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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 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

An Entropy-Maximization Approach to Automated Training Set Generation for Interatomic Potentials

Machine learning-based interatomic potentials are currently garnering a lot of attention as they strive to achieve the accuracy of electronic structure methods at the computational cost of empirical potentials. Given their generic functional forms, the transferability of these potentials is highly dependent on the quality of the training set, the generation of which can be highly labor-intensive. Good training sets should at once contain a very diverse set of configurations while avoiding redundancies that incur cost without providing benefits. We formalize these requirements in a local entropy-maximization framework and propose an automated sampling scheme to sample from this objective function. We show that this approach generates much more diverse training sets than unbiased sampling and is competitive with hand-crafted training sets.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Langevin Dynamics modeling of gas-phase ion-ion recombination (Final Technical Report)

A self-consistent trajectory simulation approach to model MN reactions (Fig. 1) which incorporates the probability of electron transfer as a Monte Carlo operator (Fig. 2) was developed and published as Liu et al. J. Chem. Phys. 159, 114111 (2023). The electron transfer probability p ET estimated using the two-state Landau-Zener (LZ) theory was incorporated into classical trajectory simulations to elicit predictions of MN reaction cross-section σ (vacuum) or rate constant β (finite pressure). Electronic structure calculations with multireference configuration interaction (MRCI) and large correlation consistent basis sets were used to derive inputs to the LZ theory. The key advance of our trajectory simulation approach is the incorporation of electron transfer probability and the inclusion of the effect of ion-neutral interactions on MN using a Langevin representation of the effect of neutral gas on ions. For H + – H - and Li + – H(D) - pairs, our approach quantitatively agrees with measured speed-dependent cross-sections for up to ~10 5 m/s. For the ion pair Ne + – Cl - , our predictions of the MN rate constant at ~1 torr are a factor of ~2 – 3 higher than the experimentally measured value. Similarly, for Xe + – F - in the pressure range of ~20000 – 80000 Pa, our predictions of the MN rate constant are ~20% lower but are in excellent qualitative agreement with experimental data. The paradigm of using trajectory simulations to self-consistently model MN reactions is the basis for inclusion of additional non-classical, and static magnetic and electric field effects. Subsequent work, published as Roy et al. focused on modeling recombination rate constant for three ion pairs (rare gas Ar + cation and halide anions): Ar + – Cl - , Ar + – Br - , Ar + – I - , 2) considering spin-orbit couplings in the electronic structure calculations to obtain high-fidelity estimates of the electron transfer probability and incorporated within the classical trajectory simulations to elicit predictions. In addition to calculations of ion-ion recombination rate constants, a classical trajectory simulation technique (published as Roy et al. J. Chem. Phys. 162(9), 094104 (2023)) that uses quaternions to represent orientation of non-spherical particles (ions or aerosol particles) was developed to simulate the recombination of diatomic or more generally, polyatomic molecules. Finally, several other ion pairs such as Ne + – Cl - , Kr + – Cl - , were explored using the developed semi-classical trajectory simulations to understand various challenges in tackling electronic structure calculations. Using empirical approaches to parameterize the electron transfer radius, trajectory simulations were also used to probe the effect of ion number density on MN rate constant.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

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

Multi-modal Approach to Modeling Creep Deformation in Nickel-base Superalloy

This study developed the multi-modal modeling approaches to elucidate the physical and overall mechanical properties of two complex alloy systems of Ni-based Superalloys, namely Haynes 282 and Inconel 740. The overall strategies employed systematically in different scales of modeling are based on the common structural framework of the multi phases that made up the Ni-based Superalloys, namely the matrix phase of the Gamma ($\gamma$) phase which is embedded with ordered Gamma prime ($\gamma$’) precipitates and decorated with the dispersions of mostly carbide precipitates. With this in mind, we had set up the modeling platforms to incorporate a wide range of scales, starting from electronic structures to the continuum level via the crystal plasticity model.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2021

Are All Post-starbursts Mergers? HST Reveals Hidden Disturbances in the Majority of PSBs

How do galaxies transform from blue, star-forming spirals to red, quiescent early-type galaxies? To answer this question, we analyzed a set of 26 gas-rich, shocked post-starburst galaxies with Hubble Space Telescope (HST) imaging in $B$, $I$, and $H$ bands and Sloan Digital Sky Survey (SDSS) $i$-band imaging of similar depth but lower resolution. We found that post-starbursts in our sample have intermediate morphologies between disk- and bulge dominated (Sérsic $n$ = ${1.7}_{-0.0}^{+0.3}$ ) and have red bulges, likely due to dust obscuration in the cores. A majority of galaxies in our sample are more morphologically disturbed than regular galaxies (88%, corresponding to >3$σ$ significance) when observed with HST, with asymmetry and Sérsic residual flux fraction being the most successful measures of disturbance. Most disturbances are undetected at the lower resolution of SDSS imaging. Although ~27% galaxies are clear merger remnants, we found that disturbances in another ~30% of the sample are internal, caused by small-scale perturbations or dust substructures rather than tidal features, and require high-resolution imaging to detect. We found 2.8$σ$ evidence that asymmetry features fade on timescales ~200 Myr, and may vanish entirely after ~750 Myr, so we do not rule out a possible merger origin of all post-starbursts given that asymmetric features may have already faded. This work highlights the importance of small-scale disturbances, detected only in high-resolution imaging, in understanding structural evolution of transitioning galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Bayesian chain graph models to characterize microbe-environment dynamics

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data.

compositional data↗
DOE OSTI2021

Assessment of Local Observation of Atomic Ordering in Alloys via the Radial Distribution Function: A Computational and Experimental Approach

As a powerful analytical technique, atom probe tomography (APT) has the capacity to acquire the spatial distribution of millions of atoms from a complex sample. However, extracting information at the Ångstrom-scale on atomic ordering remains a challenge due to the limits of the APT experiment and data analysis algorithms. The development of new computational tools enable visualization of the data and aid understanding of the physical phenomena such as disorder of complex crystalline structures. Here, we report progress towards this goal using two steps. We describe a computational approach to evaluate atomic ordering in the crystal structure by generating radial distribution functions (RDF). Atomic ordering is rendered as the Fractional Cumulative Radial Distribution Function (FCRDF) which allows for greater visibility of local compositions at short range in the structure. Further, we accommodate in the analysis additional parameters such as uncertainty in the atomic coordinates and the atomic abundance to ascertain short-range ordering in APT data sets. We applied the FCRDF analysis to synthetic and experimental APT data sets for Ni 3 Al. The ability to observe a signal of atomic ordering consistent with the known L1 2 crystal structure is heavily dependent on spatial uncertainty, irrespective of abundance. Detection of atomic ordering is subject to an upper limit of spatial uncertainty of atoms described with Gaussian distributions with a standard deviation of 1.3 Å. The FCRDF analysis was also applied to the APT data set for a six-component alloy, Al 1.3 CoCrCuFeNi. In this case, we are currently able to visualize elemental segregation at the nanoscale, though unambiguous identification of atomic ordering at the Ångstrom (nearest-neighbor) scale remains a goal.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Design principles for site-selective hydroxylation by a Rieske oxygenase

Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Calculating the grain boundary inclination of voxelated grain structures using a smoothing algorithm

We have developed a flexible method for calculating the grain boundary (GB) inclinations of voxelated grain structure data using smoothing algorithms. We compared the performance of four algorithms: the linear interpolation, Allen–Cahn, level-set, and vertex algorithms. We assessed their accuracy using 2D and 3D cases with known inclinations. The vertex algorithm provided the best balance between accuracy and efficiency for 2D structures while the linear interpolation algorithm provided the best balance for 3D structures. We compared the GB inclinations calculated using our smoothing method on a 3D high energy X-ray diffraction microscopy (HEDM) dataset to those determined by meshing the GBs. The two approaches determined similar GB plane distributions, though they varied significantly at triple junctions. In conclusion, the smoothing method was demonstrated for two sources of 3D voxelated grain structures: HEDM data and results from Monte Carlo Potts grain growth simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗
DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2024

Harmonic analysis of discrete tracers of large-scale structure

It is commonplace in cosmology to analyze fields projected onto the celestial sphere, and in particular density fields that are defined by a set of points e.g. galaxies. When performing an harmonic-space analysis of such data (e.g. an angular power spectrum) using a pixelized map one has to deal with aliasing of small-scale power and pixel window functions. We compare and contrast the approaches to this problem taken in the cosmic microwave background and large-scale structure communities, and advocate for a direct approach that avoids pixelization. We describe a method for performing a pseudo-spectrum analysis of a galaxy data set and show that it can be implemented efficiently using well-known algorithms for special functions that are suited to acceleration by graphics processing units (GPUs). The method returns the same spectra as the more traditional map-based approach if in the latter the number of pixels is taken to be sufficiently large and the mask is well sampled. The method is readily generalizable to cross-spectra and higher-order functions. It also provides a convenient route for distributing the information in a galaxy catalog directly in harmonic space, as a complement to releasing the configuration-space positions and weights, and a route to spectral apodization. Finally, we make public a code enabling the application of our method to existing and upcoming datasets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Discontinuous Galerkin discretization for quantum simulation of chemistry

All-electron electronic structure methods based on the linear combination of atomic orbitals method with Gaussian basis set discretization offer a well established, compact representation that forms much of the foundation of modern correlated quantum chemistry calculations—on both classical and quantum computers. Despite their ability to describe essential physics with relatively few basis functions, these representations can suffer from a quartic growth of the number of integrals. Recent results have shown that, for some quantum and classical algorithms, moving to representations with diagonal two-body operators can result in dramatically lower asymptotic costs, even if the number of functions required increases significantly. We introduce a way to interpolate between the two regimes in a systematic and controllable manner, such that the number of functions is minimized while maintaining a block-diagonal structure of the two-body operator and desirable properties of an original, primitive basis. Techniques are analyzed for leveraging the structure of this new representation on quantum computers. Empirical results for hydrogen chains suggest a scaling improvement from O(N 4.5 ) in molecular orbital representations to O(N 2.6 ) in our representation for quantum evolution in a fault-tolerant setting, and exhibit a constant factor crossover at 15 to 20 atoms. Moreover, we test these methods using modern density matrix renormalization group methods classically, and achieve excellent accuracy with respect to the complete basis set limit with a speedup of 1–2 orders of magnitude with respect to using the primitive or Gaussian basis sets alone. These results suggest our representation provides significant cost reductions while maintaining accuracy relative to molecular orbital or strictly diagonal approaches for modest-sized systems in both classical and quantum computation for correlated systems.

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

Six-dimensional matching of intense beam with linear accelerating structure

Beam matching is a common technique that is routinely employed in accelerator design with the aim of minimizing beam losses and preservation of beam brightness. Despite being widely used, a full theoretical understanding of beam matching in 6D remains elusive. In this work, we present an analytical treatment of 6D beam matching of a high-intensity beam onto an RF structure. We begin our analysis within the framework of a linear model, and apply the averaging method to a set of 3D beam envelope equations. Accordingly, we obtain a matched solution that is comprised of smoothed envelopes and periodic terms, describing envelope oscillations with the period of the focusing structure. We then consider the nonlinear regime, where the beam size is comparable with the separatrix size. Stating with a Hamiltonian analysis in 6D phase space, we attain a self-consistent beam profile and show that it is significantly different from the commonly used ellipsoidal shape. Subsequently, we analyze the special case of an equilibrium with equal space charge depression between all degrees of freedom. Comparison of beam dynamics for equipartitioned, equal space charge depression, and equal emittances beams is given. Finally, we present experimental results on beam matching in the LANSCE linac.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Salt-Induced Polymorphs Observed in Colloidal Single Crystals

Polymorphs are solid materials with the same chemical composition but different crystallographic structures. A unique aspect of polymorphs is that they exhibit different physical properties, such as solubility, melting point, density, color, hardness, and bioavailability. Here, we synthesized polymorphs of colloidal crystals engineered with DNA by slow-cooling gold nanoparticle-core programmable atom equivalents (PAEs, particles with DNA sequences that control their bonding characteristics) under salt concentrations ranging from 0.5 to 4 M NaCl. This approach yielded a diverse set of single-crystalline phases with cubic, tetragonal, and hexagonal lattice symmetries. The structural transitions observed here arise solely from the modulation of interparticle repulsion via ionic strength and thermal processing. Notably, in certain cases, we observed diffusionless phase transformations, wherein the superlattices evolve from cubic to lower-symmetry tetragonal lattices. By tuning the thermal stability and salt concentration, we captured intermediate, metastable body-centered tetragonal structures during the slow-cool process, indicating that subtle changes in free energy can direct crystallization to low-symmetry phases. In conclusion, this study demonstrates that thermal and ionic parameters can be tuned to access and stabilize colloidal crystal polymorphs with emergent structures and interesting functional properties.

Colloidal crystallization↗
DOE OSTI2025

Density Functional Tight Binding Insights into Plasmonic Silver–Platinum Nanoparticles and Alloys for Enhanced Photocatalysis

Developing accurate and efficient Slater-Koster (SK) tight-binding parameter sets is essential for quantum plasmonic studies of alloyed metal nanoparticles, as conventional time dependent density functional theory (TD-DFT) calculations are computationally prohibitive for larger clusters. In this work, we develop and validate density functional tight binding (DFTB) parameter sets for both ground state (GS-SK) and excited state (ES-SK) calculations to study the structural, electronic, and optical properties of silver (Ag), platinum (Pt), and Ag–Pt nanoalloys. Our investigation of the ground state properties demonstrates that the GS-SK parameters enable DFTB to closely reproduce the electronic structures of platinum clusters with diverse sizes and geometries – showing qualitative agreement with DFT for density of states (DOS) profiles and energy levels. The ES-SK parameters accurately describe excited-state properties compared to TD-DFT reference calculations, including the broad, featureless absorption profiles of Pt that are dominated by interband transitions. Using the ES-SK parameters within a real-time TD-DFTB framework, we compute size-dependent optical absorption spectra of Ag, Pt and Ag-Pt nanocubes containing up to 1099 atoms (size ∼4.18 nm). A detailed study of Ag–Pt and Pt-Ag core–shell nanoparticles shows quenching of the Ag plasmon resonance even at monolayer coverage for Ag-Pt, but not for Pt-Ag. We also show how to define submonolayer Ag-core Pt-shell cubic structures that have similar optical properties to those generated experimentally for much larger particles, which offers potential for describing plasmon-enhanced photocatalysis. Collectively, the GS-SK and ES-SK parameter sets provide an accurate, computationally efficient approach for modeling the complex optical and electronic behavior of noble–transition metal nanostructures and their alloys.

SPR↗
DOE OSTI2022

Review of Residual Stresses in Spent Nuclear Fuel Canisters

This report compiles the set of published results on the welding residual stress (WRS) distributions across the thickness section at the welds in spent nuclear fuel (SNF) canisters before and after a repair is done. The WRS information for similar steel structures with thick (~ 12.7 mm (0.5 inch)) large plate construction are also compiled to provide a comprehensive set of information on: methods to quantify; modeling to estimate; and methods to reduce WRS.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗