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DOE OSTI2025

Atomic-Scale Behavior of Radiation-Resistant ZnO under High-Energy Electron Bombardment

Understanding the atomic structure and defect characteristics of ZnO thin films is crucial for optimizing their electronic properties and performance in advanced applications. Here, we investigate the atomic structure and defect characteristics of atomic layer deposition (ALD)-grown ZnO thin films by using aberration-corrected scanning transmission electron microscopy (STEM). Atomic-resolution imaging identifies prevalent stacking faults, dipole disorder, and various grain boundary types, which are believed to influence the electronic properties of ZnO. Additionally, real-time electron beam exposure experiments demonstrate structural transformations, including crystal growth and surface rearrangements. These findings provide insights into the growth mechanisms of ALD ZnO under high-energy electron irradiation conditions, an important finding for the use of polycrystalline ZnO wide bandgap semiconductors in space-like conditions. In conclusion, our results underscore the capability of STEM in directly visualizing and quantifying atomic-scale defects and beam-induced transformations in radiation-resistant ZnO.

Defects↗

DOE OSTI2026

Substrate-Directed Underlayer Growth of Bilayer MoS 2 Revealed by Mo Isotope Labeling

Direct control over the vertical formation sequence and stacking registry in van der Waals (vdW) bilayers is essential for device performance and moiré engineering yet difficult to resolve unambiguously with conventional probes. Here, we use Mo isotope labeling in a two-step chemical vapor deposition process to synthesize bilayer MoS 2 and trace its vertical formation on common substrates. By combining site-selective laser thinning, Raman spectroscopy, time-of-flight secondary ion mass spectrometry, and atomic-resolution scanning transimission electron microscopy (STEM), we find a clear substrate dependence: on SiO 2 /Si, the second layer nucleates and grows beneath the first (underlayer), whereas on sapphire, it forms on top (overlayer). Density functional theory indicates that a larger equilibrium interfacial separation and weaker MoS 2 –substrate interactions on amorphous SiO 2 permit confined interfacial diffusion and underlayer nucleation, whereas stronger interactions and smaller separations on sapphire favor overlayer growth. On SiO 2 , confined epitaxy templates commensurate 2H, 3R, and mixed bilayers, as confirmed by second harmonic generation spectroscopy and STEM. During underlayer coalescence, embedded mirror-twin grain boundaries stitch atomically sharp 2H|3R junctions via alternating 4|8 ring motifs. Molecular-dynamics simulations reveal that these alternating 4|8 motifs accommodate interlayer vdW coupling and locally modulate the stacking registry. These results provide mechanistic insight into confined epitaxial growth and establish isotope labeling as a powerful probe of two-dimensional materials synthesis.

MoS2↗

DOE OSTI2025

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

An Atom-Precise Approach to Damp First-Order Phase Transitions and Its Implications for Neuromorphic Signal Processing

Neuromorphic computing inspired by mammalian intelligence aims to emulate the nonlinear dynamics of biological neurons and synapses to achieve fast, low-energy, and highly efficient information processing. Brain-inspired computing relies on the design and discovery of materials exhibiting nonlinear current–voltage profiles, frequently underpinned by electronic state transitions, to achieve spiking neurons and dynamically tunable synapses. A signature challenge in the design of artificial neurons is controlling the steepness of first-order transitions in active elements, as abrupt transitions are at risk of driving unstable voltage and temperature oscillations, which result in catastrophic device failure. A critical knowledge gap is the lack of structure–function correlations mapping the composition and atomistic structure of crystalline solids to nonlinear dynamical response characteristics. Here, we address the key question of how modification of atomistic structure correlates with alteration of neuron-like functionality. Constructing oscillator circuits from millimeter-scale single crystals enables high-resolution atomic structure solutions, which we use to demonstrate that the selective positioning of Pb cations modifies charge ordering along a one-dimensional CuxV2O5 framework even at low insertion stoichiometries, thereby providing an atom-precise design parameter for damping first-order transitions. We use temperature-variant X-ray diffraction and X-ray spectroscopy to elucidate the suppression of Cu-ion shuttling based on the precise positioning of Pb ions in seven-coordinated tunnel interstitial sites as the mechanistic basis for transition broadening, thus bridging a critical gap between statistical mechanics and quantum chemical descriptions of phase transitions. Such mechanistic understanding thus paves the way to site-selective modification strategies for modulating the sharpness of first-order transitions, with an exemplary demonstration here in tuning neuronal signal processing.

Crystal structure↗

DOE OSTI2024

Strain‐Driven Stabilization of a Room‐Temperature Chiral Multiferroic with Coupled Ferroaxial and Ferroelectric Order

Noncollinear ferroic materials are sought after as testbeds to explore the intimate connections between topology and symmetry, which result in electronic, optical, and magnetic functionalities not observed in collinear ferroic materials. For example, ferroaxial materials have rotational structural distortions that break mirror symmetry and induce chirality. When ferroaxial order is coupled with ferroelectricity arising from a broken inversion symmetry, it offers the prospect of electric-field-control of the ferroaxial distortions and opens up new tunable functionalities. However, chiral multiferroics, especially ones stable at room temperature, are rare. A strain-stabilized, room-temperature chiral multiferroic phase in single crystals of BaTiS 3 is reported here. Using first-principles calculations, the stabilization of this multiferroic phase having P6 3 space group for biaxial tensile strains exceeding 1.5% applied on the basal ab-plane of the room temperature P6 3 cm phase of BaTiS 3 is predicted. The chiral multiferroic phase is characterized by rotational distortions of TiS 6 octahedra around the long c-axis and polar displacement of Ti atoms along the c-axis. Furthermore, the ferroaxial and ferroelectric distortions and their domains in P6 3 -BaTiS 3 are directly resolved using atomic resolution scanning transmission electron microscopy. Landau-based phenomenological modeling predicts a strong coupling between the ferroelectric and the ferroaxial order making P6 3 -BaTiS 3 an attractive test bed for achieving electric-field-control of chirality.

Chalcogenide↗

DOE OSTI2024

Accelerating the Electrochemical Formation of the δ Phase in Manganese-Rich Rocksalt Cathodes

Mn-rich disordered rocksalt materials with Li-excess (DRX) materials have emerged as a promising class of earth-abundant and energy-dense next-generation cathode materials for lithium-ion batteries. Recently, an electrochemical transformation to a spinel-like “δ” phase has been reported in Mn-rich DRX materials, with improved capacity, rate capability, and cycling stability compared with previous DRX compositions. However, this transformation unfolds slowly over the course of cycling, complicating the development and understanding of these materials. In this work, it is reported that the transformation of Mn-rich DRX materials to the promising δ phase can be promoted to occur much more rapidly by electrochemical pulsing at elevated temperature, rate, and voltage. To extend this concept, micron-sized single-crystal DRX particles are also transformed to the δ phase by the same method, possessing greatly improved cycling stability in the first demonstration of cycling for large, single-crystal DRX particles. To shed light on the formation and specific structure of the δ phase, X-ray diffraction, scanning electron nanodiffraction (SEND) and atomic resolution STEM-HAADF are used to reveal a nanodomain spinel structure with minimal remnant disorder.

25 ENERGY STORAGE↗

DOE OSTI2024

Birefringent Color Filter by Layered Metal‐Organic Chalcogenides: In‐Plane Anisotropy and Odd/Even Effect

Anisotropic 2D materials are gaining interest recently as building blocks for angular‐dependent optical/electrical devices. However, the fundamental understanding of their structure‐property‐relationship is limited, which hinders further modulation of their unique characteristics via structure tailoring. Here the in‐plane structural anisotropy and the tunable optical/electrical properties of a series of radiation‐sensitive (X‐ray, e‐beam) metal‐organic chalcogenide (MOC) single crystals are comprehensively revealed with ligands of variable length/parity. Their monoclinic crystallography is determined at atomic resolution by a simple method that couples X‐ray/electron diffraction with first‐principles calculations. The in‐plane inorganic backbone of the MOCs exhibits a strong lattice anisotropy with odd/even alternations, which originates from that of the out‐of‐plane organic motifs via organic/inorganic accommodation. Such structural anisotropy is implied mechanically by the preferred orientation of crystal cleavage. It triggers a maximum ≈8 × distinction of in‐plane electrical conductivity of the semiconducting MOCs, plus a distinct birefringence (maximum Δn ≈ 0.03) with a dispersive orientation of dielectric axes, which rotate up to 25.7° from UV to visible‐light regime, inspiring an emerging pathway for color filtering via single crystal rotation. Such in‐plane optical characteristics also exhibit odd/even alternation and can be flexibly tuned by the designable out‐of‐plane ligands.

birefringence↗

DOE OSTI2025

SnSe 1-x S x Alloys: Anisotropic Van der Waals Semiconductors with Tunable Bandgaps

Alloying is one of the main tools of bandgap engineering, allowing the tuning of crystal structure, lattice parameters, and electronic structure of 3D and 2D/layered semiconductors. Among the latter, it can play a key role in tailoring the properties of tin monochalcogenides, a class of van der Waals semiconductors of interest for optoelectronics, thermoelectrics, ferroelectrics, and valleytronics. Here, the study investigates the synthesis and properties of large flakes of the anion substitution alloys SnSe 1-x S x . Alloy flakes across a wide range of compositions are obtained systematically by repeated growth from the same mixed (SnS, SnSe) powder precursor. Combined experiment and theory show full miscibility for all compositions, along with tunable lattice constants, bandgaps, and vibrational modes. Atomic resolution imaging demonstrates the accumulation of S and Se in alternating layers in the SnSe 1-x S x unit cell, attributed to growth kinetics. Polarized Raman spectroscopy confirms anisotropic vibrational modes; the calculated and measured band structure shows systematic changes in the band edge energies and anisotropic electronic structure due to the anisotropic in-plane lattice of the monochalcogenides. Cathodoluminescence, finally, indicates that a unique configuration of two non-degenerate, direct valleys along orthogonal k-space directions persists all the way from SnS to SnSe, making SnSe 1-x S x alloys interesting for valleytronics.

36 MATERIALS SCIENCE↗

DOE OSTI2025

On the distribution of stacking faults at dissociated medium-angle grain boundaries: Crystallographic geometry and metastability

Grain boundaries in FCC metals with low stacking-fault energy can form in dissociated configurations of stacking faults. Perhaps the most studied example is 9R stacking at boundaries near Σ3{112}, where the distribution of stacking faults is related to the emission of Shockley partial dislocations. Here, we combine atomic-resolution electron microscopy, atomistic simulations, and dislocation theory to demonstrate that boundaries vicinal to Σ33a support the stabilization of dissociated 9R stacking within a narrow range of inclinations. This boundary is interesting since its misorientation (20.05°) lies in the medium-angle regime, just past the upper misorientation limit for low-angle boundaries, motivating questions for how best to describe it in terms of dislocations. Our HAADF-STEM observations of thin film bicrystals, supported by atomistic modeling, reveal that this inclination dependence arises from specific geometric constraints on the arrangement of Shockley partial dislocations at the interface. Quantification of stacking-fault distributions across multiple boundaries indicates that the density and spacing of faults closely follow the ideal 9R motif, with subtle variations reflecting the complex energy landscape of these boundaries. Through energetic analysis, we establish the presence of competing metastable states enabled by variations in stacking sequences, emphasizing the significant role of crystallographic geometry. We generalize our analysis as a function of misorientation, showing how 9R at the Σ33a boundary is related to previous observations and calculations of HCP at a 29.7° boundary. This study provides a crystallographically grounded framework connecting dislocation structures, stacking-fault distributions, and metastability at grain boundaries in FCC metals.

Atomistic modeling↗

DOE OSTI2026

Oxide nucleation via threshold-driven volume instability in Ni oxidation

Oxide nucleation dictates the onset of metal oxidation, yet the atomistic pathways bridging initial oxygen adsorption to bulk phase transformation remain elusive. Here, we utilize in-situ atomic-resolution imaging to directly capture the nucleation of nickel oxide, revealing a threshold-driven, cooperative transformation of Ni into NiO. Our observations identify a distinct incubation period during which oxygen progressively accumulates in subsurface layers. Once a critical concentration and penetration depth are reached, a collective lattice reconfiguration is triggered, abruptly converting multiple Ni layers into NiO. Atomistic simulations corroborate this mechanism, identifying a cooperative lattice instability induced by subsurface oxygen saturation. These results establish subsurface oxygen incorporation as the missing mechanistic link between surface adsorption and three-dimensional oxide formation, providing an atomistic framework to understand and control reactive phase transformations in materials synthesis, catalysis, and degradation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Scanning tunneling microscope tip-induced formation of Bi bilayers on Bi 2 Te 3

We report the formation of Bi(111) bilayer islands and crater structures on Bi 2 Te 3 (111) surfaces induced by voltage pulses from a scanning tunneling microscope tip. Pulses above a threshold voltage (+3 V) produce craters ∼0.5μm in diameter, similar to the size of the tip. Redeposited material self-assembles into a network of atomically ordered islands with a lattice constant identical to the underlying Bi2Te3 surface. The island size monotonically decreases over several micrometers from the pulse site, until the pristine Bi 2 Te 3 surface is recovered. We assign these islands to Bi bilayer based on atomic resolution images, analysis of step heights, and tunneling spectroscopy. Here, the dependence of bilayer formation on bias polarity and the evidence for defect diffusion together suggest a mechanism driven by the interplay of field evaporation and tunneling-current-induced Joule heating.

Bi bilayer↗

DOE OSTI2024

Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms

Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. In this study, we propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗

DOE OSTI2026

KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics

KRAS4a and KRAS4b are important regulators of signaling, and their interactions with the plasma membrane are dynamic and influenced by lipid composition. KRAS 4a and 4b have nearly identical globular domains but differ in their membrane-associated hyper variable region (HVR). The functional distinctions between these isoforms remain unclear, particularly with regards to their dependence on specific lipids and the membrane environment. Previous work showed that the membrane orientation of KRAS4b affects its ability to bind to RAF kinase RBDCRD and that the KRAS–RBDCRD complex adopts different poses on the membrane as well as influences the size and composition of the lipid environment. To model differences between KRAS 4a and 4b protein–lipid interactions, we extended the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to incorporate continuum simulations in the grand canonical ensemble, enabling sampling across macroscopic, coarse-grained, and all-atom resolutions. Using this framework, we systematically altered PIP2 concentrations, KRAS 4a versus 4b, and RAF RBDCRD complexation to assess impacts on membrane–protein interactions and dynamics. Our results reveal that reducing PIP2 shifts and broadens the membrane orientational preference of both KRAS 4b and 4a, with stronger effects on 4b HVR localization versus 4a. We demonstrate that with depletion of the strong negatively charged PIP2 lipid, the less charged phosphatidylserine replaces PIP2. Our findings highlight similarities and distinctions in the dynamics and lipid dependency of KRAS isoforms and suggest that ordering of the local lipid composition by HVRs is a shared property and key modulator of RAS-mediated signaling at the plasma membrane.

Biological and medical sciences↗

DOE OSTI2026

A solid-state extrusion pathway extensible to upcycling aluminum scrap and end-of-life permanent magnets into ductile Al-6061/SmCo 5 structural magnetic composites

Permanent magnets offer strong potential for multifunctional structural components, but their inherent brittleness limits direct integration. Here, SolidStir® Extrusion (SSE) is used to embed SmCo5 powder into AA6061 in the solid state, and the resulting microstructure, interfacial chemistry, mechanical properties, and magnetic response are systematically characterized. SSE fragments the initial SmCo 5 powder into predominantly fine particles dispersed within an ultrafine Al matrix, with a volume fraction of ∼ 4–6 % in this proof-of-concept study. Interfacial reactions form a continuous Al–Co reaction layer, with local atomic-resolution indexing consistent with Al 13 Co 4 , together with Sm–Si-rich reaction products, while the matrix contains Sm–Co–Si-rich precipitates and Mg 2 Si, producing features from nanometers to micrometers. Compared with an Al extrudate, this architecture increases yield strength by ∼ 42 % and tensile strength by ∼ 31 %, while preserving uniform elongation, and it sustains work hardening in compression from 150 to 400 °C. The composite retained hard-magnetic behavior, with axial magnetization of 12.7 A·m 2 kg −1 at 6 T and intrinsic coercivity of 9.6 kOe. These findings demonstrate that SSE can produce Al-based load-bearing magnetic composites while preserving useful SmCo5 functionality.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Development of a liquid-helium free cryogenic sample holder with mK temperature control for autonomous electron microscopy

The automated and autonomous cryogenic transmission electron microscopy (Cryo-EM) demands a sample holder capable of maintaining temperatures below 10 K with precise control, long holding times, and minimal helium use. Rising to this challenge, we initiated an ambitious project to develop a novel closed-cycle cryocooler-based cryogenic sample holder that operates without the use of liquid helium and the consumption of gaseous helium. Here, this article presents the design, construction, and experimental testing of the initial prototype, which achieves an ultimate temperature of 5.6 K with exceptional stability close to 1mK, while providing a wide temperature control range from 295 K to 5.6 K, marking a clear advancement in cryo-EM holder development. While the prototype was not designed for atomic resolution imaging and thus lacks a sturdy support system to mitigate mechanical vibrations from the cryocooler's pulsed tube, this innovative approach successfully demonstrates proof of concept. It offers unprecedented capabilities for state-of-the-art cryogenic microscopy and microanalysis in materials and biological sciences.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Site-specific plan-view (S)TEM sample preparation from thin films using a dual-beam FIB-SEM

To fully evaluate the atomic structure, and associated properties of materials using transmission electron microscopy, examination of samples from three non-collinear orientations is needed. This is particularly challenging for thin films and nanoscale devices built on substrates due to limitations with plan-view sample preparation. In this work, a new method for preparation of high-quality, site-specific, plan-view TEM samples from thin-films grown on substrates, is presented and discussed. Here, it is based on using a dual-beam focused ion beam scanning electron microscope (FIB-SEM) system. To demonstrate the method, the samples were prepared from thin films of perovskite oxide BaSnO 3 grown on a SrTiO 3 substrate and metal oxide IrO 2 on a TiO 2 substrate, ranging from 20–80 nm in thicknesses using molecular beam epitaxy. While the method is optimized for the thin films, it can be extended to other site-specific plan-view samples and devices build on wafers. Aberration-corrected STEM was used to evaluate the quality of the samples and their applicability for atomic-resolution imaging and analysis.

BaSnO3↗

DOE OSTI2024

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies – two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy – and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

59 BASIC BIOLOGICAL SCIENCES↗