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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unusual plastic strain-induced phase transformation phenomena in silicon

Pressure-induced phase transformations (PTs) in Si, the most important electronic material, have been broadly studied, whereas strain-induced PTs have never been studied in situ. Here, we reveal in situ various important plastic strain-induced PT phenomena. A correlation between the direct and inverse Hall-Petch effect of particle size on yield strength and pressure for strain-induced PT is predicted theoretically and confirmed experimentally for Si-I→Si-II PT. For 100 nm particles, the strain-induced PT Si-I→Si-II initiates at 0.3 GPa under both compression and shear while it starts at 16.2 GPa under hydrostatic conditions. The Si-I→Si-III PT starts at 0.6 GPa but does not occur under hydrostatic pressure. Pressure in small Si-II and Si-III regions of micron and 100 nm particles is ~5–7 GPa higher than in Si-I. For 100 nm Si, a sequence of Si-I → I + II → I + II + III PT is observed, and the coexistence of four phases, Si-I, II, III, and XI, is found under torsion. Retaining Si-II and single-phase Si-III at ambient pressure and obtaining reverse Si-II→Si-I PT demonstrates the possibilities of manipulating different synthetic paths. The obtained results corroborate the elaborated dislocation pileup-based mechanism and have numerous applications for developing economic defect-induced synthesis of nanostructured materials, surface treatment (polishing, turning, etc.), and friction.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Transforming jet flavour tagging at ATLAS

Jet flavour tagging enables the identification of jets originating from heavy-flavour quarks in proton–proton collisions at the Large Hadron Collider, playing a critical role in its physics programmes. This paper presents GN2, a transformer-based flavour tagging algorithm deployed by the ATLAS Collaboration that represents a different methodology compared to previous approaches. Designed to classify jets based on the flavour of their constituent particles, GN2 processes low-level tracking information in an end-to-end architecture and incorporates physics-informed auxiliary training objectives to enhance both interpretability and performance. Its performance is validated in both simulation and collision data. The measured c-jet (light-jet) rejection in data is improved by a factor of 3.5 (1.8) for a 70% b-jet tagging efficiency, compared to the previous algorithm. GN2 provides substantial benefits for physics analyses involving heavy-flavour jets, such as measurements of Higgs boson pair production and the couplings of bottom and charm quarks to the Higgs boson, and demonstrates the impact of advanced machine learning methods in experimental particle physics.

Characterization and analytical techniques↗
DOE OSTI2023

Uncertainty-aware molecular dynamics from Bayesian active learning for phase transformations and thermal transport in SiC

Abstract Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomistic dynamics. Active learning methods have been recently developed to train force fields efficiently and automatically. Among them, Bayesian active learning utilizes principled uncertainty quantification to make data acquisition decisions. In this work, we present a general Bayesian active learning workflow, where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion descriptors. To circumvent the high computational cost of the sparse Gaussian process uncertainty calculation, we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of magnitude. We demonstrate the autonomous active learning workflow by training a Bayesian force field model for silicon carbide (SiC) polymorphs in only a few days of computer time and show that pressure-induced phase transformations are accurately captured. The resulting model exhibits close agreement with both ab initio calculations and experimental measurements, and outperforms existing empirical models on vibrational and thermal properties. The active learning workflow readily generalizes to a wide range of material systems and accelerates their computational understanding.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Quantitative kinetic rules for plastic strain-induced α - ω phase transformation in Zr under high pressure

Plastic strain-induced phase transformations (PTs) and chemical reactions under high pressure are broadly spread in modern technologies, friction and wear, geophysics, and astrogeology. However, because of very heterogeneous fields of plastic strain $E$ p and stress σ tensors and volume fraction c of phases in a sample compressed in a diamond anvil cell (DAC) and impossibility of measurements of σ and $E$ p , there are no strict kinetic equations for them. Here, we develop a kinetic model, finite element method (FEM) approach, and combined FEM-experimental approaches to determine all fields in strongly plastically predeformed Zr compressed in DAC, and specific kinetic equation for α-ω PT consistent with experimental data for the entire sample. Since all fields in the sample are very heterogeneous, data are obtained for numerous complex 7D paths in the space of 3 components of the plastic strain tensor and 4 components of the stress tensor. Kinetic equation depends on accumulated plastic strain (instead of time) and pressure and is independent of plastic strain and deviatoric stress tensors, i.e., it can be applied for various above processes. Our results initiate kinetic studies of strain-induced PTs and provide efforts toward more comprehensive understanding of material behavior in extreme conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Reversible transformations between the non-porous phases of a flexible coordination network enabled by transient porosity

Abstract Flexible metal–organic materials that exhibit stimulus-responsive switching between closed (non-porous) and open (porous) structures induced by gas molecules are of potential utility in gas storage and separation. Such behaviour is currently limited to a few dozen physisorbents that typically switch through a breathing mechanism requiring structural contortions. Here we show a clathrate (non-porous) coordination network that undergoes gas-induced switching between multiple non-porous phases through transient porosity, which involves the diffusion of guests between discrete voids through intra-network distortions. This material is synthesized as a clathrate phase with solvent-filled cavities; evacuation affords a single-crystal to single-crystal transformation to a phase with smaller cavities. At 298 K, carbon dioxide, acetylene, ethylene and ethane induce reversible switching between guest-free and gas-loaded clathrate phases. For carbon dioxide and acetylene at cryogenic temperatures, phases showing progressively higher loadings were observed and characterized using in situ X-ray diffraction, and the mechanism of diffusion was computationally elucidated.

Chemistry↗
DOE OSTI2025

Transforming an ATP-dependent enzyme into a dissipative, self-assembling system

Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5'-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Furthermore we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Double-pulse speckle contrast correlations with near Fourier transform limited free-electron laser light using hard X-ray split-and-delay

Abstract The ability to deliver two coherent X-ray pulses with precise time-delays ranging from a few femtoseconds to nanoseconds enables critical capabilities of probing ultra-fast phenomena in condensed matter systems at X-ray free electron laser (FEL) sources. Recent progress made in the hard X-ray split-and-delay optics developments now brings a very promising prospect for resolving atomic-scale motions that were not accessible by previous time-resolved techniques. Here, we report on characterizing the spatial and temporal coherence properties of the hard X-ray FEL beam after propagating through split-and-delay optics. Speckle contrast analysis of small-angle scattering measurements from nanoparticles reveals well-preserved transverse coherence of the beam. Measuring intensity fluctuations from successive X-ray pulses also reveals that only single or double temporal modes remain in the transmitted beam, corresponding to nearly Fourier transform limited pulses.

42 ENGINEERING↗
DOE OSTI2026

Roadmap for transforming heterogeneous catalysis with artificial intelligence

Artificial intelligence (AI) is poised to transform heterogeneous catalysis, opening avenues for catalytic materials discovery. By uncovering intricate patterns in high-dimensional data, AI has been reshaping our pursuit of sustainable catalytic processes across the energy, environmental and chemical sectors. This promise, however, hinges on overcoming fundamental barriers, including limitations in data availability and quality, challenges in the generalizability and interpretability of data-augmented decisions, and the persistent gap between in silico predictions and experiments. Furthermore, we outline a forward-looking roadmap for deeply integrating AI into heterogeneous catalysis with an AI-ready data ecosystem, multimodal foundation models, and ultimately autonomous laboratories to accelerate the development of next-generation catalytic technologies via AI-empowered human–machine collaboration.

Computational methods↗
DOE OSTI2021

Direct visualization of radiation-induced transformations at alkali halide–air interfaces

Radiation driven reactions at mineral/air interfaces are important to the chemistry of the atmosphere, but experimental constraints (e.g. simultaneous irradiation, in situ observation, and environmental control) leave process understanding incomplete. Using a custom atomic force microscope equipped with an integrated X-ray source, transformation of potassium bromide surfaces to potassium nitrate by air radiolysis species was followed directly in situ at the nanoscale. Radiolysis initiates dynamic step edge dissolution, surface composition evolution, and ultimately nucleation and heteroepitaxial growth of potassium nitrate crystallites mediated by surface diffusion at rates controlled by adsorbed water. Finally, in contrast to in situ electron microscopy and synchrotron-based imaging techniques where high radiation doses are intrinsic, our approach illustrates the value of decoupling irradiation and the basis of observation.

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

Structure of a seeded palladium nanoparticle and its dynamics during the hydride phase transformation

Palladium absorbs large volumetric quantities of hydrogen at room temperature and ambient pressure, making the palladium hydride system a promising candidate for hydrogen storage. Here, we use Bragg coherent diffraction imaging to map the strain associated with defects in three dimensions before and during the hydride phase transformation of an individual octahedral palladium nanoparticle, synthesized using a seed-mediated approach. The displacement distribution imaging unveils the location of the seed nanoparticle in the final nanocrystal. By comparing our experimental results with a finite-element model, we verify that the seed nanoparticle causes a characteristic displacement distribution of the larger nanocrystal. During the hydrogen exposure, the hydride phase is predominantly formed on one tip of the octahedra, where there is a high number of lower coordinated Pd atoms. Our experimental and theoretical results provide an unambiguous method for future structure optimization of seed-mediated nanoparticle growth and in the design of palladium-based hydrogen storage systems.

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

Structural transformation of metal oxo species within UiO-66 type metal–organic frameworks

Studying the coordination of actinide-based metal oxo clusters can provide valuable insights for nuclear energy technologies and radioactive waste containment. Metal–organic frameworks serve as a platform to directly interrogate the structure and properties of understudied actinide elements, including thorium. Examples of structural evolutions within Th oxo species within MOFs are rare yet relevant for nuclear waste speciation in solution. Herein, we report the serendipitous discovery of the structural evolution of Th-UiO-66 containing a hexanuclear Th node to a mononuclear Th(bdc) 2 (dmf) 2 upon the evaporation of solvent from the reaction. We observe a partial reversal of Th(bdc) 2 (dmf) 2 back to Th-UiO-66 upon hydrothermal treatment, indicating the complex dynamics of Th oxo species in solution. As a result, we report that isolated Ce-UiO-66 similarly transforms to a newly isolated 1D Ce III carboxylate chain MOF named NU-351 under the same conditions as Th-UiO-66, while Zr-UiO-66 and Hf-UiO-66 retain their structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural stability, dihydrogen bonding, and pressure-induced polymorphic transformations in hydrazine borane

Hydrazine borane (N 2 H 4 BH 3 ) has attracted considerable interest as a promising solid-state hydrogen storage material owing to its high hydrogen content and easy preparation. In this work, pressure-induced phase transitions of N 2 H 4 BH 3 were investigated using a combination of vibrational spectroscopy, X-ray diffraction, and density functional theory (DFT) up to 30 GPa. Our results showed that N 2 H 4 BH 3 exhibits remarkable structural stability in a very broad pressure region up to 15 GPa, and then two phase transitions were identified: the first one is from the ambient-pressure Pbcn phase to a Pbca phase near 15 GPa; the second is from the Pbca phase to a Pccn phase near 25 GPa. As revealed by DFT calculations, the unusual stability of N 2 H 4 BH 3 and the late phase transformations were attributed to the pressure-mediated evolutions of dihydrogen bonding frameworks, the compressibility and the enthalpies of the high-pressure polymorphs. In conclusion, our findings provide new insight into the structures and bonding properties of N 2 H 4 BH 3 that are important for hydrogen storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗