscopy to be carried out in the electron microscope.

Atomic-scale imaging of cation ordering in inverse spinel Zn2SnO4 nanowires.

By using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) coupled with density functional theory (DFT) calculations, we demonstrate the atomic-level imaging of cation ordering in inverse spinel Zn2SnO4 nanowires. This cation ordering was identified as 1:1 ordering of Zn(2+) and Sn(4+) at the octahedral sites of the inverse spinel crystal with microscopic symmetry transition from original cubic Fd3̅m to orthorhombic Imma group. This ordering generated a 67.8% increase in the elastic modulus and 1-2 order of magnitude lower in the electric conductivity and electron mobility compared to their bulk counterpart.

Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans.

Introduction: Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions. Methods: In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria. Results and Discussion: Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.