Mineralization of microbial biomass is a common phenomenon in geothermal habitats, but knowledge of the structure of the minerals formed in these environments is limited. A combination of spectroscopic, microscopic, and stable isotopic methods, as well as the chemical analysis of spring water, were employed in the present study to characterize calcium carbonate minerals deposited in filamentous cyanobacterial mats in different locations of La Duke hot spring, a circumneutral thermal feature near the north entrance of Yellowstone National Park, Montana, USA. Calcite was the primary crystalline mineral phase associated with biofilm-containing deposits closest to the source of the spring and the suspended microbial biomass in a pool further from the source. The carbonate minerals at all sites occurred as aggregated granules, ~2 μm in diameter, in close association with the microbial biomass. Only in the deposits closest to the source were the granules organized as laminated structures interspersed with microbial biomass. The calcium carbonate grains contained two distinct regions: a dense monolithic calcite core and a porous dendritic periphery containing organic matter (OM). Electron energy loss spectroscopy (EELS) indicated that the voids were infilled with OM and carbonates. The EELS technique was employed to distinguish the source of carbon in the organic matter and carbonate mixture. The studies of carbon isotope compositions of the calcium carbonates and the saturation indices for calcite in the spring waters suggest that processes (abiotic vs. biotic) controlling the carbonate formation may vary among the sampling sites.

The development and implementation of high-stability monochromators in state-of-the-art aberration-corrected scanning transmission electron microscopes has enabled materials characterization with an energy resolution as good as 3 meV. This allows the vibrational modes, which would otherwise be obscured by the energy spread of the electron beam, to be probed with very high precision in molecular materials. Since the vibrational energies depend on the weight of the atomic nuclei, vibrational spectroscopy can distinguish isotopes whose only difference lies in their neutron content. This opens up isotopic analysis and mapping in transmission electron microscopy as two important new research areas. Here, we review the monochromated electron energy loss spectroscopy (EELS) instrumentation, discuss optimal methods for probing beam-sensitive materials without destroying them, and review key nanoscale isotope-resolved results.

Using high intensity beams of fast electrons, the transmission electron microscope (TEM) and scanning transmission electron microscope (STEM) enable comprehensive characterization of rocks and minerals at micrometre to sub-nanometre scales. This review outlines the ways in which samples of Earth and planetary materials can be rendered sufficiently thin for TEM and STEM work, and highlights the significant advances in site-specific preparation enabled by the focused ion beam (FIB) technique. Descriptions of the various modes of TEM and STEM imaging, electron diffraction and X-ray and electron spectroscopy are outlined, with an emphasis on new technologies that are of particular relevance to geoscientists. These include atomic-resolution Z-contrast imaging by high-angle annular dark-field STEM, electron crystallography by precession electron diffraction, spectrum mapping using X-rays and electrons, chemical imaging by energy-filtered TEM and true atomic-resolution imaging with the new generation of aberration-corrected microscopes. Despite the sophistication of modern instruments, the spatial resolution of imaging, diffraction and X-ray and electron spectroscopy work on many natural materials is likely to remain limited by structural and chemical damage to the thin samples during TEM and STEM.

In Pixar’s Inside Out, the character Joy proclaims, “Do you ever look at someone and wonder what’s going on inside?” Driven by similar curiosity, the scientific community has developed remarkable in situ characterization tools to visualize the inner workings of complex, dynamic systems, elucidating their functions and enabling next-generation technologies. This article describes our research developing plasmonic techniques to visualize dynamic chemical transformations in situ with nanometer-scale resolution. As a model system, we investigated the hydrogenation and dehydrogenation of palladium nanocrystals. Using environmental electron microscopy and spectroscopy, we monitored this reaction with sub-2-nm spatial resolution and millisecond time resolution. Particles of different sizes, shapes, and crystallinities exhibit distinct thermodynamic and kinetic properties, highlighting several important design principles for next-generation catalysts and energy-storage devices.

Phase separation of InxGa1−xN into Ga-rich and In-rich regions has been studied by electron energy-loss spectroscopy (EELS) in a monochromated, aberration corrected scanning transmission electron microscope (STEM). We analyze the full spectral information contained in EELS of InGaN, combining for the first time studies of high-energy and low-energy ionization edges, plasmon, and valence losses. Elemental maps of the N K, In M4,5 and Ga L2,3 edges recorded by spectrum imaging at 100 kV reveal sub-nm fluctuations of the local indium content. The low energetic edges of Ga M4,5 and In N4,5 partially overlap with the plasmon peaks. Both have been fitted iteratively to a linear superimposition of reference spectra for GaN, InN, and InGaN, providing a direct measurement of phase separation at the nm-scale. Bandgap measurements are limited in real space by scattering delocalization rather than the electron beam size to ∼10 nm for small bandgaps, and their energetic accuracy by the method of fitting the onset of the joint density of states rather than energy resolution. For an In0.62Ga0.38N thin film we show that phase separation occurs on several length scales.

The field of plasmonics has transformed the ability to control nanoscale light-matter interactions with applications ranging from high-efficiency photovoltaic modules to ultrasensitive biodetectors, electromagnetic cloaks, and subwavelength integrated photonic circuits. This article summarizes my group’s efforts to contribute to this burgeoning field, with emphasis on our research in quantum plasmonics and optical-frequency magnetism. First, we explore the plasmon resonances of individual nanoparticles as they transition from a classical to a quantum-influenced regime. We then utilize these results to directly monitor hydrogen absorption and desorption in individual palladium nanocrystals. Subsequently, using real-time manipulation of plasmonic particles, we investigate plasmonic coupling between pairs of particles separated by nanometer- and angstrom-scale gaps. For sufficiently small separations, we observe the effects of quantum tunneling between particles on their plasmonic resonances. Finally, using the properties of coupled metallic nanoparticles, we demonstrate the colloidal synthesis of an isotropic metafluid or “metamaterial paint” that exhibits a strong optical-frequency magnetic response and the potential for negative permeabilities and negative refractive indices.

The dehydrogenated microstructure of the lithium borohydride-yttrium hydride (LiBH4-YH3) composite obtained at 350°C under 0.3 MPa of hydrogen and static vacuum was investigated by transmission electron microscopy combined with a focused ion beam technique. The dehydrogenation reaction between LiBH4 and YH3 into LiH and YB4 takes place under 0.3 MPa of hydrogen, which produces YB4 nano-crystallites that are uniformly distributed in the LiH matrix. This microstructural feature seems to be beneficial for rehydrogenation of the dehydrogenation products. On the other hand, the dehydrogenation process is incomplete under static vacuum, leading to the unreacted microstructure, where YH3 and YH2 crystallites are embedded in LiBH4 matrix. High resolution imaging confirmed the presence of crystalline B resulting from the self-decomposition of LiBH4. However, Li2B12H12, which is assumed to be present in the LiBH4 matrix, was not clearly observed.

By measuring the energy losses of high-energy electrons transmitted through a thin sample, electron energy-loss spectroscopy provides information on the local electronic structure in materials. Using electron beams smaller than 0.1 nm, the technique provides exquisite sensitivity to changes in valence and coordination of the excited atoms such that local changes in the bonding environment are probed with a resolution approaching the Ångstrøm level, with an energy resolution competitive with complementary techniques such as x-ray absorption spectroscopy. With the development of spectroscopic imaging in the scanning transmission electron microscope, this technique can be used to map, at the atomic level, the composition of atomic columns and the valence of atoms at defects, interfaces, and surfaces. Recent applications of this technique are provided as examples showing the potential of the method for materials research.

We evaluate the probe forming capability of a JEOL 2200FS transmission electron microscope equipped with a spherical aberration (Cs) probe corrector. The achievement of a real space sub-Angstrom (0.1 nm) probe for scanning transmission electron microscopy (STEM) imaging is demonstrated by acquisition and modeling of high-angle annular dark-field STEM images. We show that by optimizing the illumination system, large probe currents and large collection angles for electron energy loss spectroscopy (EELS) can be combined to yield EELS fine structure data spatially resolved to the atomic scale. We demonstrate the probe forming flexibility provided by the additional lenses in the probe corrector in several ways, including the formation of nanometer-sized parallel beams for nanoarea electron diffraction, and the formation of focused probes for convergent beam electron diffraction with a range of convergence angles. The different probes that can be formed using the probe corrected STEM opens up new applications for electron microscopy and diffraction.

We examine chemical mapping of reaction phases in a Cu-Al multilayer system using low-loss electron energy loss spectroscopy spectrum imaging and image spectroscopy techniques. The sensitivity of the plasmon peak position and shape to various crystal structures and phases is exploited using postprocessing of spectra into second derivative plasmon maps and line scans. Analytical transmission electron microscopy is complemented by studies of the orientation relationship of the multilayer system using high-resolution electron microscopy of interfaces and selected area diffraction. The techniques have been applied to the Cu-Al multilayer sample and sharply bound epitaxial phases are found, before and after heat treatment.

Electron energy loss spectroscopy (EELS), X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy have been used to study iron catalysts for Fischer–Tropsch synthesis. When silica-containing iron oxide precursors are activated in flowing CO, the iron phase segregates into iron carbide crystallites, leaving behind some unreduced iron oxide in an amorphous state coexisting with the silica binder. The iron carbide crystallites are found covered by characteristic amorphous carbonaceous surface layers. These amorphous species are difficult to analyze by traditional catalyst characterization techniques, which lack spatial resolution. Even a surface-sensitive technique such as XPS shows only broad carbon or iron peaks in these catalysts. As we show in this work, EELS allows us to distinguish three different carbonaceous species: reactive amorphous carbon, graphitic carbon, and carbidic carbon in the bulk of the iron carbide particles. The carbidic carbon K edge shows an intense “π*” peak with an edge shift of about 1 eV to higher energy loss compared to that of the π* of amorphous carbon film or graphitic carbon. EELS analysis of the oxygen K edge allows us to distinguish the amorphous unreduced iron phase from the silica binder, indicating these are two separate phases. These results shed light onto the complex phase transformations that accompany the activation of iron catalysts for Fischer–Tropsch synthesis.

Principal components analysis (PCA) factor filtering is implemented for the improvement of background removal in noisy spectra. When PCA is used as a method for filtering before background removal in electron energy loss spectroscopy elemental maps, an improvement in the accuracy of the background fit with very short fitting intervals is achieved, leading to improved quality of elemental maps from noisy spectra. This opens the possibility to use shorter exposure times for elemental mapping, leading to fewer problems with, for example, drift and beam damage.

Organic semiconductors on single-crystalline metal surfaces are model systems for injection contacts in organic field-effect transistors (OFET) and light-emitting diodes. They allow us to classify possible metal–organic interaction scenarios and to elucidate general tendencies, which most likely will also be found at metal–organic interfaces in real devices. In this contribution, we report a comprehensive investigation of the interface of perylene, a promising material for OFETs, with the close-packed noble metal surface Ag(111), using high-resolution electron energy loss spectroscopy, low-energy electron diffraction, and scanning tunneling microscopy as surface analytical techniques. The most important findings are: In the monolayer, molecules are oriented flat and form an incommensurate, most probably fluid overlayer. The molecules interact electronically with the substrate and become weakly metallic. Scanning tunneling microscopy reveals a propensity of perylene molecules toward a specific adsorption site on Ag(111), if the influence of intermolecular interactions is inhibited. Film growth at room temperature is similar to Stranski–Krastanov type. Finally, co-planar adsorption of perylene on Ag(111) is metastable, and annealing the monolayer at 420 K leads to a structural transformation of the film. The perylene–Ag(111) interface can therefore be classified as weakly interacting.

This work concerns the use of parallel electron energy loss spectroscopy (PEELS) to investigate the detection, distribution, and quantification of carbon in various steel microstructures generated by rapid cooling rates or by isothermal transformation. The feasibility of detecting C in steels containing very small amounts of carbon was first examined by calculating the minimum detectable mass fraction for a variety of binary Fe-C alloy specimen thicknesses and microscope conditions. These theoretical studies indicated that the detection of carbon in steel microconstituents containing about 0.01 wt.% (or even less) was easily possible with an analytical transmission electron microscope equipped with a LaB6 emitter and a PEEL spectrometer. These theoretical calculations seemed to be reasonable, as it proved possible to make a quantitative PEELS study of the partitioning between the microconstituents ferrite, retained austenite, and martensite found in an ultralow carbon (0.03 wt.%) steel weld metal provided care was taken to avoid hydrocarbon contamination. Studies of both carbon and molybdenum segregation to ferrite/martensite interfaces in an isothermally transformed Fe-C-Mo alloy were also carried out in order to investigate the nature of the “solute drag” effect in this alloy system.

Reduction of Cr(VI) by the bacterium, Shewanella oneidensis (previously classified Shewanella putrefaciens strain MR-1), was studied by absorption spectrophotometry and in situ, environmental cell–transmission electron microscopy (EC-TEM) coupled with electron energy loss spectroscopy (EELS). Bacteria from rinsed cultures were placed directly in the environmental cell of the transmission electron microscope and examined under 100 Torr pressure. Bright field EC-TEM images show two distinct populations of S. oneidensis in incubated cultures containing Cr(VI)O42−: those that exhibit low image contrast and heavily precipitateencrusted cells exhibiting high image contrast. Several EELS techniques were applied to determine the oxidation state of Cr associated with encrusted cells. The encrusted cells are shown to contain a reduced form of Cr in oxidation state +3 or lower. These results demonstrate the capability to determine the chemistry and valence state of reduction products associated with unfixed, hydrated bacteria in an environmental cell transmission electron microscope.

This article will discuss the importance of Raimond Castaing’s thesis on the genesis of a nondestructive and truly quantitative microanalytical method that assisted the scientific community in moving forward in the development of microanalytical instruments. I will also share with you my recollection of the decades of improvement in the electron probe microanalyzer (EPMA), that has allowed us to reach our present level of instrument sophistication, and I will explore with you my thoughts on the future evolution of this technique. To conclude, I will present the current status of related microanalysis techniques developed under Castaing in Orsay in the 1960s, as Castaing’s interest in microanalysis was not limited to electron probe microanalysis alone.

Compositional imaging with electron energy loss spectroscopy (EELS) can be performed in both the energy-filtering transmission electron microscope (EFTEM) and in the scanning transmission electron microscope (STEM). Quantitative elemental distributions are obtained from core-edges produced by inner-shell excitations, although more detailed information about chemical bonding and electronic structure is also available from the fine structure associated with valence electron excitations. The fixed-beam EFTEM can provide data from large numbers of pixels very rapidly and offers an advantage for analysis of extended specimen regions containing relatively high atomic concentrations. Acquisition of entire spectra at each pixel in the field-emission STEM (spectrum-imaging technique) provides improved flexibility and accuracy despite the longer recording times. Spectrum-imaging allows post facto data processing with parameters that can be varied after acquisition is completed. In suitably thin specimens, EELS compositional mapping can provide a sensitivity of a few atoms for certain elements.