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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Atomistic Mechanics of Torn Back Folded Edges of Triangular Voids in Monolayer WS 2

Triangular nanovoids in 2D materials transition metal dichalcogenides have vertex points that cause stress concentration and lead to sharp crack propagation and failure. Here, the atomistic mechanics of back folding around triangular nanovoids in monolayer WS 2 sheets is examined. Combining atomic-resolution images from annular dark-field scanning transmission electron microscopy with reactive molecular modelling, it is revealed that the folding edge formation has statistical preferences under geometric conditions based on the orientation mismatch. It is further investigated how loading directions and strong interlayer friction, interplay with WS 2 lattice's crack preference, govern the deformation and fracture pattern around folding edges. Finally, these results provide fundamental insights into the combination of fracture and folding in flexible monolayer crystals and the resultant Moiré lattices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Migration Kinetics of Surface Ions in Oxygen-Deficient Perovskite During Topotactic Transitions

Oxygen diffusivity and surface exchange kinetics underpin the ionic, electronic, and catalytic functionalities of complex multivalent oxides. Towards understanding and controlling the kinetics of oxygen transport in emerging technologies, it is highly desirable to reveal the underlying lattice dynamics and ionic activities related to oxygen variation. In this study, the evolution of oxygen content is identified in real-time during the progress of a topotactic phase transition in La 0.7 Sr 0.3 MnO 3-δ epitaxial thin films, both at the surface and throughout the bulk. Using polarized neutron reflectometry, a quantitative depth profile of the oxygen content gradient is achieved, which, alongside atomic-resolution scanning transmission electron microscopy, uniquely reveals the formation of a novel structural phase near the surface. Surface-sensitive X-ray spectroscopies further confirm a significant change of the electronic structure accompanying the transition. The anisotropic features of this novel phase enable a distinct oxygen diffusion pathway in contrast to conventional observation of oxygen motion at moderate temperatures. The results provide insights furthering the design of solid oxygen ion conductors within the framework of topotactic phase transitions.

36 MATERIALS SCIENCE↗
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 OSTI2021

Understanding the local structure of disordered carbons from cellulose and lignin

An electron microscopy investigation was performed to understand the relationship between the microstructure and properties of carbonized cellulose and lignin (softwood kraft lignin) relative to the structure of the original biomass components. Structure details at micro- and molecular levels were investigated by scanning transmission electron microscopy. Atomic-resolution images revealed the presence of random disordered carbon in carbonized cellulose (C-CNC) and of large domains of well-ordered carbon with graphite sheet structure in carbonized lignin (C-Lignin). These structural differences explain why C-CNC exhibits higher surface area and porosity than C-Lignin. The presence of certain well-ordered carbon in carbonized lignin indicates some of the carbon in lignin are graphitized with heat treatment temperature up to 950 °C. This result is encouraging for future endeavors of attaining acceptable modulus of carbon fiber from lignin given suitable modifications to the chemistry and structure of lignin. The results of this research contribute to an improved understanding of the carbonization mechanism of the key cellulose and lignin components of biomass materials.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Human Monoclonal IgE Antibodies—a Major Milestone in Allergy

This review provides an overview of this major milestone in allergy, the first atomic resolution structure of an authentic human IgE epitope. The molecular insights that IgE epitopes provide will allow for structure-based design approaches to the development of novel diagnostics, antibody therapeutics, and immunotherapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor

IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85 MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of < 1 mm 3 and unit cell edges of < 150 Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm 2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Accommodating a hexagonal ζ- phase Mn 2 N film on a cubic MgO (001) substrate

The thin films of c -plane dominated hexagonal ζ- phase Mn 2 N were successfully grown on a cubic MgO (001) substrate directly using plasma-assisted molecular beam epitaxy. The surface was comprehensively studied through experimental and theoretical approaches. Reflection high energy electron diffraction revealed two pseudo-cubic domains along [100] MgO and [110] MgO , and one hexagonal domain, which is 30° apart from the [100] MgO direction. Scanning tunneling microscopy was used to image and resolve the high-quality surface, revealing a distorted hexagonal surface structure. Furthermore, atomic resolution of the hexagonal domain with a 2 × 2 reconstructed surface is presented. For c-plane surface, theoretical investigations were carried out using first principles studies to determine the surface formation energy for various reconstructed surfaces. The theoretical study shows that the nitrogen terminated 2 × 2 structure with a manganese adatom on the surface as the most stable reconstruction that reproduces the experimental results. A corresponding simulated scanning tunneling microscopy model is also presented, providing strong support for the experimentally observed in-plane lattice structures. Furthermore, the manganese: nitrogen stoichiometry within the bulk and surface is in good agreement with the expected ratio of 2:1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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 OSTI2023

Single molecule insights into interfacial molecular recognition for model electrochemical DNA biosensors

Electrochemical sensors that use surface-immobilized DNA to bind analytes and transduce the binding into electrochemical signals, have the potential for rapid, specific, and sensitive detection of bioanalytes via a compact and portable platform. However, accessing the structure of these surfaces/interfaces at the relevant spatial scale (< 10 nm), which determines the interfacial interactions and ultimately sensing performance, remains an unsolved challenge. Here, we review studies that have used high resolution atomic force microscope imaging and spatial statistical analysis tools to understand crowding interactions between thiolated DNA probes immobilized on gold electrodes and how such interactions impact target binding. We also review related studies that attempt to control the nanoscale spatial arrangement of the immobilized recognition elements to optimize sensing performance. Furthermore, these efforts have led to new advances in understanding of the structure-function relationships of DNA-based electrochemical biosensors to move the field toward rational engineering of these biosensing interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2021

Evolution of the structure and chemical composition of the interface between multi-component silicate glasses and yttria-stabilized zirconia after 40,000 h exposure in air at 800 °C

The chemical and structural stability of two commercial multicomponent silicate glasses (SCN and G6) in contact with yttria-stabilized zirconia (YSZ) was investigated after exposure times of up to 40,000 h in air at 800 °C. With exposure time, interfacial layers develop at the SCN-YSZ and G6-YSZ interfaces, which were characterized in detail using both quantitative chemical analysis and atomic-resolution imaging. At the SCN-YSZ interface, a Ca-Ba-Si-O reaction phase was found to grow by diffusion control. In G6-YSZ, Raman spectroscopy and electron microscopy revealed a disorganized interfacial reaction later between G6 and YSZ, and the occurrence of cubic to tetragonal to monoclinic phase transformations in YSZ. Finally, this microstructural evolution is discussed in terms of devitrification resistance of glass and diffusion processes at interfaces.

36 MATERIALS SCIENCE↗
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↗