Phase-contrast imaging of multiply-scattering extended objects at atomic resolution by reconstruction of the scattering matrix
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Engineering topics
Publications and source records attributed to Ciston, Jim.
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Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.
We report that a scanning electron nanobeam diffraction, or 4D-STEM (four-dimensional scanning transmission electron microscopy), is a flexible and powerful approach to elucidate structure from "soft" materials that are challenging to image in the transmission electron microscope because their structure is easily damaged by the electron beam. In a 4D-STEM experiment, a converged electron beam is scanned across the sample, and a pixelated camera records a diffraction pattern at each scan position. This four-dimensional data set can be mined for various analyses, producing maps of local crystal orientation, structural distortions, crystallinity, or different structural classes. Holding the sample at cryogenic temperatures minimizes diffusion of radicals and the resulting damage and disorder caused by the electron beam. The total fluence of incident electrons can easily be controlled during 4D-STEM experiments by careful use of the beam blanker, steering of the localized electron dose, and by minimizing the fluence in the convergent beam thus minimizing beam damage. This technique can be applied to both organic and inorganic materials that are known to be beam-sensitive; they can be highly crystalline, semicrystalline, mixed phase, or amorphous. One common example is the case for many organic materials that have a π-π stacking of polymer chains or rings on the order of 3.4-4.2 Å separation. If these chains or rings are aligned in some regions, they will produce distinct diffraction spots (as would other crystalline spacings in this range), though they may be weak or diffuse for disordered or weakly scattering materials. We can reconstruct the orientation of the π-π stacking, the degree of π-π stacking in the sample, and the domain size of the aligned regions. This Account summarizes illumination conditions and experimental parameters for 4D-STEM experiments with the goal of producing images of structural features for materials that are beam-sensitive. We will discuss experimental parameters including sample cooling, probe size and shape, fluence, and cameras. 4D-STEM has been applied to a variety of materials, not only as an advanced technique for model systems, but as a technique for the beginning microscopist to answer materials science questions. It is noteworthy that the experimental data acquisition does not require an aberration-corrected TEM but can be produced on a variety of instruments with the right attention to experimental parameters.
Van der Waals heteroepitaxy allows deterministic control over lattice mismatch or azimuthal orientation between atomic layers to produce long-wavelength superlattices. The resulting electronic phases depend critically on the superlattice periodicity and localized structural deformations that introduce disorder and strain. In this study we used Bragg interferometry to capture atomic displacement fields in twisted bilayer graphene with twist angles < 2°. Nanoscale spatial fluctuations in twist angle and uniaxial heterostrain were statistically evaluated, revealing the prevalence of short-range disorder in moiré heterostructures. By quantitatively mapping strain tensor fields, we uncovered two regimes of structural relaxation and disentangled the electronic contributions of constituent rotation modes. Further, we found that applied heterostrain accumulates anisotropically in saddle-point regions, generating distinctive striped strain phases. Our results establish the reconstruction mechanics underpinning the twist-angle-dependent electronic behaviour of twisted bilayer graphene and provide a framework for directly visualizing structural relaxation, disorder and strain in moiré materials.
Topological solitary fields, such as magnetic and polar skyrmions, are envisioned to revolutionize microelectronics. These configurations have been stabilized in solid-state materials with a global inversion symmetry breaking, which translates in magnetic materials into a vector spin exchange known as the Dzyaloshinskii–Moriya interaction (DMI), as well as spin chirality selection and isotropic solitons. This work reports experimental evidence of 3D chiral spin textures, such as helical spins and skyrmions with different chirality and topological charge, stabilized in amorphous Fe–Ge thick films. These results demonstrate that structurally and chemically disordered materials with a random DMI can resemble inversion symmetry broken systems with similar magnetic properties, moments, and states. In conclusion, disordered systems are distinguished from systems with global inversion symmetry breaking by their degenerate spin chirality that allows for forming isotropic and anisotropic topological spin textures at remanence, while offering greater flexibility in materials synthesis, voltage, and strain manipulation.
Nucleation in atomic crystallization remains poorly understood, despite advances in classical nucleation theory. The nucleation process has been described to involve a nonclassical mechanism that includes a spontaneous transition from disordered to crystalline states, but a detailed understanding of dynamics requires further investigation. In situ electron microscopy of heterogeneous nucleation of individual gold nanocrystals with millisecond temporal resolution shows that the early stage of atomic crystallization proceeds through dynamic structural fluctuations between disordered and crystalline states, rather than through a single irreversible transition. Our experimental and theoretical analyses support the idea that structural fluctuations originate from size-dependent thermodynamic stability of the two states in atomic clusters. These findings, based on dynamics in a real atomic system, reshape and improve our understanding of nucleation mechanisms in atomic crystallization.
Topological solitary fields, such as magnetic and polar skyrmions, are envisioned to revolutionize microelectronics. These configurations have been stabilized in solid-state materials with a global inversion symmetry breaking, which translates in magnetic materials into a vector spin exchange known as the Dzyaloshinskii-Moriya interaction (DMI), as well as spin chirality selection and isotropic solitons. This work reports experimental evidence of 3D chiral spin textures, such as helical spins and skyrmions with different chirality and topological charge, stabilized in amorphous Fe-Ge thick films. Overall, these results demonstrate that structurally and chemically disordered materials with a random DMI can resemble inversion symmetry broken systems with similar magnetic properties, moments, and states. Disordered systems are distinguished from systems with global inversion symmetry breaking by their degenerate spin chirality that allows for forming isotropic and anisotropic topological spin textures at remanence, while offering greater flexibility in materials synthesis, voltage, and strain manipulation.
Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data and transcends the prevalent structure retrieval algorithm assumption of a very thin specimen homogenous along the optic axis. We demonstrate this approach by reconstructing the different layers of a lead iridate (Pb$_2$Ir$_2$O$_7$) and yttrium-stabilized zirconia (Y$_{0.095}$Zr$_{0.905}$O$_2$) heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction.
Multiple electron scattering and the nonintuitive nature of image formation with coherent radiation complicate the interpretation of conventional transmission electron microscopy images. Precession of the illuminating beam in transmission electron microscopy (TEM) can lead to more robust and interpretable images with some penalty to image contrast, a technique known as dynamic hollow-cone illumination TEM. Here, we demonstrate direct and robust imaging of light and heavy atoms in a crystalline environment with this technique. This method is similar to the annular bright-field technique in scanning transmission electron microscopy, via the principle of reciprocity. Dynamic hollow-cone illumination TEM is challenging in practice due to sensitivity to the misalignment of the precession axis, microscope objective aperture, and crystal zone axis.
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Complexes with neighboring metal centers in isolated pairs and their analogues on surfaces are drawing increasing attention as catalysts. These include molecular homogeneous catalysts incorporating various ligands, enzymes, and solids that include pairs of metal atoms mounted on supports. Catalysts in this broad class are active for numerous reactions and offer unexplored opportunities to address challenging reactions, such as oxidation of methane and oxidation of water in artificial photosynthesis. The subject of supported metal pair-site catalysts is in its infancy, facing challenges in (a) precise synthesis, (b) structure determination at the atomic scale, and (c) stabilization in reactive atmospheres. In this Perspective, we summarize key characteristics of molecular and enzymatic catalysts that incorporate neighboring metal centers and build on this foundation to assess the emerging literature of metal pair-site catalysts on various supports. The supported catalysts include those synthesized by anchoring molecular dinuclear precursors to support surfaces and those synthesized by selective formation of dinuclear surface species from mononuclear surface species. Examples of metals in this class are rhodium and iridium, and examples of supports are MgO and Fe 2 O 3 . We summarize characterization of these materials by electron microscopy and spectroscopy, emphasizing atomic-resolution aberration-corrected scanning transmission electron microscopy and spectroscopies that provide atomic-scale structural information and allow characterization of functioning catalysts, especially X-ray absorption spectroscopy. Finally, we list some opportunities for research, including suggestions that might lead to structurally well-defined supported metal pair-sites with new catalytic properties.
Structure and chemistry of metal/metal-oxide interfaces are critical for many catalytic processes and sensing. Pristine interfaces of Pt and γ-Al 2 O 3 were fabricated using high-energy ion implantation and thermal processing. Amorphous regions of alumina develop in single crystal α-alumina during Pt+ implantation and an 800 °C thermal treatment crystalizes amorphized alumina to γ-Al 2 O 3 and allows Pt ions to precipitate within the developing γ-alumina, yielding Pt nanoparticle tetrahedra terminated by {111} surfaces. The phase of alumina that developed and the distribution, morphology, and orientation of Pt nanoparticles was determined using x-ray diffraction, Rutherford backscattering spectrometry, transmission electron microscopy and scanning transmission electron microscopy.
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Ultrathin ferroelectric materials could potentially enable low-power logic and nonvolatile memories. As ferroelectric materials are made thinner, however, the ferroelectricity is usually suppressed. Size effects in ferroelectrics have been thoroughly investigated in perovskite oxides—the archetypal ferroelectric system. Perovskites, however, have so far proved unsuitable for thickness scaling and integration with modern semiconductor processes. In this paper we report ferroelectricity in ultrathin doped hafnium oxide (HfO 2 ), a fluorite-structure oxide grown by atomic layer deposition on silicon. We demonstrate the persistence of inversion symmetry breaking and spontaneous, switchable polarization down to a thickness of one nanometre. Our results indicate not only the absence of a ferroelectric critical thickness but also enhanced polar distortions as film thickness is reduced, unlike in perovskite ferroelectrics. This approach to enhancing ferroelectricity in ultrathin layers could provide a route towards polarization-driven memories and ferroelectric-based advanced transistors. This work shifts the search for the fundamental limits of ferroelectricity to simpler transition-metal oxide systems—that is, from perovskite-derived complex oxides to fluorite-structure binary oxides—in which ‘reverse’ size effects counterintuitively stabilize polar symmetry in the ultrathin regime.
Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
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The operating conditions of functional materials usually involve varying stress fields, resulting in structural changes, whether intentional or undesirable. Complex multiscale microstructures including defects, domains, and new phases, can be induced by mechanical loading in functional materials, providing fundamental insight into the deformation process of the involved materials. On the other hand, these microstructures, if induced in a controllable fashion, can be used to tune the functional properties or to enhance certain performance. In situ nanomechanical tests conducted in scanning/transmission electron microscopes (STEM/TEM) provide a critical tool for understanding the microstructural evolution in functional materials. In our study, select results on a variety of functional material systems in the field are presented, with a brief introduction into some newly developed multichannel experimental capabilities to demonstrate the impact of these techniques.