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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 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Computational investigation of hysteresis and phase equilibria of n-alkanes in a metal-organic framework with both micropores and mesopores

Abstract Adsorption hysteresis is a phenomenon related to phase transitions that can impact applications such as gas storage and separations in porous materials. Computational approaches can greatly facilitate the understanding of phase transitions and phase equilibria in porous materials. In this work, adsorption isotherms for methane, ethane, propane, and n-hexane were calculated from atomistic grand canonical Monte Carlo (GCMC) simulations in a metal-organic framework having both micropores and mesopores to better understand hysteresis and phase equilibria between connected pores of different size and the external bulk fluid. At low temperatures, the calculated isotherms exhibit sharp steps accompanied by hysteresis. As a complementary simulation method, canonical (NVT) ensemble simulations with Widom test particle insertions are demonstrated to provide additional information about these systems. The NVT+Widom simulations provide the full van der Waals loop associated with the sharp steps and hysteresis, including the locations of the spinodal points and points within the metastable and unstable regions that are inaccessible to GCMC simulations. The simulations provide molecular-level insight into pore filling and equilibria between high- and low-density states within individual pores. The effect of framework flexibility on adsorption hysteresis is also investigated for methane in IRMOF-1.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ultra-low field 13 C MRI of hyperpolarized pyruvate

Medicine is evolving beyond therapy largely predicated on anatomical information and towards incorporating patient-specific molecular biomarkers of disease for more accurate diagnosis and effective treatment. The complementary combination of hyperpolarization by spin-lock induced crossing signal amplification by reversible exchange (SLIC SABRE) and low field magnetic resonance imaging (MRI) can enable accessible metabolic imaging to advance personalized medicine. Hyperpolarized 13 C-enriched pyruvate has demonstrated promise for imaging metabolism in cancer, heart disease and neurodegenerative disorders; however, broader clinical adoption awaits validated clinical indications, and is further constrained by the cost and limited availability of current hyperpolarization technology. Parahydrogen-based polarization techniques, paired with low-cost high-performance MRI at millitesla fields, offer a means of broadening the reach of metabolic imaging. Here we show results demonstrating in situ hyperpolarization of pyruvate at 6.5 mT by SLIC SABRE, followed by immediate readout without field cycling or sample shuttling. We achieve 13 C signal enhancements several million times above thermal equilibrium at 6.5 mT, corresponding to polarization levels of approximately 3%. Leveraging this enhancement, we perform 13 C MRI and acquire NMR spectra with resolution sufficient to distinguish chemical shifts between pyruvate isotopomers. These results show a viable pathway towards accessible metabolic imaging with hyperpolarized 13 C MRI at ultra-low field.

Medical and clinical diagnostics↗
DOE OSTI2021

Matryoshka phonon twinning in α-GaN

Understanding lattice dynamics is crucial for effective thermal management in electronic devices because phonons dominate thermal transport in most semiconductors. α -GaN has become a focus of interest as one of the most important third-generation power semiconductors, however, the knowledge on its phonon dynamics remains limited. Here we show a Matryoshka phonon dispersion of α -GaN with the complementary inelastic X-ray and neutron scattering techniques and the first-principles calculations. Such Matryoshka twinning throughout the basal plane of the reciprocal space is demonstrated to amplify the anharmonicity of the related phonons through creating abundant three-phonon scattering channels and cutting the lifetime of affected modes by more than 50%. Such phonon topology contributes to reducing the in-plane thermal transport, thus the anisotropic thermal conductivity of α -GaN. The results not only have implications for engineering the thermal performance of α -GaN, but also offer valuable insights on the role of anomalous phonon topology in thermal transport of other technically semiconductors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Discovering nuclear models from symbolic machine learning

Numerous phenomenological nuclear models have been proposed to describe specific observables within different regions of the nuclear chart. However, developing a unified model that describes the complex behavior of all nuclei remains an open challenge. Here, we explore whether symbolic Machine Learning (ML) can rediscover traditional nuclear physics models or identify alternatives with improved simplicity, fidelity, and predictive power. To address this challenge, we developed a Multi-objective Iterated Symbolic Regression approach that handles symbolic regressions over multiple target observables, accounts for experimental uncertainties and is robust against high-dimensional problems. As a proof of principle, we applied this method to describe the nuclear binding energies and charge radii of light and medium mass nuclei. Our approach identified simple analytical relationships based on the number of protons and neutrons, providing interpretable models with precision comparable to state-of-the-art nuclear models. Additionally, we integrated this ML-discovered model with an existing complementary model to estimate the limits of nuclear stability. These results highlight the potential of symbolic ML to develop accurate nuclear models and guide our description of complex many-body problems.

Nuclear structure↗
DOE OSTI2025

Global tuning of hadronic interaction models with accelerator-based and astroparticle data

In high-energy and astroparticle physics, event generators play an essential role, even in the simplest data analyses. As analysis techniques become more sophisticated, e.g. based on deep neural networks, their correct description of the observed event characteristics becomes even more important. Physical processes occurring in hadronic collisions are simulated within a Monte Carlo framework. A major challenge is the modeling of hadron dynamics at low momentum transfer, which includes the initial and final phases of every hadronic collision. QCD-inspired phenomenological models used for these phases cannot guarantee completeness or correctness over the full phase space. These models usually include parameters which must be tuned to suitable experimental data. Until now, event generators have been developed and tuned mainly on the basis of data from high-energy physics experiments at accelerators. The wealth of data available from the latest generation of astroparticle experiments has not yet been fully exploited, and in many cases is not satisfactorily described. Both kinds of data sets are complementary as astroparticle experiments provide sensitivity especially to hadrons produced nearly parallel to the collision axis and cover center-of-mass energies up to several hundred TeV, well beyond those reached at colliders so far. In this report, we provide an overview of state-of-the-art event generators and their tuning, including the most relevant inputs from high-energy accelerator and astroparticle experiments. We present a road map that shows, for the first time, how the unified tuning of event generators with accelerator-based and astroparticle data can be performed.

Albrecht, J. [Ruhr U., Bochum, RAPP Ctr.; Ruhr U.,↗
DOE OSTI2026

Radioactive molecules as laboratories of fundamental physics

Radioactive molecules provide a new platform in the search for new physics, at energy scales complementary to those probed by high-energy particle colliders. Here, by combining enhancements from nuclear properties with the sensitivity and control offered by molecular structure, experiments with radioactive molecules offer great reach in the search for physics beyond the standard model. Progress in this field is being driven by advances in the production and control of radioactive molecules, alongside the development of new experimental tools and theoretical techniques. In this Perspective, we discuss the current status and future prospects of this rapidly developing, interdisciplinary field at the intersection of nuclear physics, atomic and molecular physics and particle physics.

Jadbabaie, A. [Massachusetts Institute of Technolo↗
DOE OSTI2023

Hybrid microstructure of smectite clay gels revealed using neutron and synchrotron X-ray scattering

Aqueous suspensions of swelling clays display a nematic sol-gel transition at very low solid concentrations. The underlying microstructure of the gel has remained a point of contention since the time of Irving Langmuir and has been a major obstacle to fully realizing the potential of clays for practical applications. Here, we comprehensively probe the microstructure of a smectite clay suspension using ultra-small angle neutron/X-ray scattering and find that the nematic gel is structurally ordered and contains entities that are at least an order of magnitude larger than the individual particles. Complementary cryo-electron microscopy shows the presence of domains having particle-particle ordering responsible for nematic texture and regions of particle-particle aggregation responsible for gel-like behavior. We find that the smectic clay gels have a hybrid microstructure with co-existing repulsive nematic domains and attractive disordered domains.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Tracking the dynamics of catalytic Pt/CeO2 active sites during water-gas-shift reaction

Abstract Understanding the atomistic structure of the active site during catalytic reactions is of paramount importance in both fundamental studies and practical applications, but such studies are challenging due to the complexity of heterogeneous systems. Here, we use Pt/CeO 2 as an example to study the dynamic nature of active sites during the water-gas-shift reaction (WGSR) by combining multiple in situ characterization tools. We show that the different concentrations of interfacial Pt δ+ – O – Ce 4+ moieties at Pt/CeO 2 interfaces are responsible for the rank of catalytic performance of Pt/CeO 2 catalysts: Pt/CeO 2 -rod > Pt/CeO 2 -cube > Pt/CeO 2 -oct. For all the catalysts, metallic Pt is formed during the WGSR, leading to the transformation of the active sites to Pt 0 – O v – Ce 3+ and interface reconstruction. These findings shed light on the nature of the active site for the WGSR on Pt/CeO 2 and highlight the importance of combining complementary in situ techniques for establishing structure-performance relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Quantum defects in carbon nanotubes as single-photon sources

Single-photon emitters are essential components of emerging quantum technologies, including secure communication and quantum computing. Single-walled carbon nanotubes (SWCNTs) have emerged as a promising platform for quantum light sources due to their quasi-one-dimensional excitonic host structure and compatibility with telecom photonic systems. Recent advances in deterministic defect engineering—most notably the development of organic color centers (OCCs)—have enabled stable, chemically controllable, and spectrally tunable single-photon emission. OCC-based emitters have demonstrated single-photon purity exceeding 99% and, more recently, room-temperature photon indistinguishability, placing them among the few solid-state systems with quantum-grade performance under ambient conditions. This review surveys progress in the field from three complementary perspectives: chemical synthesis and quantum defect engineering, computational studies of structure-property relationships and excitonic behavior, and experimental investigations of quantum optical properties. We also discuss alternative approaches, including air-suspended SWCNTs and hybrid van der Waals heterostructures, highlighting opportunities and open challenges for scalable integration into quantum photonic platforms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

A Permanently Porous Chalcogen-Bonded Organic Framework

The nature of connectivity between constituent atomic or molecular building blocks is fundamental in shaping the properties and functionality of materials. The extrapolation of emergent interatomic interactions to enable functional materials has driven transformative technological advancements. However, the bonding interactions used in material design have been largely static since the emergence of dynamic covalent chemistry ~30 years ago. Here we demonstrate that non-covalent chalcogen bonding (Ch-bonding) is a distinct mode of interatomic connectivity for constructing functional materials by design. This is established by leveraging self-complementary assembly of 1,2,5-telluradiazole moieties to construct a honeycomb-type permanently porous Ch-bonded organic framework, assembled and stabilized solely through non-covalent Te...N contacts. Empirical and computational studies of electronic structure, structural healing and lattice dynamics highlight the pi-type electronic communication, controlled assembly and modulated lattice dynamics in Trip3Tez-I arising directly from the unique nature of the Te...N Ch-bonding that holds substantial implications for next generation crystalline semiconductors. In addition to introducing a distinct class of permanently porous frameworks, this work establishes Ch-bonding as a programmable molecular tool for constructing functional materials with distinct properties.

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

Mapping of the mechanical response in Si/SiGe nanosheet device geometries

Abstract The performance of next-generation, nanoelectronic devices relies on a precise understanding of strain within the constituent materials. However, the increased flexibility inherent to these three-dimensional device geometries necessitates direct measurement of their deformation. Here we report synchrotron x-ray diffraction-based non-destructive nanoscale mapping of Si/SiGe nanosheets for gate-all-around structures. We identified two competing mechanisms at different length scales contributing to the deformation. One is consistent with the in-plane elastic relaxation due to the Ge lattice mismatch with the surrounding Si. The second is associated with the out-of-plane layering of the Si and SiGe regions at a length scale of film thickness. Complementary mechanical modeling corroborated the qualitative aspects of the deformation profiles observed across a variety of nanosheet sample widths. However, greater deformation is observed in the SiGe layers of the nanosheets than the predicted distributions. These insights could play a role in predicting carrier mobilities of future devices.

Murray, Conal E. (ORCID:0000000199014290)↗
DOE OSTI2020

Is Cs 2 TiBr 6 a promising Pb-free perovskite for solar energy applications?

In a quest for Pb-free perovskites suitable for solar energy applications, Cs 2 TiBr 6 has recently been reported as a promising compound, with appropriate optical and electrical properties as well as high stability under environmental stresses. In this study, we pursue investigation on this compound, demonstrating phase pure Cs 2 TiBr 6 powder formation using solution synthesis and providing complementary experimental characterization and theoretical calculations. An experimental absorption onset of around 2.0 eV is extracted and a weak broad photoluminescence is measured. Density functional theory calculations predict an indirect bandgap, parity-forbidden for both the direct and indirect transitions, which explains the weak and Stokes shifted luminescence. Additionally, we highlight the strong instability of Cs 2 TiBr 6 powder in ambient atmosphere. Therefore, our experimental results supported by theoretical calculations differ from previous results and raise doubts on the suitability of Cs 2 TiBr 6 in its pristine form for solar energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Iminoguanidines: from anion recognition and separation to carbon capture

Iminoguanidines, first reported in 1898, have received renewed attention in the last 5 years due to their ability to recognize and separate anions from competitive aqueous environments. Iminoguanidines display high recognition abilities towards hydrophilic oxyanions (e.g., sulfate, chromate, carbonate) through strong and complementary hydrogen bonding from the guanidinium groups. Here, this feature article reviews the fundamental anion recognition chemistry of iminoguanidines, as well as real-world applications including sulfate removal from seawater and CO 2 capture for climate change mitigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Formic acid catalyzed isomerization and adduct formation of an isoprene-derived Criegee intermediate: experiment and theory

Isoprene is the most abundant non-methane hydrocarbon emitted into the Earth's atmosphere. Ozonolysis is an important atmospheric sink for isoprene, which generates reactive carbonyl oxide species (R 1 R 2 C[double bond, length as m-dash]O + O – ) known as Criegee intermediates. This study focuses on characterizing the catalyzed isomerization and adduct formation pathways for the reaction between formic acid and methyl vinyl ketone oxide (MVK-oxide), a four-carbon unsaturated Criegee intermediate generated from isoprene ozonolysis. syn-MVK-oxide undergoes intramolecular 1,4 H-atom transfer to form a substituted vinyl hydroperoxide intermediate, 2-hydroperoxybuta-1,3-diene (HPBD), which subsequently decomposes to hydroxyl and vinoxylic radical products. In this paper, we report direct observation of HPBD generated by formic acid catalyzed isomerization of MVK-oxide under thermal conditions (298 K, 10 torr) using multiplexed photoionization mass spectrometry. The acid catalyzed isomerization of MVK-oxide proceeds by a double hydrogen-bonded interaction followed by a concerted H-atom transfer via submerged barriers to produce HPBD and regenerate formic acid. The analogous isomerization pathway catalyzed with deuterated formic acid (D2-formic acid) enables migration of a D atom to yield partially deuterated HPBD (DPBD), which is identified by its distinct mass (m/z 87) and photoionization threshold. In addition, bimolecular reaction of MVK-oxide with D 2 -formic acid forms a functionalized hydroperoxide adduct, which is the dominant product channel, and is compared to a previous bimolecular reaction study with normal formic acid. Complementary high-level theoretical calculations are performed to further investigate the reaction pathways and kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Sulfur Kβ X-ray emission spectroscopy: comparison with sulfur K-edge X-ray absorption spectroscopy for speciation of organosulfur compounds

Until recently, sulfur was known as a “spectroscopically silent” element because of a paucity of convenient spectroscopic probes suitable for in situ chemical speciation. In recent years the technique of sulfur K-edge X-ray absorption spectroscopy (XAS) has been used extensively in sulfur speciation in a variety of different fields. With an initial focus on reduced forms of organic sulfur, we have explored a complementary X-ray based spectroscopy – sulfur Kβ X-ray emission spectroscopy (XES) – as a potential analytical tool for sulfur speciation in complex samples. In this work, we compare and contrast the sensitivity of sulfur Kβ XES with that of sulfur K-edge XAS, and find differing sensitivities for the two techniques. In some cases an approach involving both sulfur K-edge XAS and sulfur Kβ XES may be a powerful combination for deducing sulfur speciation in samples containing complex mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A non-perturbative pairwise-additive analysis of charge transfer contributions to intermolecular interaction energies

Energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs) decomposes the interaction energy between molecules into physically interpretable components like geometry distortion, frozen interactions, polarization, and charge transfer (CT, also sometimes called charge delocalization) interactions. In this work, a numerically exact scheme to decompose the CT interaction energy into pairwise additive terms is introduced for the ALMO-EDA using density functional theory. Unlike perturbative pairwise charge-decomposition analysis, the new approach does not break down for strongly interacting systems, or show significant exchange–correlation functional dependence in the decomposed energy components. Both the energy lowering and the charge flow associated with CT can be decomposed. Complementary occupied–virtual orbital pairs (COVPs) that capture the dominant donor and acceptor CT orbitals are obtained for the new decomposition. It is applied to systems with different types of interactions including DNA base-pairs, borane-ammonia adducts, and transition metal hexacarbonyls. While consistent with most existing understanding of the nature of CT in these systems, we report the results also reveal some new insights into the origin of trends in donor–acceptor interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗