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DOE OSTI2018

Imaging Unstained Synthetic Polymer Crystals and Defects on Atomic Length Scales Using Cryogenic Electron Microscopy

Properties of soft crystalline materials such as synthetic polymers are governed by locations of constituent atoms. Determining atomic-scale structures in these materials is difficult because they degrade rapidly when studied by electron microscopy, and techniques such as x-ray scattering average over volumes much larger than coherent blocks of the unit cells. We obtained cryo-electron microscopy images of self-assembled nanosheets of a peptoid polymer, made by solid-phase synthesis, in which we see a variety of crystalline motifs. A combination of crystallographic and single particle methods, developed for cryo-electron microscopy of biological macromolecules, was used to obtain high resolution images of the crystals. Individual crystals contain grains that are mirror images of each other with concomitant grain boundaries. We have used molecular dynamic simulations to build an atomic model of the crystal structure to facilitate the interpretation of electron micrographs. Direct visualization of crystalline grains and grain boundaries on atomic length scales represents a new level of information for the polymer field.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Nanoscale Resolution 3D Snapshot Particle Tracking by Multifocal Microscopy

Accurate, precise, and rapid particle tracking in three dimensions remains a challenge; yet, its achievement will significantly enhance our understanding of living systems. We developed a multifocal microscopy (MFM) that allows snapshot acquisition of the imaging data, and an associated image processing approach, that together allow simultaneous 3D tracking of many fluorescent particles with nanoscale resolution. The 3D tracking was validated by measuring a known trajectory of a fluorescent bead with an axial accuracy of 19 nm through an image depth (axial range) of 3 pm and 4 nm precision of axial localization through an image depth of 4 pm. A second test obtained a uniform axial probability distribution and Brownian dynamics of beads diffusing in solution. We also validated the MFM approach by imaging fluorescent beads immobilized in gels and comparing the 3D localizations to their "ground truth" positions obtained from a confocal microscopy z-stack of finely spaced images. Finally, we applied our MFM and image processing approach to obtain 3D trajectories of insulin granules in pseudoislets of MIN6 cells to demonstrate its compatibility with complex biological systems. Our study demonstrates that multifocal microscopy allows rapid (video rate) and simultaneous 3D tracking of many "particles" with nanoscale accuracy and precision in a wide range of systems, including over spatial scales relevant to whole live cells.

3D Tracking↗

DOE OSTI2017

Breaking the Time Barrier in Kelvin Probe Force Microscopy: Fast Free Force Reconstruction Using the G-Mode Platform

The atomic force microscope (AFM) offers unparalleled insight into structure and material functionality across nanometer length scales. However, the spatial resolution afforded by the AFM tip is counterpoised by slow detection speeds compared to other common microscopy techniques (e.g. optical, scanning electron microscopy etc.). In this work, we develop an AFM imaging approach allowing ultrafast reconstruction of the tip-sample forces having ~2 orders of magnitude higher time resolution than standard detection methods. Fast free force recovery (F3R) overcomes the widely-viewed temporal bottleneck in AFM, i.e. the mechanical bandwidth of the cantilever, enabling time-resolved imaging at sub-bandwidth speeds. We demonstrate quantitative recovery of electrostatic forces with ~10 µs temporal resolution, free from cantilever ring-down effects. We further apply the F3R method to Kelvin probe force microscopy (KPFM) measurements. F3R-KPFM is an open loop imaging approach (i.e. no bias feedback), allowing ultrafast surface potential measurements (e.g. < 20 µs) to be performed at regular KPFM scan speeds. F3R-KPFM is demonstrated for exploration of ion migration in organometallic halide perovskites materials and shown to allow spatio-temporal imaging of positively charged ion migration under applied electric field, as well as subsequent formation of accumulated charges at the perovskite/electrode interface. In this work we demonstrate quantitative F3R-KPFM measurements – however, we fully expect the F3R approach to be valid for all modes of non-contact AFM operation, including non-invasive probing of ultrafast electrical and magnetic dynamics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues

Abstract Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.

Science & Technology - Other Topics↗

DOE OSTI2022

Bridging microscopy with molecular dynamics and quantum simulations: an atomAI based pipeline

Recent advances in (scanning) transmission electron microscopy have enabled a routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for atomistic simulations. In this fashion, the theory will address experimentally emerging structures, as opposed to the full range of theoretically possible atomic configurations. However, this challenge is highly nontrivial due to the extreme disparity between intrinsic timescales accessible to modern simulations and microscopy, as well as latencies of microscopy and simulations per se. Addressing this issue requires as a first step bridging the instrumental data flow and physics-based simulation environment, to enable the selection of regions of interest and exploring them using physical simulations. Here we report the development of the machine learning workflow that directly bridges the instrument data stream into Python-based molecular dynamics and density functional theory environments using pre-trained neural networks to convert imaging data to physical descriptors. Additionally, the pathways to ensure structural stability and compensate for the observational biases universally present in the data are identified in the workflow. This approach is used for a graphene system to reconstruct optimized geometry and simulate temperature-dependent dynamics including adsorption of Cr as an ad-atom and graphene healing effects. However, it is universal and can be used for other material systems.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Resolution-enhanced X-ray fluorescence microscopy via deep residual networks

Abstract Multimodal hard X-ray scanning probe microscopy has been extensively used to study functional materials providing multiple contrast mechanisms. For instance, combining ptychography with X-ray fluorescence (XRF) microscopy reveals structural and chemical properties simultaneously. While ptychography can achieve diffraction-limited spatial resolution, the resolution of XRF is limited by the X-ray probe size. Here, we develop a machine learning (ML) model to overcome this problem by decoupling the impact of the X-ray probe from the XRF signal. The enhanced spatial resolution was observed for both simulated and experimental XRF data, showing superior performance over the state-of-the-art scanning XRF method with different nano-sized X-ray probes. Enhanced spatial resolutions were also observed for the accompanying XRF tomography reconstructions. Using this probe profile deconvolution with the proposed ML solution to enhance the spatial resolution of XRF microscopy will be broadly applicable across both functional materials and biological imaging with XRF and other related application areas.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Modeling Si/SiGe quantum dot variability induced by interface disorder reconstructed from multiperspective microscopy

SiGe heteroepitaxial growth yields pristine host material for quantum dot qubits, but residual interface disorder can lead to qubit-to-qubit variability that might pose an obstacle to reliable SiGe-based quantum computing. By convolving data from scanning tunneling microscopy and high-angle annular dark field scanning transmission electron microscopy, we reconstruct 3D interfacial atomic structure and employ an atomistic multi-valley effective mass theory to quantify qubit spectral variability. The results indicate (1) appreciable valley splitting (VS) variability of ~50% owing to alloy disorder and (2) roughness-induced double-dot detuning bias energy variability of order 1–10 meV depending on well thickness. For measured intermixing, atomic steps have negligible influence on VS, and uncorrelated roughness causes spatially fluctuating energy biases in double-dot detunings potentially incorrectly attributed to charge disorder. Our approach yields atomic structure spanning orders of magnitude larger areas than post-growth microscopy or tomography alone, enabling more holistic predictions of disorder-induced qubit variability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗

DOE OSTI2019

Second harmonic microscopy of poled x-cut thin film lithium niobate: Understanding the contrast mechanism

Thin film lithium niobate has been of great interest recently, and an understanding of periodically poled thin films is crucial for both fundamental physics and device developments. Second-harmonic (SH) microscopy allows for the noninvasive visualization and analysis of ferroelectric domain structures and walls. While the technique is well understood in bulk lithium niobate, SH microscopy in thin films is largely influenced by interfacial reflections and resonant enhancements, which depend on film thicknesses and substrate materials. We present a comprehensive analysis of SH microscopy in x-cut lithium niobate thin films, based on a full three-dimensional focus calculation and accounting for interface reflections. We show that the dominant signal in backreflection originates from a copropagating phase-matched process observed through reflections, rather than direct detection of the counterpropagating signal as in bulk samples. We simulate the SH signatures of domain structures by a simple model of the domain wall as an extensionless transition from a −χ(2) to a +χ(2) region. This allows us to explain the main observation of domain structures in the thin-film geometry, and, in particular, we show that the SH signal from thin poled films allows to unambiguously distinguish areas, which are completely or only partly inverted in depth.

Rüsing, M. (ORCID:0000000346824577)↗

DOE OSTI2019

Electrostatic potential mapping at ferroelectric domain walls by low-temperature photoemission electron microscopy

Low-temperature X-ray photoemission electron microscopy (X-PEEM) is used to measure the electric potential at domain walls in improper ferroelectric Er 0.99 Ca 0.01 MnO 3 . Here, by combining X-PEEM with scanning probe microscopy and theory, we develop a model that relates the detected X-PEEM contrast to the emergence of uncompensated bound charges, explaining the image formation based on intrinsic electronic domain-wall properties. In contrast to previously applied low-temperature electrostatic force microscopy (EFM), X-PEEM readily distinguishes between positive and negative bound charges at domain walls. Finally, our study introduces an X-PEEM-based approach for low-temperature electrostatic potential mapping, facilitating nanoscale spatial resolution and data acquisition times on the order of 0.1-1 s.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Spectral and polarization based imaging in deep-ultraviolet excited photoelectron microscopy

Using photoelectron emission microscopy, nanoscale spectral imaging of atomically thin MoS2 buried between Al2O3 and SiO2 is achieved by monitoring the wavelength and polarization dependence of the photoelectron signal excited by deep-ultraviolet light. Although photons induce the photoemission, images can exhibit resolutions below the photon wavelength as electrons sense the response. To validate this concept, the dependence of photoemission yield on the wavelength and polarization of the exciting light was first measured and then compared to simulations of the optical response quantified with classical optical theory. A close correlation between experiment and theory indicates that photoemission probes the optical interaction of UV-light with the material stack directly. The utility of this probe is then demonstrated when both the spectral and polarization dependence of photoemission observe spatial variation consistent with grains and defects in buried MoS2. Taken together, these new modalities of photoelectron microscopy allow mapping of optical property variation at length scales unobtainable with conventional light-based microscopy.

Beechem, Thomas E. (ORCID:0000000275360719)↗

DOE OSTI2023

EMDB—the Electron Microscopy Data Bank

Abstract The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Simulating noncontact atomic force microscopy images

A scanning probe with an atomically sharp tip is used in atomic force microscopy. As the probe is rastered over the specimen of interest, changes in its vibration mode can be ascribed to changes in the interatomic forces between the specimen and the tip. Various modes for implementing atomic force measures exist. One of the most successful modes is frequency-modulation noncontact atomic force microscopy. Here we address the role of replicating accurate forces on the probe tip to simulate images within this mode. In this work, we examine several approaches. One involves the use of classical force fields based on interatomic potentials, where the potentials are often fit to experiment. Other approaches center on the use of forces generated from quantum-based calculations. We consider the development of a “virtual tip” approximation wherein the probe tip senses electrostatic forces generated by the specimen. This approach treats the specimen quantum mechanically, while the tip is treated as a classical object. We also consider the use of an embedding approximation to avoid direct computations of the specimen in the presence of the tip. In this method, the tip and specimen are treated quantum mechanically. However, the electronic structure of the specimen is computed in the absence of the probe tip. The electronic density of the specimen is then fixed and the electronic structure of the tip is then computed in the presence of the fixed density. As a general approach, we outline new methods for the full computation of quantum forces between the tip and specimen. We note that quantum-based forces are particularly important as they directly contain the chemical nature of the forces present without the use of any adjustable parameters. We illustrate recent algorithmic developments to computing quantum forces that can produce accurate simulations of atomic force microscopy images for large and complex molecular species. We also suggest new pathways to overcome current challenges in this rapidly evolving field.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Buried Interface and Luminescent Coupling Analysis with Time-Resolved Two-Photon Excitation Microscopy in II-VI and III-V Semiconductor Heterostructures

Semiconductor heterostructures are used in high-efficiency solar cells and in other electronic devices. Solar cells can't reach thermodynamic efficiency limits in part due to the charge carrier recombination, and efforts are applied to understand and reduce recombination. We describe a novel experimental approach to identify and quantify recombination losses at semiconductor interfaces. Using time-resolved two-photon excitation microscopy, we generate carriers at well-defined absorber depths and find that the red spectral shift of the photoluminescence (PL) emission can be used as a 'spectroscopic ruler' to identify recombination depth up to 30 um. We apply this analysis to quantify Shockley-Read-Hall recombination at the buried CdTe/CdTe interface, where 15 um thick epitaxial CdTe is grown by the molecular beam epitaxy on the single crystal CdTe substrate. We also measure luminescent coupling between the GaInP and GaAs layers in heterostructures grown by the metal-organic chemical vapor deposition. Our results resolve important limitations for accurate 3D charge carrier lifetime tomography. Earlier we analyzed recombination due to extended defects and grain boundaries with the lateral resolution sufficient to resolve such features (approximately 0.5 um), but interpretation of the carrier lifetime microscopy data for buried interfaces and buried semiconductor layers was a challenge. Using methods described here, the axial (z) coordinate for the PL microscopy measurements becomes as well defined as the lateral (x, y) coordinates, enabling accurate 3D identification and analysis of the charge carrier recombination locations in semiconductor heterostructures.

14 SOLAR ENERGY↗

DOE OSTI2020

Microwave Microscopy and Its Applications

Understanding the nanoscale electrodynamic properties of a material at microwave frequencies is of great interest for materials science, condensed matter physics, device engineering, and biology. With specialized probes, sensitive detection electronics, and improved scanning platforms, microwave microscopy has become an important tool for cutting-edge materials research in the past decade. In this article, we review the basic components and data interpretation of microwave imaging and its broad range of applications. In addition to the general-purpose mapping of permittivity and conductivity, microwave microscopy is now exploited to perform quantitative measurements on semiconductor devices, photosensitive materials, ferroelectric domains and domain walls, and acoustic-wave systems. Implementation of the technique in low-temperature and high-magnetic-field chambers has also led to major discoveries in quantum materials with strong correlation and topological order. We conclude the review with an outlook of the ultimate resolution, operation frequency, and future industrial and academic applications of near-field microwave microscopy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

XRF-ROI Finder: Machine Learning to Guide Region-of-Interest Scanning for X-ray Fluorescence Microscopy

The ROI-finder software is being developed for use by several Microscopy Group beamlines at Argonne National Laboratory, including 2-ID microprobes and 9-ID-B Bionanoprobe which use multi-scale scanning fluorescence microscopy to acquire elemental maps (multi-modal image data). Microscopy experiments require scan of samples at a coarse resolution followed by ROI identification using feature detection based on domain expertise. Finer resolution scans are then conducted based on identified ROI. The decision-making process based on domain expertise will be difficult to perform for faster data rates and much larger sampling volumes anticipated after APS-U necessitating the need for the ROI-finder software. The ROI- finder detects regions of interest through a continuous learning process, starting with a unsupervised representation learning and improving its recommendations through supervised learning and an interactive tool for user annotation. The scope of ongoing development efforts includes the integration of image registration module to correlate optical and X-ray images, extraction of feature morphology as well as elemental signatures in the image space and incorporation of beamtime streaming data by the scanning probe via EPICS.

CHOWDHURY, M. ARSHAD ZAHANGIR↗

DOE OSTI2025

Confocal Raman Microscopy for Measuring In Situ Temperature-Dependent Structural Changes in Poly(Ethylene Oxide) Thin Films

Crystallization from the melt is a critical process governing the properties of semi-crystalline polymeric materials. While structural analyses of melting and crystallization transitions in bulk polymers have been widely reported, in contrast, those in thin polymer films on solid supports have been underexplored. Herein, in situ Raman microscopy and self-modeling curve resolution (SMCR) analysis are applied to investigate the temperature-dependent structural changes in poly(ethylene oxide) (PEO) films during melting and crystallization phase transitions. By resolving complex overlapping sets of spectra, SMCR analysis reveals that the thermal transitions of 50 µm thick PEO films comprise two structural phases: an ordered crystalline phase and a disordered amorphous phase. The ordered structure of the crystalline PEO film entirely disappears as the polymer is heated; conversely, the disordered structure of the amorphous PEO film reverts to the ordered structure as the polymer is cooled. Broadening of the Raman bands was observed in PEO films above the melting temperature (67 °C), while sharpening of bands was observed below the crystallization temperature (45 °C). The temperatures at which these spectral changes occurred were in good agreement with differential scanning calorimetry (DSC) measurements, especially during the melting transition. The results illustrate that in situ Raman microscopy coupled with SMCR analysis is a powerful approach for unraveling complex structural changes in thin polymer films during melting and crystallization processes. Furthermore, we show that confocal Raman microscopy opens opportunities to apply the methodology to interrogate the structural features of PEO or other surface-supported polymer films as thin as 2 µm, a thickness regime beyond the reach of conventional thermal analysis techniques.

Koh, Miharu [Department of Chemistry, University o↗

DOE OSTI2025

Applications of ultrafast nano-spectroscopy and nano-imaging with tip-based microscopy

Innovation in microscopy has often been critical in advancing both fundamental science and technological progress. Notably, the evolution of ultrafast near-field optical nano-spectroscopy and nano-imaging has unlocked the ability to image at spatial scales from nanometers to ångströms and temporal scales from nanoseconds to femtoseconds. This approach revealed a plethora of fascinating light-matter states and quantum phenomena, including various species of polaritons, quantum phases, and complex many-body effects. This review focuses on the working principles and state-of-the-art development of ultrafast tip-enhanced and near-field microscopy, integrating diverse optical pump-probe methods across the terahertz (THz) to ultraviolet (UV) spectral ranges. It highlights their utility in examining a broad range of materials, including two-dimensional (2D), organic molecular, and hybrid materials. The review concludes with a spatio-spectral-temporal comparison of ultrafast nano-imaging techniques, both within already well-defined domains, and offering an outlook on future developments of ultrafast tip-based microscopy and their potential to address a wider range of materials.

Zhao, Zhichen [Tongji University, Shanghai (China)↗