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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗
DOE OSTI2025

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Midlik, Adam [European Bioinformatics Institute (U↗
NASA NTRS1990

Deformation of as-cast LiF-22 mol pct CaF2 hypereutectic salt between 500 and 1015 K

Results are presented on compression tests conducted on as-cast LiF-22 mol pct CaF2 hypereutectic specimens at nominal strain rates between 1.8 x 10 to the -6th/sec and 0.25/sec over the temperature range 500-1015 K. In all instances, the stress-strain curves showed broad maxima, with negative strain-hardening rates after the peak stress sigma(max). It was found that, at low temperatures and high stresses, the CaF2 lamellae are rigid while the LiF matrix exhibits extensive transgranular cavitation, while at high temperatures and low stresses the CaF2 lamellae break down and spheroidize while the LiF matrix does not cavitate. It was concluded that the mechanical properties of the as-cast hypereutectic LiF-22 mol pct CaF2 are governed by the rate of deformation of the CaF2 phase. It is suggested that, for thermal energy storage applications, a spheroidal microstructure is more desirable than a lamellar structure.

Raj, S. V.↗
DOE OSTI2021

Mutual Diffusion Coefficients of Na 2 SO 4 at C = 0.02989 mol·dm -3 and 298.15 K by Using Rayleigh Interferometry with Free Diffusion Boundary Conditions: Experimental Test of the Effect of the C 3/2 Concentration Dependence of Refractive Index at Low Concentration

Rayleigh interferometry is one of the most precise and accurate methods for the experimental determination of the mutual diffusion coefficients of both electrolytes and non-electrolytes in liquid solutions. For binary solutions at moderate and high concentrations where the concentration dependences of both diffusion coefficient and refractive index can be assumed to be linear or almost linear and the concentration difference ΔC between a pair of solutions undergoing free diffusion is not large compared to their average concentration, and by using proper combinations of the interference fringe positions as they vary with time, under these conditions diffusion coefficients are obtained that are independent of the size of ΔC. However, this situation becomes more complicated at low concentrations for electrolyte solutions where the concentration dependences of both the diffusion coefficient and refractive index are non-linear, with C 1/2 dependence for the diffusion coefficient and C 3/2 dependence for the refractive index. As a test of these effects on calculated mutual diffusion of electrolyte solutions at low concentrations as measured by Rayleigh interferometry, apparent mutual diffusion coefficients D v,a (volume-fixed reference frame) were measured for fixed average concentrations C=(0.02989 ± 0.00001) mol·dm –3 of Na 2 SO 4 (aq) at 298.15 K while varying ΔC/C from 0.66673 to 2, a threefold variation. The dependence of the diffusion coefficient on ΔC/C was found to be linear, yielding D v = 1.041 6 × 10 –9 m 2 ·s –1 for an infinitely small concentration difference between the diffusing solutions.

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

On the Arrhenius-like behavior of conductivity during flash sintering of 3 mol% yttria stabilized zirconia ceramics

Here, we discuss the Arrhenius behavior of electrical conductivity σ during flash sintering of 3 mol% yttria stabilized zirconia (3YSZ). In situ x-ray diffraction is used to determine sample temperature. Sintering contribution to σ is excluded by investigating the flash event on a dense ceramic. We show that total conductivity follows an Arrhenius-like equation in both dense and green samples, even during Stage II of flash. The non-linearity often verified during flash sintering of 3YSZ is therefore related to the furnace temperature instead of the sample temperature when building the ln(σ) vs. 1/T plots. Furthermore, we verified a change in the activation energy for conduction prior to the ignition of the flash event and discussed the possible mechanisms. For instance, the decrease in activation energy from Stage I to II in the dense sample is attributed to a contribution from electronic carriers.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Adhesive evaluation of thin films of LARC-TPI and LARC-TPI with 5 mol % ODA

A commercially available LARC-TPI film and an experimentally prepared film of LARC-TPI with 5 mol % of 4,4'-oxydianiline (ODA), designated as LARC-TPI/ODA in the report, supplied by Mitsui Toatsu Chemicals, Incorporated (MTCI), Japan, were evaluated as thermoplastic adhesive films for bonding Ti-6Al-4V. The LARC-TPI/ODA had been shown by MTCI to possess more flow than thermoplastic LARC-TPI and was, therefore, evaluated and compared to the LARC-TPI. Lap shear strength was used to evaluate the materials as adhesives. They were characterized after fracture by determining the glass transition temperature, Tg. The mode of failure was also reported. Thermal exposure at 204C for 500 and 1000 hrs and a 72-hour water-boil were conducted on lap shear specimens prepared with the two adhesive films. Lap shear tests were conducted at RT, 177C, 204C, and 232C before and after exposures.

Progar, D. J.↗
NASA NTRS1999

Effects of CO2 on stomatal conductance: do stomata open at very high CO2 concentrations?

Potato and wheat plants were grown for 50 d at 400, 1000 and 10000 micromoles mol-1 carbon dioxide (CO2). and sweetpotato and soybean were grown at 1000 micromoles mol-1 CO2 in controlled environment chambers to study stomatal conductance and plant water use. Lighting was provided with fluorescent lamps as a 12 h photoperiod with 300 micromoles m-2 s-1 PAR. Mid-day stomatal conductances for potato were greatest at 400 and 10000 micromoles mol-1 and least at 1000 micromoles mol-1 CO2. Mid-day conductances for wheat were greatest at 400 micromoles mol-1 and least at 1000 and 10000 micromoles mol-1 CO2. Mid-dark period conductances for potato were significantly greater at 10000 micromoles mol-1 than at 400 or 1000 micromoles mol-1, whereas dark conductance for wheat was similar in all CO2 treatments. Temporarily changing the CO2 concentration from the native 1000 micromoles mol-1 to 400 micromoles mol-1 increased mid-day conductance for all species, while temporarily changing from 1000 to 10000 micromoles mol-1 also increased conductance for potato and sweetpotato. Temporarily changing the dark period CO2 from 1000 to 10000 micromoles mol-1 increased conductance for potato, soybean and sweetpotato. In all cases, the stomatal responses were reversible, i.e. conductances returned to original rates following temporary changes in CO2 concentration. Canopy water use for potato was greatest at 10000, intermediate at 400, and least at 1000 micromoles mol-1 CO2, whereas canopy water use for wheat was greatest at 400 and similar at 1000 and 10000 micromoles mol-1 CO2. Elevated CO2 treatments (i.e. 1000 and 10000 micromoles mol-1) resulted in increased plant biomass for both wheat and potato relative to 400 micromoles mol-1, and no injurious effects were apparent from the 10000 micromoles mol-1 treatment. Results indicate that super-elevated CO2 (i.e. 10000 micromoles mol-1) can increase stomatal conductance in some species, particularly during the dark period, resulting in increased water use and decreased water use efficiency.

NASA Discipline Life Support Systems↗
NASA NTRS2000

Growth, pod, and seed yield, and gas exchange of hydroponically grown peanut in response to CO2 enrichment

The effects of elevated CO2 on growth, pod, and seed yield, and gas exchange of 'Georgia Red' peanut (Arachis hypogaea L.) were evaluated under controlled environmental conditions. Plants were exposed to concentrations of 400 (ambient), 800, and 1200 micromoles mol-1 CO2 in reach-in growth chambers. Foliage fresh and dry weights increased with increased CO2 up to 800 micromoles mol-1, but declined at 1200 micromoles mol-1. The number and the fresh and dry weights of pods also increased with increasing CO2 concentration. However, the yield of immature pods was not significantly influenced by increased CO2. Total seed yield increased 33% from ambient to 800 micromoles mol-1 CO2, and 4% from 800 to 1200 micromoles mol-1 CO2. Harvest index increased with increasing CO2. Branch length increased while specific leaf area decreased linearly as CO2 increased from ambient to 1200 micromoles mol-1. Net photosynthetic rate was highest among plants grown at 800 micromoles mol-1. Stomatal conductance decreased with increased CO2. Carboxylation efficiency was similar among plants grown at 400 and 800 micromoles mol-1 and decreased at 1200 micromoles mol-1 CO2. These results suggest that CO2 enrichment from 400 to 800 micromoles mol-1 had positive effects on peanut growth and yield, but above 800 micromoles mol-1 enrichment seed yield increased only marginally.

NASA Discipline Life Support Systems↗
DOE OSTI2023

Analysis and Thermal Property Investigations into Ternary Actinide Chloride Salt Systems Containing UCl3 and PuCl3

While regulators, the scientific community, and MSR developers still lack access to literature data on the thermal properties of clean fuel salts, even less information is available on the properties of fuel salts containing impurities. It is essential to understand, benchmark, and predict crucial data on the changes in thermal properties of fuel salt systems due to impurities arising from moisture, corrosion, and reactor operation (i.e., fission products). This research focuses on two actinide fuel salts (1) to investigate a worst-case scenario buildup of actinide fission product in a NaCl-UCl3 eutectic fuel salt and (2) to investigate NaCl-PuCl3 eutectic salt after 1000 hours of operation in a natural circulation flow loop flow to determine if corrosion or atmospheric (moisture/oxygen) products are present. For the first salt, a conservative assumption or worst-case scenario, for fission product buildup in a fuel salt was investigated by adding PuCl3 to eutectic 67 mol% NaCl – 33 mol% UCl3 salt resulting in a ternary salt having a composition of 61 mol% NaCl – 30 mol% UCl3 – 9mol% PuCl3. Addition of PuCl3 to eutectic NaCl-UCl3 resulted in a ternary salt that had a higher melting temperature than either the NaCl-PuCl3 or NaCl-UCl3 binary eutectic mixture. Addition of PuCl3 also resulted in an increase in density which was expected. The second salt was extracted from a micro loop. The composition of the fuel (primary) salt prior to flow loop operations was determined to be 64 mol% NaCl – 36 mol% PuCl3, however, the post-flow loop salt showed increased levels of MgCl2 and NaCl changing the salt composition to 10 mol% MgCl2 – 63mol% NaCl – 26mol% PuCl3) indicating the primary salt interacted with the rinse salt. Analysis of the post flow loop salt detected low concentrations of Al, Ni, Co, Nb, and Zr, most likely corrosion products from the flow loop material of construction. Contamination of the fuel salt (with the rinse salt NaCl-MgCl2) decreased the density by approximately 10% and reduced the onset of melting temperature by 50 °C, from 451 °C to approximately 400 °C. Results from the fission product simulated salt (61 mol% NaCl – 30 mol% UCl3 – 9mol% PuCl3) and the corrosion product salt (10 mol% MgCl2 – 63mol% NaCl – 26mol% PuCl3) will be included in two separate manuscripts for submission to peer-reviewed journals.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Recovery of Alkaline-Earths into Liquid Bi in Ternary LiCl-KCl-SrCl 2 /BaCl 2 Electrolytes at 500 °C

Electrochemical reduction of Sr 2+ and Ba 2+ into liquid Bi was investigated in dilute concentrations of SrCl 2 /BaCl 2 (0-5 mol%) in LiCl-KCl electrolytes at 500 °C to ascertain the limit of liquid Bi electrodes for alkaline-earth recovery. Analysis of the electrodes after constant current electrolysis to the specific charge of 270 C g -1 showed Sr 2+ ions consuming 29% of charge at 5 mol% before dropping to 8%-10% of the total charge at 0.45-0.72 mol% SrCl 2 . Ba 2+ ions consumed 54% at 5 mol% BaCl 2 before decreasing to 22%-24% at 0.42-0.89 mol% BaCl 2 ; substantial co-deposition of Li was observed in all chemistries, consuming up to 53% of charge. Considering only 1% of the total charge was consumed for depositing Ba 2+ and Sr 2+ ions in ~0.1 mol% SrCl 2 /BaCl 2 electrolyte, the lower recovery limit of Bi for alkaline-earth elements is suggested to be at ~0.4 mol% SrCl 2 /BaCl 2 to achieve appreciable deposition of alkaline-earths (>1.5 mol% Ba/Sr in liquid Bi). The overpotentials of liquid Bi at 5 mol% of SrCl 2 /BaCl 2 were evaluated by electrochemical impedance spectroscopy. The co-deposition of Sr and Li exhibited the largest increase in charge transfer resistances implying sluggish charge transfer kinetics whereas the co-deposition of Ba and Li exhibited a large increase in mass transport resistances due to the slow diffusion of Ba 2+ ions in the electrolyte.

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

The highly exothermic hydrogen abstraction reaction H 2 Te + OH → H 2 O + TeH: comparison with analogous reactions for H 2 Se and H 2 S

The “gold standard” CCSD(T) method is adopted along with the correlation consistent basis sets up to aug-cc-pV5Z-PP to study the mechanism of the hydrogen abstraction reaction H 2 Te + OH. Here, the predicted geometries and vibrational frequencies for reactants and products are in good agreement with the available experimental results. With the ZPVE corrections, the transition state in the favorable pathway of this reaction energetically lies 1.2 kcal mol -1 below the reactants, which is lower than the analogous relative energies for the H 2 Se + OH reaction (-0.7 kcal mol -1 ), the H 2 S + OH reaction (+0.8 kcal mol -1 ) and the H 2 O + OH reaction (+9.0 kcal mol -1 ). Accordingly, the exothermic reaction energies for these related reactions are predicted to be 47.8 (H 2 Te), 37.7 (H 2 Se), 27.1 (H 2 S), and 0.0 (H 2 O) kcal mol -1 , respectively. Geometrically, the low-lying reactant complexes for H 2 Te + OH and H 2 Se + OH are two-center three-electron hemibonded structures, whereas those for H 2 S + OH and H 2 O + OH are hydrogen-bonded. With ZPVE and spin–orbit coupling corrections, the relative energies for the reactant complex, transition state, product complex, and the products for the H 2 Te + OH reaction are estimated to be -13.1, -1.0, -52.0, and -52.6 kcal mol -1 , respectively. Finally, twenty-eight DFT functionals have been tested systematically to assess their ability in describing the potential energy surface of the H 2 Te + OH reaction. The best of these functionals for the corresponding energetics are -9.9, -1.4, -46.4, and -45.4 kcal mol -1 (MPWB1K), or -13.1, -2.4, -57.1, and -54.6 kcal mol -1 (M06-2X), respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗