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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Multi-reward reinforcement learning based development of inter-atomic potential models for silica

Abstract Silica is an abundant and technologically attractive material. Due to the structural complexities of silica polymorphs coupled with subtle differences in Si–O bonding characteristics, the development of accurate models to predict the structure, energetics and properties of silica polymorphs remain challenging. Current models for silica range from computationally efficient Buckingham formalisms (BKS, CHIK, Soules) to reactive (ReaxFF) and more recent machine-learned potentials that are flexible but computationally costly. Here, we introduce an improved formalism and parameterization of BKS model via a multireward reinforcement learning (RL) using an experimental training dataset. Our model concurrently captures the structure, energetics, density, equation of state, and elastic constants of quartz (equilibrium) as well as 20 other metastable silica polymorphs. We also assess its ability in capturing amorphous properties and highlight the limitations of the BKS-type functional forms in simultaneously capturing crystal and amorphous properties. We demonstrate ways to improve model flexibility and introduce a flexible formalism, machine-learned ML-BKS, that outperforms existing empirical models and is on-par with the recently developed 50 to 100 times more expensive Gaussian approximation potential (GAP) in capturing the experimental structure and properties of silica polymorphs and amorphous silica.

36 MATERIALS SCIENCE↗
DOE OSTI2016

New polarisation effects in saturated absorption spectroscopy in the field of counterpropagating light waves

The effect of a double structure of saturated absorption resonance in the field of counterpropagating light waves interacting with atomic gas is considered, which was first studied experimentally and theoretically by Vasil'ev et al. [V.V. Vasil'ev et al., J. Exp. Theor. Phys., 112, 770 (2011)]. The effect manifests itself as a new nonlinear resonance formed as a peak in the absorption spectrum of the probe wave. The resonance is observed inside a 'conventional' dip in the spectrum of saturated absorption. Previously, this effect was theoretically described only in the frameworks of the two-level atomic model, i.e., without making allowance for degeneracy of atomic energy levels with respect to the projection of the total angular momentum and for the vector nature of light. We extend the theory of the effect to the case of real atomic systems with degenerate energy levels and arbitrary polarisations of light waves. In particular, on an example of the simple transition F{sub g} = 1 → F{sub e} = 0 we show that polarisation parameters of light waves may significantly affect the contrast of the new effect and the possibility of observing it at all. Conclusions of the work are confirmed both analytically and bnumerically. (laser spectroscopy)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex

The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133 55–502 ) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Low to intermediate energy elastic electron scattering from dichloromethane (CH 2 Cl 2 )

We report a theoretical-experimental investigation of electron scattering by dichloromethane (CH 2 Cl 2 ) in the low- and intermediate energy ranges. Experimental elastic differential cross sections (DCS), in the incident electron energy range of 0.5–800 eV and scattering angle range of 10°–130°, were measured using a crossed beam relative flow technique. Integral and momentum-transfer cross sections were determined from the experimental DCS. Theoretical elastic differential, integral, and momentum-transfer, as well as grand-total, and total absorption cross sections were also calculated for impact energies ranging from 0.5 to 500 eV. A complex optical Hartree–Fock potential represented the electron-target interaction and a single-center expansion method combined with a Padé approximation was used to solve the scattering equations. Three resonances: a 2 A 1 C–Cl k σ * resonance centered at about 3.5 eV, a 2 B 2 C–Cl k σ * resonance centered at about 5 eV and a broad 2 A 1 C–H k σ * resonance at about 10 eV were detected in our calculation. Further calculations of DCS were performed at an intermediate energy range of 50–800 eV, using the independent-atom model in which the atomic complex optical potential and partial-wave method were used to obtain atomic scattering amplitudes. In conclusion, comparisons of our experimental and theoretical data with very recent experimental and theoretical results are made.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Artificial intelligence for advanced functional materials: exploring current and future directions

This perspective addresses the topic of harnessing the tools of artificial intelligence (AI) for boosting innovation in functional materials design and engineering as well as discovering new materials for targeted applications in energy storage, biomedicine, composites, nanoelectronics or quantum technologies. It gives a current view of experts in the field, insisting on challenges and opportunities provided by the development of large materials databases, novel schemes for implementing AI into materials production and characterization as well as progress in the quest of simulating physical and chemical properties of realistic atomic models reaching the trillion atoms scale and with near ab initio accuracy.

36 MATERIALS SCIENCE↗
NASA NTRS1992

On the calculation of atomic term populations

The usefulness of calculations on model atomic term systems which can give spectral multiplet intensities is emphasized, in contrast to more detailed level calculations which are not always feasible because of lack of appropriate atomic data. A more general expression for the multiplet radiative transition rate is proposed to facilitate term representations. The differences between term and level representations are discussed quantitatively with respect to a model three-level atom and real examples of the C III and Ne IV ions. It is shown that term representations fail at lower densities when level inverse lifetimes within terms differ by only a few orders of magnitude. In such cases one must resort to other methods; a hybrid calculation is therefore proposed to fill this need and is carried out for the C III ion to demonstrate its feasibility and validity.

Kastner, S. O.↗
DOE OSTI2017

Polder maps: Improving OMIT maps by excluding bulk solvent

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX .

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

Efficient structure-factor modeling for crystals with multiple components

Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by an atomic model alone, i.e . using point scatterers. Indeed, entities such as disordered (bulk) solvent, semi-ordered solvent ( e.g. lipid belts in membrane proteins, ligands, ion channels) and disordered polymer loops require other types of modeling than a collection of individual atoms. This results in the model structure factors containing multiple contributions. Most macromolecular applications assume two-component structure factors: one component arising from the atomic model and the second one describing the bulk solvent. A more accurate and detailed modeling of the disordered regions of the crystal will naturally require more than two components in the structure factors, which presents algorithmic and computational challenges. Here an efficient solution of this problem is proposed. All algorithms described in this work have been implemented in the computational crystallography toolbox ( CCTBX ) and are also available within Phenix software. These algorithms are rather general and do not use any assumptions about molecule type or size nor about those of its components.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Simulation of Tip-Sample Interaction in the Atomic Force Microscope

Recent simulations of the interaction between planar surfaces and model Atomic Force Microscope (AFM) tips have suggested that there are conditions under which the tip may become unstable and 'avalanche' toward the sample surface. Here we investigate via computer simulation the stability of a variety of model AFM tip configurations with respect to the avalanche transition for a number of fcc metals. We perform Monte-Carlo simulations at room temperature using the Equivalent Crystal Theory (ECT) of Smith and Banerjea. Results are compared with recent experimental results as well as with our earlier work on the avalanche of parallel planar surfaces. Our results on a model single-atom tip are in excellent agreement with recent experiments on tunneling through mechanically-controlled break junctions.

Good, Brian S.↗