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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure

The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure , 27 , 1137–1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103 kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77 Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, |Δ ano |/σΔ ano ( d ′′/sig), approaches 1.4 at 3.4 Å resolution. The highly redundant, 11 000 000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP 4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP 4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix , SHELXC / D and PRASA as implemented in the CRANK 2 program suite were each employed to determine the sulfur substructure. All of these approaches were effective, although HySS , as a component of the phenix.autosol tool, required data from all crystals to find the positions of the sulfur atoms. Critical contributors in this case study to successful phase determination by SAD included (i) the high-flux FMX beamline, featuring helical-mode data collection and a helium-filled beam path, (ii) as recognized by many authors, a very highly redundant, multiple-crystal data set and (iii) the inclusion within that data set of data from crystals that were scanned over large ω ranges, yielding highly isomorphous and highly redundant intensity measurements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data Science in Chemical Engineering: Applications to Molecular Science

Chemical engineering is being rapidly transformed by the tools of data science. On the horizon, artificial intelligence (AI) applications will impact a huge swath of our work, ranging from the discovery and design of new molecules to operations and manufacturing and many areas in between. Early adoption of data science, machine learning, and early examples of AI in chemical engineering has been rich with examples of molecular data science—the application tools for molecular discovery and property optimization at the atomic scale. Here, we summarize key advances in this nascent subfield while introducing molecular data science for a broad chemical engineering readership. We introduce the field through the concept of a molecular data science life cycle and discuss relevant aspects of five distinct phases of this process: creation of curated data sets, molecular representations, data-driven property prediction, generation of new molecules, and feasibility and synthesizability considerations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

An interactive machine learning platform for analyzing multi-particle coincidence data from cold target recoil ion momentum spectroscopy

We present SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training), a comprehensive software platform for analyzing tabulated high-dimensional multi-particle coincidence data from Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) experiments. The software addresses critical challenges in modern momentum spectroscopy by integrating advanced machine learning techniques with physics-informed analysis in an interactive web-based environment. SCULPT implements uniform manifold approximation and projection for non-linear dimensionality reduction to reveal correlations in high-dimensional data. We also discuss potential extensions to deep autoencoders for feature learning and genetic programming for automated discovery of physically meaningful observables. A novel adaptive confidence scoring system provides quantitative reliability assessments by evaluating user-selected clustering quality metrics with predefined weights that reflect each metric’s robustness. The platform features configurable molecular profiles for different experimental systems, interactive visualization with selection tools, and comprehensive data filtering capabilities. Utilizing a subset of SCULPT’s capabilities, we analyze photo-double-ionization data measured using the COLTRIMS method for three-body dissociation of the D 2 O molecule, revealing distinct fragmentation channels and their correlations with physics parameters. The software’s modular architecture and web-based implementation make it accessible to the broader atomic and molecular physics community, significantly reducing the time required for complex multi-dimensional analyses. This opens the door to finding and isolating rare events exhibiting non-linear correlations on the fly during experimental measurements, which can help steer exploration and improve the efficiency of experiments.

Artificial neural networks↗
DOE OSTI2021

Nuclear Science for the Manhattan Project and Comparison to Today’s ENDF Data

Nuclear physics advances in the United States and Britain from 1939 to 1945 are described. The Manhattan Project’s work led to an explosion in our knowledge of nuclear science. A conference in April 1943 at Los Alamos provided a simple formula used to compute critical masses and laid out the research program needed to determine the key nuclear constants. In short order, four university accelerators were disassembled and reassembled at Los Alamos, and methods were established to make measurements on extremely small samples owing to the initial lack of availability of enriched 235U and plutonium. I trace the program that measured fission cross sections, fission-emitted neutron multiplicities and their energy spectra, and transport cross sections, comparing the measurements with our best understanding today as embodied in the Evaluated Nuclear Data File ENDF/B-VIII.0. The large nuclear data uncertainties at the beginning of the project, which often exceeded 25% to 50%, were reduced by 1945 often to less than 5% to 10%. Uranium-235 and plutonium-239 fission cross-section assessments in the fast mega-electron-volt range were reduced following more accurate measurements, and the neutron multiplicity $\overline{v}$ increased. By a lucky coincidence of canceling errors, the initial critical mass estimates were close to the final estimated masses. Some images from historical documents from our Los Alamos archives are shown. Many of the original measurements from these early years have not previously been widely available. Through this work, these data have now been archived in the international experimental nuclear reaction data library (EXFOR) in a collaboration with the International Atomic Energy Agency and Brookhaven National Laboratory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗
DOE OSTI2021

Bayesian automated weighting of aggregated DFT, MD, and experimental data for candidate thermodynamic models of aluminum with uncertainty quantification

Atomic-scale modeling methods such as density functional theory (DFT) and molecular dynamics (MD) can predict the thermodynamic properties of materials at a lower cost than experimental measurements. However, their regular usage in thermodynamic model construction is hampered by the lack of quantitative agreement with experimental measurements and the lack of uncertainty estimates on the data. To make regular usage of this atomistic simulation data, it is important to assess whether the atomistic simulation datasets, by themselves or in combination with experimental measurements, result in the same physics-informed models best supported by experimental measurements alone. Here, models of aluminum thermodynamic properties are discussed using three data sources: atomistic calculations (DFT and MD), experiments, and a combination of atomistic calculations and experiments. The study shows that, after ensuring self-consistency in predicting key invariant points, both experimental measurements and atomistic calculations can significantly contribute to an optimal model.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Deep potential molecular dynamics simulations of ion-enhanced etching of silicon by atomic chlorine

The continued development of plasma-assisted processing techniques requires a fundamental understanding of plasma-surface interactions. Molecular dynamics (MD) simulations have been employed to complement experimental studies and better understand the properties of such systems. Recently, machine learning (ML) methods have enabled the development of ab initio-based interatomic potentials, which can be generalized to complex combinations of multiple atom types. In this work, we use ML potentials developed using the Deep Potential Molecular Dynamics (DeepMD) framework to provide a model of ion-enhanced etching of Si by Cl atoms. We demonstrate the importance of proper selection of the training data set to the accuracy of the DeepMD model and compare our results to MD results using empirical potentials, as well as to experimental measurements. Exposure of undoped Si at 300 K to thermal Cl atoms yields a steady-state Cl coverage of 1.25 monolayers, which is slightly lower than the value obtained in previous experimental studies. Predictions of Si etch yields by simultaneous Cl atom and Ar + ion impacts as a function of ion energy, neutral to ion flux ratio, and angle of incidence of the ions are in reasonably good agreement with classical MD results and experimental measurements. Finally, etch yields and SiCl x mixed layer thicknesses during simultaneous bombardment of the Si(100) surface by Cl atoms and Cl + ions are in good agreement with experimental data. In conclusion, the present work is a necessary condition for the extension of the DeepMD procedure to more complex systems of interest in plasma-surface interactions.

Artificial neural networks↗
DOE OSTI2024

Massive all-atom analysis of 2D materials with quantum properties (Final report)

Improvements in microscopy have enabled the acquisition of data at a scale that is difficult to process manually, making automated machine learning approaches to analyzing experimental images essential. In this project, we developed and applied machine learning (ML) workflows for atomic resolution scanning transmission electron microscopy (STEM) images. This development included improving both methodology as well as generating user-friendly codes. We developed machine learning architectures which, after training, automatically identify the location and types of defects throughout a material. We used these data to produce class-averaged images of 2D atomic coordinates with up to 0.3 pm precision, uncovering the structure and oscillations of long-range strain fields around point defects in WSe 2-2x Te 2x . We also resolved a long-standing problem in this field in the training of ML models, a lack of labeled experimental data, by developing a cycle-GAN that transformed simulated-generated labeled data into labeled data indistinguishable from experiment and therefore suitable for training. This removed the remaining parts of the ML data processing workflow where human intervention was still critical and therefore a bottleneck to working at scale. Codes have been developed and released for this full machine learning workflow. ML approaches to partially automate STEM acquisition were also developed. Finally we applied ML and other advanced data processing methods to several materials science problems in two-dimensional materials, including studying the evolution of hyperuniformity with defect concentration in WSe2, understanding phase transformations in transition metal dichalcogenides during in-situ heating in the STEM, and exploring how 2D interfaces transform from twisted into aligned structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Long-Range Ordered Amorphous Atomic Chains as Building Blocks of a Superconducting Quasi-One-Dimensional Crystal

Crystalline and amorphous structures are two of the most common solid-state phases. Crystals having orientational and periodic translation symmetries are usually both short-range and long-range ordered, while amorphous materials have no long-range order. Short-range ordered but long-range disordered materials are generally categorized into amorphous phases. In contrast to the extensively studied crystalline and amorphous phases, the combination of short-range disordered and long-range ordered structures at the atomic level is extremely rare and so far has only been reported for solvated fullerenes under compression. Here, a report on the creation and investigation of a superconducting quasi-1D material with long-range ordered amorphous building blocks is presented. Using a diamond anvil cell, monocrystalline (TaSe4)(2)I is compressed and a system is created where the TaSe(4)atomic chains are in amorphous state without breaking the orientational and periodic translation symmetries of the chain lattice. Strikingly, along with the amorphization of the atomic chains, the insulating (TaSe4)(2)I becomes a superconductor. The data provide critical insight into a new phase of solid-state materials. The findings demonstrate a first ever case where superconductivity is hosted by a lattice with periodic but amorphous constituent atomic chains.

combination of crystalline and amorphous structure↗
DOE OSTI2023

Review of the 1st EUV Light Sources Code Comparison Workshop

We review the results of the 1 st Extreme Ultraviolet (EUV) Light Sources Code Comparison Workshop. The goal of this workshop was to provide a platform for specialists in EUV light source plasma modeling to benchmark and validate their numerical codes using well-defined case studies. Detailed consideration of a plethora of atomic collisional and radiative processes is required for modeling EUV light source plasmas. Eight institutions spanning four countries contributed data to the workshop. Two topics were addressed, namely (i) the atomic kinetics and radiative properties of tin plasmas under EUV-generating conditions and (ii) laser absorption in a fully ionized, one-dimensional hydrogen plasma. In this paper, we summarize the key findings of the workshop and outline plans for future iterations of the code comparison activity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

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

Measuring the oscillator strength of intercombination lines of helium-like V ions in a laser-produced-plasma

In this work, we present results of measurements of the oscillator strength of intercombination lines of He-like Vanadium ions in high energy density (HED) laser-produced-plasmas and compare them with the simulations from commonly used codes and data from the NIST database. Whilst not yet sufficiently accurate to constrain different trusted atomic-physics models for the particular system studied, our results are in agreement with the available data within experimental error bars, yet differ from cruder approximations of the oscillator strength used in certain atomic-kinetics packages, suggesting that this general method could be further extended to be used as a measurement of the oscillator strength of additional atomic transitions under the extreme conditions that are achieved in HED experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

The electronic structure of the actinide oxides and their singly and doubly charged cations: A ligand field approach

Abstract Ligand field theory (LFT) calculations of energy levels were performed for the neutral actinide monooxides ( An O) and their singly and doubly ionized cations ( An O + and An O 2+ ) by treating the molecular electronic states as An m+ free‐ion energy levels (where An ∈ Th through Lr and m = 1, 2, 3, or 4) perturbed by the electric field of O 2− or O − . LFT parameters obtained from fits to the energy levels of ThO, ThO + , UO, and UO + were used to compute molecular energy levels for the lowest energy (maximum S c , maximum L c ) 5 f ‐core states of An 4+ , An 3+ , An 2+ , and An + for the majority of the An 4+ O 2− , An 3+ O − , An 3+ O 2− , An 2+ O − , An 2+ O 2− , and An + O − electronic configurations. Simple linear relationships enabled predictions of the dissociation energies for An O, An O + and An O 2+ (where An ∈ Bk through Lr) and ionization energies for An O and An O + (where An ∈ Bk through Lr), mainly based on recent accurate experimental data for the ionization energies of An atoms (where An ∈ Fm, Md, No, and Lr) and correlations with the energetics of the atoms and ions.

Kaledin, Leonid A.↗
DOE OSTI2023

Comparison and multi-model inference of excess risks models for radiation-related solid cancer

In assessments of detrimental health risks from exposures to ionising radiation, many forms of risk to dose–response models are available in the literature. The usual practice is to base risk assessment on one specific model and ignore model uncertainty. The analysis illustrated here considers model uncertainty for the outcome all solid cancer incidence, when modelled as a function of colon organ dose, using the most recent publicly available data from the Life Span Study on atomic bomb survivors of Japan. Seven recent publications reporting all solid cancer risk models currently deemed plausible by the scientific community have been included in a model averaging procedure so that the main conclusions do not depend on just one type of model. The models have been estimated with different baselines and presented for males and females at various attained ages and ages at exposure, to obtain specially computed model-averaged Excess Relative Risks (ERR) and Excess Absolute Risks (EAR). Monte Carlo simulated estimation of uncertainty on excess risks was accounted for by applying realisations including correlations in the risk model parameters. Three models were found to weight the model-averaged risks most strongly depending on the baseline and information criteria used for the weighting. Fitting all excess risk models with the same baseline, one model dominates for both information criteria considered in this study. Based on the analysis presented here, it is generally recommended to take model uncertainty into account in future risk analyses.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2500+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with an emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with experimental data obtained from X-ray diffraction, infrared spectroscopy and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Analytical characterization of laser induced plasmas towards uranium isotopic analysis in gaseous uranium hexafluoride

To perform direct enrichment assay on gaseous uranium hexafluoride (UF 6 ) with laser induced breakdown spectroscopy (LIBS), the dominant spectral-line features, evolution of the signal and background of the U II 424.437 nm line, and its Stark width and shift, were studied as a function of UF 6 gas pressure and pulse energy of a nanosecond Nd:YAG laser. In this work, vapor pressure of UF 6 was found to be the most important parameter for LIBS analysis of gaseous UF 6 . Spectral congestion with numerous U lines of high excitation potential was observed and signal-to-background ratio (SBR) was low for measurements with 80 Torr UF 6 . Only when both UF 6 vapor pressure and laser pulse energy were low, for example, less than 20 Torr pressure and 30 mJ pulse energy, the resultant LIBS spectra from gaseous UF 6 resembled those obtained from solid U samples. The experimental data also suggest that U and F atoms recombine back to UF 6 after the laser pulse. The U emission was found to decay fast with a persistent background signal, degrading SBR with delay time. Systematic positive biases were found for UF 6 enrichment assays performed with the 235 U– 238 U line pair at 424.412–424.437 nm, which was confirmed to be caused by self-absorption. Even with optimization of experimental parameters and incorporation of a self-absorption term into the spectral-fitting algorithm, to reduce and compensate for self-absorption, self-absorption is still a main factor limiting accurate UF 6 enrichment assay. The use of another spectral window which contains no resonance lines is a prospective solution for the self-absorption issue.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

f-Orbital Mixing in the Octahedral f 2 Compounds UX 6 2– [X = F, Br, Cl, I] and PrCl 6 3–

Understanding how interactions between the f orbitals and ligand orbitals in lanthanide and actinide systems affect their physical properties is the central issue in f-element chemistry. A wide variety of approaches including both theoretical and experimental tools have been used to study these relationships. Among the most widely used tools has been crystal field theory (CFT), which bridges theory and experiment in that it is a model based largely on atomic theory that is parametrized using experimental data. Crystal field theory is quite accurate for the lanthanides, due in part to the highly contracted nature of the 4f orbitals. For actinides, crystal field theory is less accurate, potentially due to the treatment of orbital mixing. In CFT, orbital mixing is handled implicitly by allowing the electron repulsion parameters (Slater F k parameters) and the spin–orbit coupling constant to vary. As a result, orbital mixing in CFT is isotropic in that the F k parameters and the spin–orbit coupling constant affect all f orbitals equally. This approximation works well for the lanthanides due to the limited degree of orbital mixing in these complexes. In actinide complexes, the 5f orbitals have greater overlap with the ligand orbitals, and this approximation is less accurate than in the lanthanides. In this work, we report a modification of CFT that includes the effect of orbital mixing on electron repulsion and spin–orbit coupling for each f orbital. The model is applied to the tetravalent uranium hexahalide dianions and PrCl 6 3– for which the energies of many low-lying excited states are known. The new model generally fits the data as well the traditional CFT although with fewer parameters. However, the new model does not fit the data better than the more complex CFT models of Faucher and co-workers. The results of the model show in detail how changes in overlap and orbital energies influence the energies of the bonding and antibonding orbitals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Combined Machine Learning and Molecular Dynamics Reveal Two States of Hydration of a Single Functional Group of Cationic Polymeric Brushes

The state of hydration of a macromolecular system regulates a plethora of different properties of such a system. In this article, we develop a novel machine learning (ML) approach, based on the unsupervised clustering algorithm, for probing the hydration behavior of the {N(CH 3 ) 3 } + functional group of the PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] polyelectrolyte (PE) brush system. The PE brushes and the brush-supported water molecules and counterions (chloride ions) are first described using all-atom molecular dynamics (MD) simulations. The simulation data is subsequently used in our ML framework to identify that (1) the {N(CH 3 ) 3 } + functional groups of the PMETAC brushes have two distinct hydration states with one state (state 1) being characterized by less structured water molecules and the other state (state 2) being characterized by more structured water molecules and (2) an enhancement in the brush grafting density leads to the progressive dissapparenace of state 2. An increase in the grafting density increases the number of chloride counterions in a given volume around the {N(CH 3 ) 3 } + functional group and increases the number of shared water molecules between the {N(CH 3 ) 3 } + and Cl - . The chloride counterions are associated with a hydration layer with much less structured water molecules. Therefore, with an increase in the grafting density, an increase in the percentage of shared water molecules leads to the prevalence of the hydration state [of the {N(CH 3 ) 3 } + moiety] with less structured water molecules. Finally, we explain how the present findings are commensurate with two key previous related results, namely a significantly large chloride ion mobility inside the PMETAC brush layer and the {N(CH 3 ) 3 } + -Cl - average distance remaining independent of the PMETAC brush grafting density. Furthermore, we anticipate that the combined ML-MD-simulation approach proposed in this study can be adapted to probe other soft matter systems to reveal new insights of the underlying mechanisms of emergent phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗