Serial sectioning methods for 3D investigations in materials science

Correlative Fluorescent Scanning Probe Nanotomography Used to Study the Intracellular Distribution of Doxorubicin in MCF-7 Human Breast Adenocarcinoma Cells

Developing technologies for efficient targeted drug delivery for oncotherapy requires new methods to analyze the features of micro- and nanoscale distributions of antitumor drugs in cells and tissues. A new approach to three-dimensional analysis of the intracellular distribution of cytostatics was developed using fluorescence scanning optical-probe nanotomography. A correlative analysis of the nanostructure and distribution of injected doxorubicin in MCF-7 human breast adenocarcinoma cells revealed the features of drug penetration and accumulation in the cell. The technology is based on the principles of scanning optical probe nanotomography and is applicable to studying the distribution patterns of various fluorescent or fluorescence-labelled substances in cells and tissues.

Three-dimensional SEM, TEM, and STEM for analysis of large-scale biological systems

A major aim in structural cell biology is to analyze intact cells in three dimensions, visualize subcellular structures, and even localize proteins at the best possible resolution in three dimensions. Though recently developed electron microscopy tools such as electron tomography, or three-dimensional (3D) scanning electron microscopy, offer great resolution in three dimensions, the challenge is that, the better the resolution, usually the smaller the volume under investigation. Several different approaches to overcome this challenge were presented at the Microscopy Conference in Vienna in 2021. These tools include array tomography, batch tomography, or scanning transmission electron tomography, all of which can nowadays be extended toward correlative light and electron tomography, with greatly increased 3D information. Here, we review these tools, describe the underlying procedures, and discuss their advantages and limits.

Advanced characterization of 3D structure and porosity of ordinary portland cement (OPC) mortar using plasma focused ion beam tomography and X-ray computed tomography

The visualization and quantification of pore networks and main phases have been critical research topics in cementitious materials as many critical mechanical and chemical properties and infrastructure reliability rely on these 3-D characteristics. In this study, we realized the mesoscale serial sectioning and analysis up to ∼80 μm by ∼90 μm by ∼60 μm on portland cement mortar using plasma focused ion beam (PFIB) for the first time. The workflow of working with mortar and PFIB was established applying a prepositioned hard silicon mask to reduce curtaining. Segmentation with minimal human interference was performed using a trained neural network, in which multiple types of segmentation models were compared. Combining PFIB analysis at microscale with X-ray micro-computed tomography, the analysis of capillary pores and air voids ranging from hundreds of nanometers (nm) to millimeters (mm) can be conducted. The volume fraction of large capillary pores and air voids are 11.5% and 12.7%, respectively. Moreover, the skeletonization of connected capillary pores clearly shows fluid transport pathways, which is a key factor determining durability performance of concrete in aggressive environments. Another interesting aspect of the FIB tomography is the reconstruction of anhydrous phases, which could enable direct study of hydration kinetics of individual cement phases. This article is protected by copyright. All rights reserved.

Three-Dimensional Morphology and Analysis of Widmanstätten Sideplates Ferrite

The three-dimensional (3D) morphology and crystal structure of Widmanstätten sideplate ferrite were simulated using a focused ion beam (FIB) scanning electron microscope equipped with electron backscatter diffraction (EBSD). The primary Widmanstätten sideplates nucleated and grew directly at the austenite grain boundary (GB). A certain included angle between the sideplates and the austenite GB was observed. The sideplates grew approximately parallel to the grain, and were separated by a small-angle GB. The primary Widmanstätten sideplates are best described as “∃” shaped, with a long intermediate ferrite strip. The interface with the austenite GB was smooth and flat, and the sideplate surface contained pits and holes. The secondary Widmanstätten sideplates nucleated and grew on the surface of the proeutectoid GB ferrite, with the sideplates and GB ferrite perpendicular to each other. Sideplates parallel to one another grew into the grain, and were separated by small-angle GB. The 3D morphology was distinguished by its “comb” shape. The sideplates’ tail was clustered and its front end remained sharp. The contact side of the GB ferrite was smooth and flat. The surface contained several uneven pits and defects.

Oxygen Loss in Layered Oxide Cathodes for Li-Ion Batteries: Mechanisms, Effects, and Mitigation

Layered lithium transition metal oxides derived from LiMO₂ (M = Co, Ni, Mn, etc.) have been widely adopted as the cathodes of Li-ion batteries for portable electronics, electric vehicles, and energy storage. Oxygen loss in the layered oxides is one of the major factors leading to cycling-induced structural degradation and its associated fade in electrochemical performance. Herein, we review recent progress in understanding the phenomena of oxygen loss and the resulting structural degradation in layered oxide cathodes. We first present the major driving forces leading to the oxygen loss and then describe the associated structural degradation resulting from the oxygen loss. We follow this analysis with a discussion of the kinetic pathways that enable oxygen loss, and then we address the resulting electrochemical fade. Finally, we review the possible approaches toward mitigating oxygen loss and the associated electrochemical fade as well as detail novel analytical methods for probing the oxygen loss.

Liposome Sterile Filtration Characterization via X-ray Computed Tomography and Confocal Microscopy

Two high resolution, 3D imaging techniques were applied to visualize and characterize sterilizing grade dual-layer filtration of liposomes, enabling membrane structure to be related with function and performance. Two polyethersulfone membranes with nominal retention ratings of 650 nm and 200 nm were used to filter liposomes of an average diameter of 143 nm and a polydispersity index of 0.1. Operating conditions including differential pressure were evaluated. X-ray computed tomography at a pixel size of 63 nm was capable of resolving the internal geometry of each membrane. The respective asymmetry and symmetry of the upstream and downstream membranes could be measured, with pore network modeling used to identify pore sizes as a function of distance through the imaged volume. Reconstructed 3D digital datasets were the basis of tortuous flow simulation through each porous structure. Confocal microscopy visualized liposome retention within each membrane using fluorescent dyes, with bacterial challenges also performed. It was found that increasing pressure drop from 0.07 MPa to 0.21 MPa resulted in differing fluorescent retention profiles in the upstream membrane. These results highlighted the capability for complementary imaging approaches to deepen understanding of liposome sterilizing grade filtration.

(Un)expected Similarity of the Temporary Adhesive Systems of Marine, Brackish, and Freshwater Flatworms

Many free-living flatworms have evolved a temporary adhesion system, which allows them to quickly attach to and release from diverse substrates. In the marine Macrostomum lignano, the morphology of the adhesive system and the adhesion-related proteins have been characterised. However, little is known about how temporary adhesion is performed in other aquatic environments. Here, we performed a 3D reconstruction of the M. lignano adhesive organ and compared it to the morphology of five selected Macrostomum, representing two marine, one brackish, and two freshwater species. We compared the protein domains of the two adhesive proteins, as well as an anchor cell-specific intermediate filament. We analysed the gene expression of these proteins by in situ hybridisation and performed functional knockdowns with RNA interference. Remarkably, there are almost no differences in terms of morphology, protein regions, and gene expression based on marine, brackish, and freshwater habitats. This implies that glue components produced by macrostomids are conserved among species, and this set of two-component glue functions from low to high salinity. These findings could contribute to the development of novel reversible biomimetic glues that work in all wet environments and could have applications in drug delivery systems, tissue adhesives, or wound dressings.

Dissecting Biological and Synthetic Soft-Hard Interfaces for Tissue-Like Systems

Soft and hard materials at interfaces exhibit mismatched behaviors, such as mismatched chemical or biochemical reactivity, mechanical response, and environmental adaptability. Leveraging or mitigating these differences can yield interfacial processes difficult to achieve, or inapplicable, in pure soft or pure hard phases. Exploration of interfacial mismatches and their associated (bio)chemical, mechanical, or other physical processes may yield numerous opportunities in both fundamental studies and applications, in a manner similar to that of semiconductor heterojunctions and their contribution to solid-state physics and the semiconductor industry over the past few decades. In this review, we explore the fundamental chemical roles and principles involved in designing these interfaces, such as the (bio)chemical evolution of adaptive or buffer zones. We discuss the spectroscopic, microscopic, (bio)chemical, and computational tools required to uncover the chemical processes in these confined or hidden soft-hard interfaces. We propose a soft-hard interaction framework and use it to discuss soft-hard interfacial processes in multiple systems and across several spatiotemporal scales, focusing on tissue-like materials and devices. We end this review by proposing several new scientific and engineering approaches to leveraging the soft-hard interfacial processes involved in biointerfacing composites and exploring new applications for these composites.

Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach

Although X-ray based 3D virtual histology is an emerging tool for the analysis of biological tissue, it falls short in terms of specificity when compared to conventional histology. Thus, the aim was to establish a novel approach that combines 3D information provided by microCT with high specificity that only (immuno-)histochemistry can offer. For this purpose, we developed a software frontend, which utilises an elastic transformation technique to accurately co-register various histological and immunohistochemical stainings with free propagation phase contrast synchrotron radiation microCT. We demonstrate that the precision of the overlay of both imaging modalities is significantly improved by performing our elastic registration workflow, as evidenced by calculation of the displacement index. To illustrate the need for an elastic co-registration approach we examined specimens from a mouse model of breast cancer with injected metal-based nanoparticles. Using the elastic transformation pipeline, we were able to co-localise the nanoparticles to specifically stained cells or tissue structures into their three-dimensional anatomical context. Additionally, we performed a semi-automated tissue structure and cell classification. This workflow provides new insights on histopathological analysis by combining CT specific three-dimensional information with cell/tissue specific information provided by classical histology.

Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples

Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.

Nondestructive Quantitative Evaluation of Yarns and Fabrics and Determination of Contact Area of Fabrics Using the X-ray Microcomputed Tomography System for Skin-Textile Friction Analysis

In different mechanical conditions, repetitive friction in combination with pressure, shear, temperature, and moisture leads to skin discomfort and imposes the risks of developing skin injuries such as blisters and pressure ulcers, frequently reported in athletes, military personnel, and in people with compromised skin conditions and/or immobility. Textiles next to skin govern the skin microclimate, have the potential to influence the mechanical contact with skin, and contribute to skin comfort and health. The adhesion-friction theory suggests that contact area is a critical factor to influence adhesion, and therefore, friction force. Friction being a surface phenomenon, most of the studies concentrated on the surface profile or topographic analysis of textiles. This study investigated both the surface profiles and the inner construction of the fabrics through X-ray microcomputed tomographic three-dimensional image analysis. A novel nondestructive method to evaluate yarn and fabric structural details quantitatively and calculate contact area (in fiber area %) experimentally has been reported in this paper. Plain and satin-woven fabrics with different thread densities and made from 100% cotton ring-spun yarns with two different linear densities (40 and 60 Ne) were investigated in this study. The measurements from the tomographic images (pixel size: 1.13 μm) and the fiber area % analysis were in good agreement to comprehend and compare the yarn and fabric properties reported. The fiber area % as reported in this paper can be used to evaluate the skin-textile interfaces and quantitatively determine the contact area under different physical, mechanical, and microclimatic conditions to understand the actual skin-textile interaction during any physical activity or sports. The proposed method can be helpful in engineering textiles to enhance skin comfort and prevent injuries, such as blisters and pressure ulcers, in diversified application areas, including but not limited to, sports and healthcare apparel, military apparel, and firefighter's protective clothing. In addition, the images were capable of precisely evaluating yarn diameters, crimp %, and packing factor as well as fabric thickness, volumetric densities, and cover factors as compared with those obtained from theoretical evaluation and existing classical test methods. All these findings suggest that the proposed new method can reliably be used to quantify the yarn and fabric characteristics, compare their functionality, and understand the structural impacts in an objective and nondestructive way.

2D single crystal Bragg-dip mapping by time-of-flight energy-resolved neutron imaging on IMAT@ISIS

The cold neutron imaging and diffraction instrument IMAT, at the second target station of the pulsed neutron and muon source ISIS, is used to investigate bulk mosaicity within as-cast single crystal CMSX-4 and CMSX-10 Ni-base superalloys. Within this study, neutron transmission spectrum is recorded by each pixel within the microchannel plate image detector. The movement of the lowest transmission wavelength within a specified Bragg-dip for each pixel is tracked. The resultant Bragg-dip shifting has enabled crystallographic orientation mapping of bulk single crystal specimens with good spatial resolution. The total acquisition time required to collect sufficient statistics for each test is ~ 3 h. In this work, the influence of a change in bulk solidification conditions on the variation in single crystal mosaicity was investigated. Misorientation of the (001) crystallographic plane has been visualised and a new spiral twisting solidification phenomena observed. This proof of concept work establishes time-of-flight energy-resolved neutron imaging as a fundamental characterisation tool for understanding and visualising mosaicity within metallic single crystals and provides the foundation for post-mortem deduction of the shape of the solid/liquid isotherm.

Slicing Spheroids in Microfluidic Devices for Morphological and Immunohistochemical Analysis

Microfluidic devices utilizing spheroids play important roles in in vitro experimental systems to closely simulate morphological and biochemical characteristics of the in vivo tumor microenvironment. For the observation and analysis of the inner structure of spheroids, sectioning is an efficient approach. However, conventional microfluidic devices are difficult for sectioning, and therefore, spheroids inside the microfluidic channels have not been sliced well. We proposed a microfluidic device created from embedding resin for sectioning. Spheroids were cultured, embedded by resin, and sectioned in the microfluidic device. Slices of the sectioned spheroids yielded clear images at the cellular level. According to morphological and immunohistochemical analyses of the slices of the spheroid, specific protein distribution was observed.

Experimental steering of electron microscopy studies using prior X-ray computed tomography

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Using microCT pre-scans to accurately steer serial block face SEM.

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High throughput screening and mapping samples to reduce time hunting for features of interest.

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Using microCT to optimise specimen preparation and staining.

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Using microCT to guide site-specific TEM sample preparation.

Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) can provide unrivalled high-resolution images of specific features and volumes of interest. However, the regions interrogated are typically very small, and sample preparation is both time-consuming and destructive. Here we consider how prior X-ray micro-computed tomography (microCT) presents an opportunity to increase the efficiency of electron microscopy in biology. We demonstrate how it can be used to; select the most promising samples and target site-specific locations; provide a wider context of the location being interrogated (multiscale correlative imaging); guide sample preparation and 3D imaging schemes; as well as quantify the effects of destructive sample preparation and staining procedures. We present a workflow utilising open source software in which microCT can be used either broadly, or precisely, to experimentally steer and inform subsequent electron microscopy studies. As automated sample registration procedures are developed to enable correlative microscopy, experimental steering by prior CT could be beneficially routinely incorporated into many experimental workflows.

Multi-modal plasma focused ion beam serial section tomography of an organic paint coating

Pigment distributions have a critical role in the corrosion protection properties of organic paint coatings, but they are difficult to image in 3D over statistically significant volumes and at sufficiently high spatial resolutions required for detailed analysis. Here we report, for the first time, large volume analytical serial sectioning tomography of an organic composite coating using a xenon Plasma Focused Ion Beam (PFIB) combined with secondary electron imaging, energy dispersive X-ray (EDX) spectrum imaging (SI) and electron backscattered diffraction (EBSD). Together these techniques provide a comprehensive quantitative description of the physical orientation and distribution of the pigments within a model marine ballast tank coating, as well as their crystallographic and elemental characterisation. Polymers and organic materials are challenging because of their propensity for ion beam damage and possible beam heating effects. Our novel, optimised block preparation technique permits automated data acquisition with minimal operator intervention, and can have significant applications for the structural and chemical characterisation of a wide range of organic materials. Our results revealed that the paint contained 7.5 vol% aluminium flakes and 25 vol% quartz particles. The aluminium flakes were oriented parallel to the substrate surface, which is beneficial in terms of the corrosion protection capability of the coating.

Correlation of Materials Property and Performance with Internal Structures Evolvement Revealed by Laboratory X-ray Tomography

Although X-rays generated from a laboratory-based tube cannot be compared with synchrotron radiation in brilliance and monochromaticity, they are still viable and accessible in-house for ex situ or interrupted in situ X-ray tomography. This review mainly demonstrates recent works using laboratory X-ray tomography coupled with the measurements of properties or performance testing under various conditions, such as thermal, stress, or electric fields. Evolvements of correlated internal structures for some typical materials were uncovered. The damage features in a graded metallic 3D mesh and a metallic glass under mechanical loading were revealed and investigated. Micro-voids with thermal treatment and void healing phenomenon with electropulsing were clearly demonstrated and quantitatively analyzed. The substance transfer around an electrode of a Li-S battery and the protective performance of a Fe-based metallic glass coating on stainless steel were monitored through electrochemical processes. It was shown that in situ studies of the laboratory X-ray tomography were suitable for the investigation of structure change under controlled conditions and environments. An extension of the research for in situ laboratory X-ray tomography can be expected with supplementary novel techniques for internal strain, global 3D grain orientation, and a fast tomography strategy.

Electron tomography-a tool for ultrastructural 3D visualization in cell biology and histology

Electron tomography (ET) was developed to overcome some of the problems associated reconstructing three-dimensional (3D) images from 2D election microscopy data from ultrathin slices. Virtual sections of semithin sample are obtained by incremental rotation of the target and this information is used to assemble a 3D image. Herein, we provide an instruction to ET including the physical principle, possibilities, and limitations. We review the development of innovative methods and highlight important investigations performed in our department and with our collaborators. ET has opened up the third dimension at the ultrastructural level and represents a milestone in structural molecular biology.

Biological serial block face scanning electron microscopy at improved z-resolution based on Monte Carlo model

Serial block-face electron microscopy (SBEM) provides nanoscale 3D ultrastructure of embedded and stained cells and tissues in volumes of up to 10⁷ µm³. In SBEM, electrons with 1–3 keV energies are incident on a specimen block, from which backscattered electron (BSE) images are collected with x, y resolution of 5–10 nm in the block-face plane, and successive layers are removed by an in situ ultramicrotome. Spatial resolution along the z-direction, however, is limited to around 25 nm by the minimum cutting thickness. To improve the z-resolution, we have extracted depth information from BSE images acquired at dual primary beam energies, using Monte Carlo simulations of electron scattering. The relationship between depth of stain and ratio of dual-energy BSE intensities enables us to determine 3D structure with a ×2 improvement in z-resolution. We demonstrate the technique by sub-slice imaging of hepatocyte membranes in liver tissue.

3D high resolution imaging for microelectronics: A multi-technique survey on copper pillars

In microelectronics, recently developed 3D integration offers the possibility to stack the dice or wafers vertically instead of putting their different parts next to one another, in order to save space. As this method becomes of greater interest, the need for 3D imaging techniques becomes higher. We here report a study about different 3D characterization techniques applied to copper pillars, which are used to stack different dice together. Destructive techniques such as FIB/SEM, FIB/FIB, and PFIB/PFIB slice and view protocols have been assessed, as well as non-destructive ones, such as laboratory-based and synchrotron-based computed tomographies. A comparison of those techniques in the specific case of copper pillars is given, taking into account the constraints linked to the microelectronics industry, mainly concerning resolution and sample throughput. Laboratory-based imaging techniques are shown to be relevant in the case of punctual analyses, while synchrotron based tomographies offer highly resolved volumes for larger batches of samples.

Time-of-Flight Three Dimensional Neutron Diffraction in Transmission Mode for Mapping Crystal Grain Structures

The physical properties of polycrystalline materials depend on their microstructure, which is the nano- to centimeter scale arrangement of phases and defects in their interior. Such microstructure depends on the shape, crystallographic phase and orientation, and interfacing of the grains constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional neutron diffraction (ToF 3DND). Compared to existing analogous X-ray diffraction techniques, ToF 3DND enables studies of samples that can be both larger in size and made of heavier elements. Moreover, ToF 3DND facilitates the use of complicated sample environments. The basic ToF 3DND setup, utilizing an imaging detector with high spatial and temporal resolution, can easily be implemented at a time-of-flight neutron beamline. The technique was developed and tested with data collected at the Materials and Life Science Experimental Facility of the Japan Proton Accelerator Complex (J-PARC) for an iron sample. We successfully reconstructed the shape of 108 grains and developed an indexing procedure. The reconstruction algorithms have been validated by reconstructing two stacked Co-Ni-Ga single crystals, and by comparison with a grain map obtained by post-mortem electron backscatter diffraction (EBSD).

A novel design of a scanning probe microscope integrated with an ultramicrotome for serial block-face nanotomography

We present a new concept of a combined scanning probe microscope (SPM)/ultramicrotome apparatus. It enables "slice-and-view" scanning probe nanotomography measurements and 3D reconstruction of the bulk sample nanostructure from series of SPM images after consecutive ultrathin sections. The sample is fixed on a flat XYZ scanning piezostage mounted on the ultramicrotome arm. The SPM measuring head with a cantilever tip and a laser-photodiode tip detection system approaches the sample for SPM measurements of the block-face surface immediately after the ultramicrotome sectioning is performed. The SPM head is moved along guides that are also fixed on the ultramicrotome arm. Thereby, relative dysfunctional displacements of the tip, the sample, and the ultramicrotome knife are minimized. The design of the SPM head enables open frontal optical access to the sample block-face adapted for high-resolution optical lenses for correlative SPM/optical microscopy applications. The new system can be used in a wide range of applications for the study of 3D nanostructures of biological objects, biomaterials, polymer nanocomposites, and nanohybrid materials in various SPM and optical microscopy measuring modes.

Cryo scanning probe nanotomography study of the structure of alginate microcarriers

Nanostructure of microparticles of decellularized rat liver ECM on spherical alginate hydrogel microcarriers is analyzed by cryo scanning probe nanotomography.

Assessing structural correlations and heterogeneity length scales in functional porous polymers from physical reconstructions

A general, model-free, quantitative approach to the key morphological properties of a porous polymer monolith is presented. After 3D reconstruction, image-based analysis delivers detailed spatial and spatially correlated information on the structural heterogeneities in the void space and the polymer skeleton. Identified heterogeneities, which limit the monolith's performance in targeted applications, are traced back to the preparation process.

Three-dimensional microstructural characterization of porous cubic zirconia

A set of cubic zirconia samples were investigated using 3-dimensional electron backscatter diffraction (3D EBSD) to analyze the grain structure, grain boundary networks and pore morphology. 3D EBSD is a variation of conventional EBSD, whereby a focused ion beam (FIB) is used in a dual beam scanning electron microscope (SEM) i.e. FIB-SEM to mill away material and to create 'serial sections' through the material being analyzed. Each new surface revealed is subject to an EBSD scan, which continues sequentially until a desired volume of material has been removed. In this manner, many consecutive 2D EBSD scans can be rendered in 3D to gain a greater insight of microstructural features and parameters. The three samples were examined in order to determine the effect of differences in the manufacturing process used for each. For each sample, a volume of ca. 15,000 μm(3) was studied. The analysis of several microstructure parameters revealed a strong dependence on manufacturing conditions. Subsequently, the results of 3D EBSD analysis were compared to conventional 2D EBSD. Significant differences between the values of microstructure parameters determined by 2D and 3D EBSD were observed.

Focused particle beam nano-machining: the next evolution step towards simulation aided process prediction

During the last decade, focused ion beam processing has been developed from traditionally used Ga(+) liquid ion sources towards higher resolution gas field ion sources (He(+) and Ne(+)). Process simulations not only improve the fundamental understanding of the relevant ion-matter interactions, but also enable a certain predictive power to accelerate advances. The historic 'gold' standard in ion-solid simulations is the SRIM/TRIM Monte Carlo package released by Ziegler, Ziegler and Biersack 2010 Nucl. Instrum. Methods B 268 1818-23. While SRIM/TRIM is very useful for a myriad of applications, it is not applicable for the understanding of the nanoscale evolution associated with ion beam nano-machining as the substrate does not evolve with the sputtering process. As a solution for this problem, a new, adapted simulation code is briefly overviewed and finally addresses these contributions. By that, experimentally observed Ne(+) beam sputter profiles can be explained from a fundamental point of view. Due to their very good agreement, these simulations contain the potential for computer aided optimization towards predictable sputter processes for different nanotechnology applications. With these benefits in mind, the discussed simulation approach represents an enormous step towards a computer based master tool for adaptable ion beam applications in the context of industrial applications.