Hydrogen Plasma Inhibits Ion Beam Restructuring of GaP.

Focused ion beam (FIB) techniques are employed widely for nanofabrication and processing of materials and devices. However, ion irradiation often gives rise to severe damage due to atomic displacements that cause defect formation, migration, and clustering within the ion-solid interaction volume. The resulting restructuring degrades the functionality of materials and limits the utility of FIB ablation and nanofabrication techniques. Here we show that such restructuring can be inhibited by performing FIB irradiation in a hydrogen plasma environment via chemical pathways that modify defect binding energies and transport kinetics, as well as material ablation rates. The method is minimally invasive and has the potential to greatly expand the utility of FIB nanofabrication techniques in processing functional materials and devices.

Rubidium and Cesium Ion-Induced Electron and Ion Signals for Scanning Ion Microscopy Applications.

Scanning ion microscopy applications of novel focused ion beam (FIB) systems based on ultracold rubidium (Rb) and cesium (Cs) atoms were investigated via ion-induced electron and ion yields. Results measured on the Rb+ and Cs+ FIB systems were compared with results from commercially available gallium (Ga+) FIB systems to verify the merits of applying Rb+ and Cs+ for imaging. The comparison shows that Rb+ and Cs+ have higher secondary electron (SE) yields on a variety of pure element targets than Ga+, which implies a higher signal-to-noise ratio can be achieved for the same dose in SE imaging using Rb+/Cs+ than Ga+. In addition, analysis of the ion-induced ion signals reveals that secondary ions dominate Cs+ induced ion signals while the Rb+/Ga+ induced signals contain more backscattered ions.

Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography.

Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the viral genome, together with the viral proteins VP24 and VP35. We employed cryo-electron tomography of cells transfected with viral proteins and infected with model Ebola virus to illuminate assembly intermediates, as well as a 9 Å map of the complete intracellular assembly. This structure reveals a previously unresolved third and outer layer of NP complexed with VP35. The intrinsically disordered region, together with the C-terminal domain of this outer layer of NP, provides the constant width between intracellular nucleocapsid bundles and likely functions as a flexible tether to the viral matrix protein in the virion. A comparison of intracellular nucleocapsids with prior in-virion nucleocapsid structures reveals that the nucleocapsid further condenses vertically in the virion. The interfaces responsible for nucleocapsid assembly are highly conserved and offer targets for broadly effective antivirals.

The molecular architecture of the nuclear basket.

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.

Microstructural characterization of gadolinium-rich phases in titanium alloys.

This study explores the microstructural characteristics of gadolinium (Gd)-rich phases in titanium (Ti) alloys through comprehensive electron microscopy analysis. The Ti alloys were produced using plasma arc melting and subsequently hot-forged. Elaborate material characterization, including scanning electron microscopy, electron backscatter diffraction, and energy dispersive spectroscopy, revealed the formation of round or angular Gd oxides and elongated Gd-rich grains within the alloy. High-magnification transmission electron microscopy and X-ray diffraction confirmed the presence of the FCC-type γ-Gd phase, influenced by the oxygen intake during casting, coexisting with Gd2O3 due to their similar crystal structures. The study also observed internal twins in the Gd grains, potentially delaying the transformation to the stable α-Gd phase. The significant mechanical property differences between the Gd-rich phases and the Ti matrix caused defects at phase interfaces during hot processing, weakening the Gd phase. This work enhances the understanding of Gd phase formation and its implications on the mechanical properties of Ti-Gd alloys.

An Integrated Solution to FIB-Induced Hydride Artifacts in Pure Zirconium.

The preparation method of transmission electron microscopy (TEM) samples for pure zirconium was successfully executed using a focused ion beam (FIB) system. These samples unveiled artifact hydrides induced during the FIB sample preparation process, which resulted from stress damage, ion implantation, and ion irradiation. An innovative solution was proposed to effectively reduce the effect of artifact hydrides for FIB-prepared samples of hydrogen-sensitive materials, such as zirconium alloys. This development lays the groundwork for further research on the micro/nanostructures of zirconium alloys after ion irradiation, thereby facilitating the study of corrosion mechanisms and the prediction of service life for nuclear fuel cladding materials. Furthermore, the solution proposed in this study is also applicable to TEM sample preparation using FIB for other hydrogen-sensitive materials such as titanium, magnesium, and palladium.

Recent technical advances in cellular cryo-electron tomography.

Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.

Level set simulation of focused ion beam sputtering of a multilayer substrate.

The evolution of a multilayer sample surface during focused ion beam processing was simulated using the level set method and experimentally studied by milling a silicon dioxide layer covering a crystalline silicon substrate. The simulation took into account the redeposition of atoms simultaneously sputtered from both layers of the sample as well as the influence of backscattered ions on the milling process. Monte Carlo simulations were applied to produce tabulated data on the angular distributions of sputtered atoms and backscattered ions. Two sets of test structures including narrow trenches and rectangular boxes with different aspect ratios were experimentally prepared, and their cross sections were visualized in scanning transmission electron microscopy images. The superimposition of the calculated structure profiles onto the images showed a satisfactory agreement between simulation and experimental results. In the case of boxes that were prepared with an asymmetric cross section, the simulation can accurately predict the depth and shape of the structures, but there is some inaccuracy in reproducing the form of the left sidewall of the structure with a large amount of the redeposited material. To further validate the developed simulation approach and gain a better understanding of the sputtering process, the distribution of oxygen atoms in the redeposited layer derived from the numerical data was compared with the corresponding elemental map acquired by energy-dispersive X-ray microanalysis.

The Microstructural Reconstruction of Variously Sintered Ni-SDC Cermets Using Focused Ion Beam Scanning Electron Microscopy Nanotomography.

This work focuses in-depth on the quantitative relationships between primary first-order microstructural parameters (i.e., volume fractions of various phases and particle size distribution) with the more complex second-order topological features (i.e., connectivity of phases, three-phase boundary length (TPBL), interfacial areas, or tortuosity). As a suitable model material, a cermet nickel/samaria-doped ceria (Ni-SDC) is used as an anode in a solid oxide fuel cell (SOFC). A microstructure description of nano-sized Ni-SDC cermets, fabricated at various sintering conditions from 1100 °C to 1400 °C, was performed using FIB-SEM nanotomography. The samples were serially sectioned employing a fully automated slicing procedure with active drift correction algorithms and an auto-focusing routine to obtain a series of low-loss BSE images. Advanced image processing algorithms were developed and applied directly to image data volume. The microstructural-topological relationships are crucial for the microstructure optimisation and, thus, the improvement of the corresponding electrode performance. Since all grains of individual phases (Ni, SDC, or pores) did not percolate, special attention was given to the visualisation of the so-called active TPBL. Based on the determined microstructure characteristics of the prepared Ni-SDC cermets, including simulations of gas flow and pressure drop, thermal treatment at 1200 °C was recognised as the most appropriate sintering temperature.

Preparation of Bunyavirus-Infected Cells for Electron Cryo-Tomography.

Cellular electron cryo-tomography (cryoET) produces high-resolution three-dimensional images of subcellular structures in a near-native frozen-hydrated state. These three-dimensional images are obtained by recording a series of two-dimensional tilt images on a transmission electron cryo-microscope that are subsequently back-projected to form a tomogram. Key to a successful experiment is however a high-quality sample. This chapter outlines a basic workflow for the preparation of cellular cryoET samples. It covers the preparation of infected cells on electron cryo-microscopy grids and the vitrification by plunge-freezing and clipping of grids into AutoGrid rims. It also provides a general overview of the workflow for thinning the vitrified cells by focused ion beam (FIB) milling. Although this book is dedicated to Rift Valley fever virus research, the present protocol may also be applied to any other research subject where high-resolution structural insight into intracellular processes is desired.

Nanoporous Gold Thin Films as Substrates to Analyze Liquids by Cryo-atom Probe Tomography.

Cryogenic atom probe tomography (cryo-APT) is being developed to enable nanoscale compositional analyses of frozen liquids. Yet, the availability of readily available substrates that allow for the fixation of liquids while providing sufficient strength to their interface is still an issue. Here, we propose the use of 1-2-µm-thick binary alloy film of gold-silver sputtered onto flat silicon, with sufficient adhesion without an additional layer. Through chemical dealloying, we successfully fabricate a nanoporous substrate, with an open-pore structure, which is mounted on a microarray of Si posts by lift-out in the focused-ion beam system, allowing for cryogenic fixation of liquids. We present cryo-APT results obtained after cryogenic sharpening, vacuum cryo-transfer, and analysis of pure water on the top and inside the nanoporous film. We demonstrate that this new substrate has the requisite characteristics for facilitating cryo-APT of frozen liquids, with a relatively lower volume of precious metals. This complete workflow represents an improved approach for frozen liquid analysis, from preparation of the films to the successful fixation of the liquid in the porous network, to cryo-APT.

Development and Fabrication of a Multi-Layer Planar Solar Light Absorber Achieving High Absorptivity and Ultra-Wideband Response from Visible Light to Infrared.

The objective of this study is to create a planar solar light absorber that exhibits exceptional absorption characteristics spanning from visible light to infrared across an ultra-wide spectral range. The eight layered structures of the absorber, from top to bottom, consisted of Al2O3, Ti, Al2O3, Ti, Al2O3, Ni, Al2O3, and Al. The COMSOL Multiphysics® simulation software (version 6.0) was utilized to construct the absorber model and perform simulation analyses. The first significant finding of this study is that as compared to absorbers featuring seven-layered structures (excluding the top Al2O3 layer) or using TiO2 or SiO2 layers as substituted for Al2O3 layer, the presence of the top Al2O3 layer demonstrated superior anti-reflection properties. Another noteworthy finding was that the top Al2O3 layer provided better impedance matching compared to scenarios where it was absent or replaced with TiO2 or SiO2 layers, enhancing the absorber's overall efficiency. Consequently, across the ultra-wideband spectrum spanning 350 to 1970 nm, the average absorptivity reached an impressive 96.76%. One significant novelty of this study was the utilization of various top-layer materials to assess the absorption and reflection spectra, along with the optical-impedance-matching properties of the designed absorber. Another notable contribution was the successful implementation of evaporation techniques for depositing and manufacturing this optimized absorber. A further innovation involved the use of transmission electron microscopy to observe the thickness of each deposition layer. Subsequently, the simulated and calculated absorption spectra of solar energy across the AM1.5 spectrum for both the designed and fabricated absorbers were compared, demonstrating a match between the measured and simulated results.

The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography.

Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.

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.

Template-assisted growth of Ga-based nanoparticle clusters on Si: effect of post-annealing process on the Ga ion beam exposed 2D arrays fabricated by focused ion beam nanolithography.

We demonstrate template-assisted growth of gallium-based nanoparticle clusters on silicon substrate using a focused ion beam (FIB) nanolithography technique. The nanolithography counterpart of the technique steers a focussed 30 kV accelerated gallium ion beam on the surface of Si to create template patterns of two-dimensional dot arrays. Growth of the nanoparticles is governed by two vital steps namely implantation of gallium into the substrate via gallium beam exposure and formation of the stable nanoparticles on the surface of the substrate by subsequent annealing at elevated temperature in ammonia atmosphere. The growth primarily depends on the dose of implanted gallium which is in the order of 107atoms per spot and it is also critically influenced by the temperature and duration of the post-annealing treatment. By controlling the growth parameters, it is possible to obtain one particle per spot and particle densities as high as 109particles per square centimetre could be achieved in this case. The demonstrated growth process, utilizing the advantages of FIB nanolithography, is categorized under the guided organization approach as it combines both the classical top-down and bottom-up approaches. Patterned growth of the particles could be utilized as templates or nucleation sites for the growth of an organized array of nanostructures or quantum dot structures.

Spatially Controlled Phase Transition in MoTe2 Driven by Focused Ion Beam Irradiations.

Phase transitions play an important role in tuning the physical properties of two-dimensional (2D) materials as well as developing their high-performance device applications. Here, we reported the observation of a phase transition in few-layered MoTe2 flakes by the irradiation of gallium (Ga+) ions using a focused ion beam (FIB) system. The semiconducting 2H phase of MoTe2 can be controllably converted to the metallic 1T'-like phase via Te defect engineering during irradiations. By taking advantage of the nanometer-sized Ga+ ion probe proved by FIB, in-plane 1T'-2H homojunctions of MoTe2 at submicrometer scale can be fabricated. Furthermore, we demonstrate the improvement of device performance (on-state current over 2 orders of magnitude higher) in MoTe2 transistors using the patterned 1T'-like phase regions as contact electrodes. Our study provides a new strategy to drive the phase transitions in MoTe2, tune their properties, and develop high-performance devices, which also extends the applications of FIB technology in 2D materials and their devices.

Quantifying Microstructure Features for High-Performance Solid Oxide Cells.

The drive for sustainable energy solutions has spurred interest in solid oxide fuel cells (SOFCs). This study investigates the impact of sintering temperature on SOFC anode microstructures using advanced 3D focused ion beam-scanning electron microscopy (FIB-SEM). The anode's ceramic-metal composition significantly influences electrochemical performance, making optimization crucial. Comparing cells sintered at different temperatures reveals that a lower sintering temperature enhances yttria-stabilized zirconia (YSZ) and nickel distribution, volume, and particle size, along with the triple-phase boundary (TPB) interface. Three-dimensional reconstructions illustrate that the cell sintered at a lower temperature exhibits a well-defined pore network, leading to increased TPB density. Hydrogen flow simulations demonstrate comparable permeability for both cells. Electrochemical characterization confirms the superior performance of the cell sintered at the lower temperature, displaying higher power density and lower total cell resistance. This FIB-SEM methodology provides precise insights into the microstructure-performance relationship, eliminating the need for hypothetical structures and enhancing our understanding of SOFC behavior under different fabrication conditions.

Facilitating Atom Probe Tomography of 2D MXene Films by In Situ Sputtering.

2D materials are emerging as promising nanomaterials for applications in energy storage and catalysis. In the wet chemical synthesis of MXenes, these 2D transition metal carbides and nitrides are terminated with a variety of functional groups, and cations such as Li+ are often used to intercalate into the structure to obtain exfoliated nanosheets. Given the various elements involved in their synthesis, it is crucial to determine the detailed chemical composition of the final product, in order to better assess and understand the relationships between composition and properties of these materials. To facilitate atom probe tomography analysis of these materials, a revised specimen preparation method is presented in this study. A colloidal Ti3C2Tz MXene solution was processed into an additive-free free-standing film and specimens were prepared using a dual beam scanning electron microscope/focused ion beam. To mechanically stabilize the fragile specimens, they were coated using an in situ sputtering technique. As various 2D material inks can be processed into such free-standing films, the presented approach is pivotal for enabling atom probe analysis of other 2D materials.

Shaping single crystalline BaTiO3nanostructures by focused neon or helium ion milling.

The realization of perovskite oxide nanostructures with controlled shape and dimensions remains a challenge. Here, we investigate the use of helium and neon focused ion beam (FIB) milling in an ion microscope to fabricate BaTiO3nanopillars of sub-500 nm in diameter starting from BaTiO3(001) single crystals. Irradiation of BaTiO3with He ions induces the formation of nanobubbles inside the material, eventually leading to surface swelling and blistering. Ne-FIB is shown to be suitable for milling without inducing surface swelling. The resulting structures are defect-free single crystal nanopillars, which are enveloped, on the top and lateral sidewalls, by a point defect-rich crystalline region and an outer Ne-rich amorphous layer. The amorphous layer can be selectively etched by dipping in diluted HF. The geometry and beam-induced damage of the milled nanopillars depend strongly on the patterning parameters and can be well controlled. Ne ion milling is shown to be an effective method to rapidly prototype BaTiO3crystalline nanostructures.

Systematic study of FIB-induced damage for the high-quality TEM sample preparation.

Nowadays, a focused Ga ion beam (FIB) with a scanning electron microscopy (SEM) system has been widely used to prepare the thin-foil sample for transmission electron microscopy (TEM) or scanning TEM (STEM) observation. An establishment of a solid strategy for a reproducible high-quality sample preparation process is essential to carry out high-quality (S)TEM analysis. In this work, the FIB damages introduced by Ga+ beam were investigated both experimentally and stopping and range of ions in matter (SRIM) simulation for silicon (Si), gallium nitride (GaN), indium phosphide (InP), and gallium arsenide (GaAs) semiconductors. It has been revealed that experimental investigations of the FIB-induced damage are in good agreement with SRIM simulation by defining the damage as not only "amorphization" but also "crystal distortion". The systematic evaluation of FIB damages shown in this paper should be indispensable guidance for reliable (S)TEM sample preparation.