arXiv subjects

Colin Ophus

Publications and source records attributed to Colin Ophus.

At least 55 records · Page 3Linked to original sources

arXiv2024

Considerations for extracting moiré-level strain from dark field intensities in transmission electron microscopy

Bragg interferometry (BI) is an imaging technique based on four-dimensional scanning electron microscopy (4D-STEM) wherein the intensities of select overlapping Bragg disks are fit or more qualitatively analyzed in the context of simple trigonometric equations to determine local stacking order. In 4D-STEM based approaches, the collection of full diffraction patterns at each real-space position of the scanning probe allows the use of precise virtual apertures much smaller and more variable in shape than those used in conventional dark field imaging, such that even buried interfaces marginally twisted from other layers can be targeted. A coarse-grained form of dark field ptychography, BI uses simple physically derived fitting functions to extract the average structure within the illumination region and is therefore viable over large fields of view. BI has shown a particular advantage for selectively investigating the interlayer stacking and associated moiré reconstruction of bilayer interfaces within complex multi-layered structures. This has enabled investigation of reconstruction and substrate effects in bilayers through encapsulating hexagonal boron nitride and of select bilayer interfaces within trilayer stacks. However, the technique can be improved to provide a greater spatial resolution and probe a wider range of twisted structures, for which current limitations on acquisition parameters can lead to large illumination regions and the computationally involved post-processing can fail. Here we analyze these limitations and the computational processing in greater depth, presenting a few methods for improvement over previous works, discussing potential areas for further expansion, and illustrating the current capabilities of this approach for extracting moiré-scale strain.

cond-mat.mtrl-sci↗

arXiv2024

Streaming Large-Scale Electron Microscopy Data to a Supercomputing Facility

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy (NCEM) generates data at a nominal rate of 480 Gbit/s (87,000 frames/s) producing a 700 GB dataset in fifteen seconds. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera's data acquisition (DAQ) system to supercomputing nodes at the National Energy Research Scientific Computing Center (NERSC), bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a post-mortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

physics.ins-det↗

arXiv2024

Tailored topotactic chemistry unlocks heterostructures of magnetic intercalation compounds

The construction of thin film heterostructures has been a widely successful archetype for fabricating materials with emergent physical properties. This strategy is of particular importance for the design of multilayer magnetic architectures in which direct interfacial spin--spin interactions between magnetic phases in dissimilar layers lead to emergent and controllable magnetic behavior. However, crystallographic incommensurability and atomic-scale interfacial disorder can severely limit the types of materials amenable to this strategy, as well as the performance of these systems. Here, we demonstrate a method for synthesizing heterostructures comprising magnetic intercalation compounds of transition metal dichalcogenides (TMDs), through directed topotactic reaction of the TMD with a metal oxide. The mechanism of the intercalation reaction enables thermally initiated intercalation of the TMD from lithographically patterned oxide films, giving access to a new family of multi-component magnetic architectures through the combination of deterministic van der Waals assembly and directed intercalation chemistry.

cond-mat.mtrl-sci↗

arXiv2024

Iterative Phase Retrieval Algorithms for Scanning Transmission Electron Microscopy

Scanning transmission electron microscopy (STEM) has been extensively used for imaging complex materials down to atomic resolution. The most commonly employed STEM modality, annular dark-field imaging, produces easily-interpretable contrast, but is dose-inefficient and produces little to no discernible contrast for light elements and weakly-scattering samples. An alternative is to use STEM phase retrieval imaging, enabled by high speed detectors able to record full images of a diffracted STEM probe over a grid of scan positions. Phase retrieval imaging in STEM is highly dose-efficient, enabling the measurement of the structure of beam-sensitive materials such as biological samples. Here, we comprehensively describe the theoretical background, algorithmic implementation details, and perform both simulated and experimental tests for three iterative phase retrieval STEM methods: focused-probe differential phase contrast, defocused-probe parallax imaging, and a generalized ptychographic gradient descent method implemented in two and three dimensions. We discuss the strengths and weaknesses of each of these approaches by comparing the transfer of information using analytical expressions and numerical results for a white-noise model. This presentation of STEM phase retrieval methods aims to make these methods more approachable, reproducible, and more readily adoptable for many classes of samples.

cond-mat.mtrl-sci↗

arXiv2024

Uncovering the Three-Dimensional Structure of Upconverting Core-Shell Nanoparticles with Multislice Electron Ptychography

In photon upconverting core-shell nanoparticles, structure strongly dictates performance. Conventional imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional imaging modes insufficient for fully characterizing these structures. Phase retrieval methods provide a promising alternative imaging mode, and in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core-shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples.

cond-mat.mtrl-sci↗

arXiv2024

A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries

An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase alpha / beta titanium alloy. The data was recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3nm step size. The results show the expected Burgers orientation relationships between the alpha laths and beta matrix, as well as the expected misorientations between alpha laths. A minor issue was found that one area was affected by 180° ambiguities in indexing occur due to this area being aligned too close to a zone axis of the alpha with 2-fold projection symmetry (not present in 3D) in the Zero Order Laue Zone, and this should be avoided in data acquisition in the future. Nevertheless, this study demonstrates a good workflow for the analysis of nanocrystalline two- or multi-phase materials, which will be of widespread use in analysing two-phase titanium and other systems and how they evolve as a function of thermomechanical treatments.

cond-mat.mtrl-sci↗

arXiv2023

High-resolution 3D phase-contrast imaging beyond the depth of field limit via ptychographic multi-slice electron tomography

Resolving single atoms in large-scale volumes has been a goal for atomic resolution microscopy for a long time. Electron microscopy has come close to this goal using a combination of advanced electron optics and computational imaging algorithms. However, atomic-resolution 3D imaging in volumes larger than the depth of field limit of the electron optics has so far been out of reach. Electron ptychography, a computational imaging method allowing to solve the multiple-scattering problem from position- and momentum-resolved measurements, provides the opportunity to surpass this limit. Here, we experimentally demonstrate atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits using multi-slice ptychographic electron tomography. We reconstruct tilt-series 4D-STEM measurements of a Co3O4 nanocube, yielding 1.75 Å resolution in a reconstructed volume of (18.2nm)^3.

cond-mat.mtrl-sci↗

arXiv2023

Imaging Atomic-Scale Chemistry from Fused Multi-Modal Electron Microscopy

Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic interactions. Here, fused multi-modal electron microscopy offers high signal-to-noise ratio (SNR) recovery of material chemistry at nano- and atomic- resolution by coupling correlated information encoded within both elastic scattering (high-angle annular dark field (HAADF)) and inelastic spectroscopic signals (electron energy loss (EELS) or energy-dispersive x-ray (EDX)). By linking these simultaneously acquired signals, or modalities, the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector hardware. In many cases, the dose requirements can be reduced by over one order of magnitude. This high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.

physics.comp-ph↗

arXiv2023

Janus icosahedral particles: amorphization driven by three-dimensional atomic misfit and edge dislocation compensation

Icosahedral nanoparticles composed of fivefold twinned tetrahedra have broad applications. The strain relief mechanism and angular deficiency in icosahedral multiply twinned particles are poorly understood in three dimensions. Here, we resolved the three-dimensional atomic structures of Janus icosahedral nanoparticles using atomic resolution electron tomography. A geometrically fivefold face consistently corresponds to a less ordered face like two hemispheres. We quantify rich structural variety of icosahedra including bond orientation order, bond length, strain tensor; and packing efficiency, atom number, solid angle of each tetrahedron. These structural characteristics exhibit two-sided distribution. Edge dislocations near the axial atoms and small disordered domains fill the angular deficiency. Our findings provide new insights how the fivefold symmetry can be compensated and the geometrically-necessary internal strains relived in multiply twinned particles.

cond-mat.mtrl-sci↗

arXiv2023

Measurement of atomic modulation direction using the azimuthal variation of first order Laue zone electron diffraction

We show that diffraction intensity into the First Order Laue Zone (FOLZ) of a crystal can have a strong azimuthal dependence, where this FOLZ ring appears solely because of unidirectional atom position modulation. Such a modulation was already known to cause the appearance of elliptical columns in atom resolution images, but we show that measurement of the angle via 4-dimensional Scanning Transmission Electron Microscopy (4DSTEM) is far more reliable and allows the measurement of the modulation direction with a precision of about 1° and an accuracy of about 3°. This method could be very powerful in characterising atomic structures in 3 dimensions by 4DSTEM, especially in cases where the structure deviates from that found in bulk crystals.

cond-mat.mtrl-sci↗

arXiv2023

Observation of Antiferroelectric Domain Walls in a Uniaxial Hyperferroelectric

Ferroelectric domain walls are a rich source of emergent electronic properties and unusual polar order. Recent studies showed that the configuration of ferroelectric walls can go well beyond the conventional Ising-type structure. Néel-, Bloch-, and vortex-like polar patterns have been observed, displaying strong similarities with the spin textures at magnetic domain walls. Here, we report the discovery of antiferroelectric domain walls in the uniaxial ferroelectric Pb$_{5}$Ge$_{3}$O$_{11}$. We resolve highly mobile domain walls with an alternating displacement of Pb atoms, resulting in a cyclic 180$^{\circ}$ flip of dipole direction within the wall. Density functional theory calculations reveal that Pb$_{5}$Ge$_{3}$O$_{11}$ is hyperferroelectric, allowing the system to overcome the depolarization fields that usually suppress antiparallel ordering of dipoles along the longitudinal direction. Interestingly, the antiferroelectric walls observed under the electron beam are energetically more costly than basic head-to-head or tail-to-tail walls. The results suggest a new type of excited domain-wall state, expanding previous studies on ferroelectric domain walls into the realm of antiferroic phenomena.

cond-mat.mtrl-sci↗

arXiv2023

Exploring the origins of perpendicular magnetic anisotropy in amorphous Tb-Co via changes in medium-range ordering

Amorphous thin films of Tb$_{17}$Co$_{83}$ (a-Tb-Co) grown by magnetron co-sputtering exhibit changes in magnetic anisotropy with varying growth and annealing temperatures. The magnetic anisotropy constant increases with increasing growth temperature, which is reduced or vanishes upon annealing at temperatures above the growth temperature. The proposed explanation for this growth-induced anisotropy in high orbital moment Tb-based transition metal alloys such as a-Tb-Co is an amorphous phase texturing with preferential in-plane and out-of-plane local bonding configurations for the rare-earth and transition metal atoms. Scanning nanodiffraction performed in a transmission electron microscope (TEM) is applied to a-Tb$_{17}$Co$_{83}$ films deposited over a range of temperatures to measure relative changes in medium-range ordering (MRO). These measurements reveal an increase in MRO with higher growth temperatures and a decrease in MRO with higher annealing temperatures. The trend in MRO indicates a relationship between the magnetic anisotropy and local atomic ordering. Tilting select films between 0$^{\circ}$ and 40$^{\circ}$ in the TEM measures variations in the local atomic structure a function of orientation within the films. The findings support claims that preferential ordering along the growth direction results from temperature-mediated adatom configurations during deposition, and that oriented MRO correlates with the larger anisotropy constants.

cond-mat.mtrl-sci↗

arXiv2023

The 4D Camera: an 87 kHz direct electron detector for scanning/transmission electron microscopy

We describe the development, operation, and application of the 4D Camera -- a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at approximately 480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10 - 700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 - 300 keV. Through electron counting, the resulting sparse data sets are reduced in size by 10 - 300x compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex 4D-STEM experiments to be accomplished with typical STEM scanning parameters.

physics.ins-det↗

arXiv2023

Defect contrast with 4D-STEM: Understanding crystalline order with virtual detectors and beam modification

Material properties strongly depend on the nature and concentration of defects. Characterizing these features may require nano- to atomic-scale resolution to establish structure-property relationships. 4D-STEM, a technique where diffraction patterns are acquired at a grid of points on the sample, provides a versatile method for highlighting defects. Computational analysis of the diffraction patterns with virtual detectors produces images that can map material properties. Here, using multislice simulations, we explore different virtual detectors that can be applied to the diffraction patterns that go beyond the binary response functions that are possible using ordinary STEM detectors. Using graphene and lead titanate as model systems, we investigate the application of virtual detectors to study local order and in particular defects. We find that using a small convergence angle with a rotationally varying detector most efficiently highlights defect signals. With experimental graphene data, we demonstrate the effectiveness of these detectors in characterizing atomic features, including vacancies, as suggested in simulations. Phase and amplitude modification of the electron beam provides another process handle to change image contrast in a 4D-STEM experiment. We demonstrate how tailored electron beams can enhance signals from short-range order and how a vortex beam can be used to characterize local symmetry.

cond-mat.mtrl-sci↗

arXiv2023

Uncovering polar vortex structures by inversion of multiple scattering with a stacked Bloch wave model

Nanobeam electron diffraction can probe local structural properties of complex crystalline materials including phase, orientation, tilt, strain, and polarization. Ideally, each diffraction pattern from a projected area of a few unit cells would produce clear a Bragg diffraction pattern, where the reciprocal lattice vectors can be measured from the spacing of the diffracted spots, and the spot intensities are equal to the square of the structure factor amplitudes. However, many samples are too thick for this simple interpretation of their diffraction patterns, as multiple scattering of the electron beam can produce a highly nonlinear relationship between the spot intensities and the underlying structure. Here, we develop a stacked Bloch wave method to model the diffracted intensities from thick samples with structure that varies along the electron beam. Our method reduces the large parameter space of electron scattering to just a few structural variables per probe position, making it fast enough to apply to very large fields of view. We apply our method to SrTiO$_3$/PbTiO$_3$/SrTiO$_3$ multilayer samples, and successfully disentangle specimen tilt from the mean polarization of the PbTiO$_3$ layers. We elucidate the structure of complex vortex topologies in the PbTiO$_3$ layers, demonstrating the promise of our method to extract material properties from thick samples.

cond-mat.mtrl-sci↗

arXiv2023

Rotational and Dilational Reconstruction in Transition Metal Dichalcogenide Moiré Bilayers

Lattice reconstruction and corresponding strain accumulation play a key role in defining the electronic structure of two-dimensional moiré superlattices, including those of transition metal dichalcogenides (TMDs). Imaging of TMD moirés has so far provided a qualitative understanding of this relaxation process in terms of interlayer stacking energy, while models of the underlying deformation mechanisms have relied on simulations. Here, we use interferometric four-dimensional scanning transmission electron microscopy to quantitatively map the mechanical deformations through which reconstruction occurs in small-angle twisted bilayer MoS2 and WSe2/MoS2 heterobilayers. We provide direct evidence that local rotations govern relaxation for twisted homobilayers, while local dilations are prominent in heterobilayers possessing a sufficiently large lattice mismatch. Encapsulation of the moiré layers in hBN further localizes and enhances these in-plane reconstruction pathways, suppressing out-of-plane corrugation. We also find that extrinsic uniaxial heterostrain, which introduces a lattice constant difference in twisted homobilayers, leads to accumulation and redistribution of reconstruction strain, demonstrating another route to modify the moiré potential.

cond-mat.mtrl-sci↗

arXiv2023

Design of Electrostatic Aberration Correctors for Scanning Transmission Electron Microscopy

In a scanning transmission electron microscope (STEM), producing a high-resolution image generally requires an electron beam focused to the smallest point possible. However, the magnetic lenses used to focus the beam are unavoidably imperfect, introducing aberrations that limit resolution. Modern STEMs overcome this by using hardware aberration correctors comprised of many multipole lenses, but these devices are complex, expensive, and can be difficult to tune. We demonstrate a design for an electrostatic phase plate that can act as an aberration corrector. The corrector is comprised of annular segments, each of which is an independent two-terminal device that can apply a constant or ramped phase shift to a portion of the electron beam. We show the improvement in image resolution using an electrostatic corrector. Engineering criteria impose that much of the beam within the probe-forming aperture be blocked by support bars, leading to large probe tails for the corrected probe that sample the specimen beyond the central lobe. We also show how this device can be used to create other STEM beam profiles such as vortex beams and beams with a high degree of phase diversity, which improve information transfer in ptychographic reconstructions.

cond-mat.mtrl-sci↗

arXiv2023

Crystal Toolkit: A Web App Framework to Improve Usability and Accessibility of Materials Science Research Algorithms

Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based apps to explore their own data or to help developers make their research algorithms accessible to a broader audience of scientists who might not have any training in computer programming and who would benefit from graphical interfaces. Crystal Toolkit comes with a library of ready-made components that can be assembled to make complex web apps: simulation of powder and single crystalline diffraction patterns, convex hull phase diagrams, Pourbaix diagrams, electronic band structures, analysis of local chemical environments and symmetry, and more. Crystal Toolkit is now powering the Materials Project website frontend, providing user-friendly access to its database of computed materials properties. In the future, it is hoped that new visualizations might be prototyped using Crystal Toolkit to help explore new forms of data being generated by the materials science community, and that this in turn can help new materials scientists develop intuition for how their data behaves and the insights that might be found within. Crystal Toolkit will remain a work-in-progress and is open to contributions from the community.

cond-mat.mtrl-sci↗