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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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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↗
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↗
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↗
DOE OSTI2023

Thermodynamic properties and superconductivity of natural carrollite (CuCo 2 S 4 )

The thermodynamic properties of natural carrollite with a formula Cu 0.92 Co 2.07 S 4 are studied using low temperature heat capacity and high temperature oxidative solution calorimetry. The standard thermodynamic functions at 298.15 K are: C p,m °, S m °, H m °, and Φ m ° are 158.48 J∙K −1 ∙mol −1 , 176.33 J∙K −1 ∙mol −1 , 28.40 kJ∙mol −1 , and 81.07 kJ∙mol −1 with an estimated error of 1%. The enthalpies (Δ f H), entropies (Δ f S), and Gibbs energies of formation (Δ f G) from elements at 298.15 K are: −344.46 ± 12.87 kJ∙mol −1 , −45.22 ± 1.81 J∙K −1 ∙mol −1 , and −331.14 ± 1.89 J∙K −1 ∙mol −1 . The stability of carrollite relative to the elements is demonstrated with a negative Gibbs energy (ΔG r °) of formation for several temperatures between 0 and 300 K. Furthermore, a superconductivity transition, which has been observed previously for synthetic carrollite, is confirmed by both the low temperature heat capacity and magnetization measurements.

Chemistry↗
DOE OSTI2021

Mechanistic Pathways for N 2 O Elimination from trans -R 3 Sn-O-N=N-O-SnR 3 and for Reversible Binding of CO 2 to R 3 Sn-O-SnR 3 (R = Ph, Cy)

The rate and mechanism of the elimination of N 2 O from trans-R 3 Sn-O-N=N-O-SnR 3 (R = Ph ( 1 Ph ) and R = Cy ( 1 Cy )) to form R 3 Sn-O-SnR 3 (R = Ph ( 2 Ph ) and R = Cy ( 2 Cy )) have been studied using both NMR and IR techniques to monitor the reactions in the temperature range of 39–79 °C in C 6 D 6 . Activation parameters for this reaction are ΔH ‡ = 15.8 ± 2.0 kcal·mol –1 and ΔS ‡ = –28.5 ± 5 cal·mol –1 ·K –1 for 1 Ph and ΔH ‡ = 22.7 ± 2.5 kcal·mol –1 and ΔS ‡ = –12.4 ± 6 cal·mol –1 ·K –1 for 1 Cy . Addition of O 2 , CO 2 , N 2 O, or PPh 3 to sealed tube NMR experiments did not alter in a detectable way the rate or product distribution of the reactions. Computational DFT studies of elimination of hyponitrite from trans-Me 3 Sn-O-N=N-O-SnMe 3 ( 1 Me ) yield a mechanism involving initial migration of the R 3 Sn group from O to N passing through a marginally stable intermediate product and subsequent N 2 O elimination. Reactions of 1 Ph with protic acids HX are rapid and lead to formation of R 3 SnX and trans-H 2 N 2 O 2 . Reaction of 1 Ph with the metal radical •Cr(CO) 3 C 5 Me 5 at low concentrations results in rapid evolution of N 2 O. At higher •Cr(CO) 3 C 5 Me 5 concentrations, evolution of CO 2 rather than N 2 O is observed. Addition of 1 atm or less CO 2 to benzene or toluene solutions of 2 Ph and 2 Cy resulted in very rapid reaction to form the corresponding carbonates R 3 Sn-O-C(=O)-O-SnR 3 (R = Ph ( 3 Ph ) and R = Cy ( 3 Cy )) at room temperature. Evacuation results in fast loss of bound CO 2 and regeneration of 2 Ph and 2 Cy . Variable temperature data for formation of 3 Cy yield ΔH o = –8.7 ± 0.6 kcal·mol –1 , ΔS o = –17.1 ± 2.0 cal·mol –1 ·K –1 , and ΔG o 298K = –3.6 ± 1.2 kcal·mol –1 . Furthermore, DFT studies were performed and provide additional insight into the energetics and mechanisms for the reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Self-Diffusivity Measurement of Eutectic F 7 LiNaK with and without Additives Using Quasi-Elastic Neutron Scattering

The atomic scale relaxation dynamics of eutectic F 7 LiNaK (46.5 LiF–11.5 NaF–42 KF mol %, Li-7 enriched) were measured using quasi-elastic neutron scattering (QENS) over a temperature range of 500–750 °C. Here, the effect of adding 0.988 mol % cerium, 0.499 mol % cesium, and 1.21 mol % zirconium individually to the dynamics of F 7 LiNaK was also investigated. The relaxation process in both pure and doped F 7 LiNaK molten salts was fit with a stretched exponential function and the temperature dependence follows an Arrhenius behavior over a wavevector transfer range of 0.4 Å –1 < Q < 0.9 Å –1 . The measured activation energy for self-diffusion is E a = 0.77 ± 0.02 eV/atom for pure molten F 7 LiNaK. The QENS response with additives added to F 7 LiNaK was also fit with a stretched exponential and the associated Arrhenius behavior was characterized with activation energies of E a = 0.88 ± 0.01 eV/atom for zirconium (1.21 mol %), E a = 1.02 ± 0.02 eV/atom for cerium (0.988 mol %), and E a = 0.71 ± 0.03 eV/atom for cesium (0.499 mol %). The measured diffusivities are compared to those simulated with a neural network force field model by Lee et al. [Lee, S.-C. Comparative Studies of the Structural and Transport Properties of Molten Salt FLiNaK Using the Machine-Learned Neural Network and Reparametrized Classical Forcefields. J. Phys. Chem. B 2021, 125(37), 10562–10570].

FLiNaK↗
DOE OSTI2024

A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction

Drug discovery is a complex and challenging process, requiring the optimization of candidate compounds to identify those with the potential to become safe and effective drugs. Predicting molecular properties is an indispensable step in the drug discovery pipeline. Traditionally, this process is costly and time-intensive, involving multiple rounds of experiments and clinical trials, rendering it impractical for every candidate compound. Deep learning techniques have emerged as a promising approach to drug discovery to reduce the cost and time required to identify novel drugs. However, prevalent research in deep learning models focused on predicting molecular properties has primarily fixated on single-modal models, which utilize a single modality of data, neglecting the potential benefits of combining different data modalities. To overcome this limitation, we introduce MRL-Mol: a deep \textbf{M}ultimodal \textbf{R}epresentation \textbf{L}earning framework for accurate \textbf{Mol}ecular properties prediction. MRL-Mol harnesses three data modalities: sequence, graph, and image, augmenting the depth of comprehension. Leveraging a large-scale unlabeled dataset~($\sim$1M unique molecules), we pretrain MRL-Mol to extract inter- and intra-modal information. Our study demonstrates the superior performance of MRL-Mol in predicting molecular properties across six benchmark datasets, including both classification and regression tasks. Notably, MRL-Mol outperforms other state-of-the-art molecular properties prediction models. These findings suggest that by combining information from multiple data modalities, MRL-Mol can comprehend molecules better than single-modal deep learning models and identify molecular properties with better accuracy.

Yang, Yuxin↗
DOE OSTI2022

Degradation in Photovoltaic Encapsulant Transmittance: Results of the Second PVQAT TG5 Artificial Weathering Study

The optical degradation of encapsulants from ultraviolet (UV) radiation has historically resulted in a significant loss in performance throughout the life of a photovoltaic (PV) module. International Electrotechnical Commission (IEC) test methods have recently been developed to screen for PV encapsulants prone to loss in optical performance. The present study was performed to benchmark polymeric packaging materials relative to IEC 62788-1-4 (covering the measurement of optical transmittance) and IEC 62788-1-7 (on the durability of transmittance), provide feedback toward improvement of the methods, and develop insight regarding optical degradation. Contemporary materials were examined, including poly(ethylene-co-vinyl acetate) (EVA), thermoplastic polyolefin (TPO), polyolefin elastomer (POE), and polyvinyl butyral (PVB) encapsulants; a poly(ethene-co-tetrafluoroethene)/poly(ethylene terephthalate) (ETFE/PET) transparent backsheet; and a polystyrene (PS) working reference material. The use of silica-, specialty-, and rolled-glass was also compared in laminated coupons. Specimen size was separately examined from 2.5 to 12.5 cm. Weathering was performed with a xenon source, using IEC TS 62788-7-2 methods A2, A3, A4, and A5 (chamber temperature of 55 degrees C, 65 degrees C, 75 degrees C, or 85 degrees C), respectively. Characterizations were made using a UV-visible-near-infrared (UV-VIS-NIR) spectrophotometer (transmittance and reflectance, with and without an integrating sphere), a UV-VIS fluorescence spectrophotometer, a camera, and an optical microscope. Performance was analyzed, including solar weighted transmittance, yellowness index, UV cut-off wavelength, and haze (scattering). Separate Arrhenius analyses were performed to assess retention of transmittance and changes in yellowness index. The activation energy for both characteristics was found to range from 15-80 kJ mol-1, with an average of 48 kJ mol-1, similar to the average of 45 kJ mol-1 identified in the previous international PV Quality Assurance Task Force (PVQAT) Task Group 5 (TG5) study of more traditional encapsulants. The separate degradation modes of discoloration and scattering were distinguished in the encapsulants using a comprehensive spectral characterization. Based on these results, the IEC 62788-1-7 pass/fail criteria of 5% change in transmittance was confirmed to identify a known bad encapsulant.

durability↗
DOE OSTI2020

Losses of CO and CO 2 upon collision-activated dissociation of substituted 2-methoxyphenoxides after methyl radical loss

Some deprotonated, substituted 2-methoxyphenols fragment by methyl radical loss followed by competing losses of CO and CO 2 upon collisional activation in linear quadrupole ion trap mass spectrometers. These reactions were examined experimentally and computationally in order to determine their mechanisms. For deprotonated vanillin, the CO loss was found to involve ring contraction, with the highest free energy barrier of 58.0 kcal mol -1 (for the syn rotamer; here, syn refers to the relationship between the aldehyde oxygen atom and the oxygen atom of the methoxy group) for the entire process. The atoms lost in this fragmentation are the oxygen atom that was bound to the first eliminated methyl group and the aromatic carbon atom bound to this oxygen. Examination of carbon-13 labeled vanillin supports these assignments. Examination of several model compounds revealed that this reaction requires the presence of an electron-withdrawing substituent in the para-position relative to the phenol moiety. In contrast, the CO 2 loss from deprotonated vanillin occurs via ring opening followed by re-cyclization and then ring contraction, leading to the loss of CO 2 in a process wherein the highest free energy barrier is 84.5 kcal mol -1 (for the syn isomer). The atoms lost in this fragmentation are the carbon and oxygen atoms from the phenoxide group and the oxygen atom that was bound to the first eliminated methyl group, which is supported by examination of carbon-13 labeled vanillin. Despite the higher total free energy requirement, the CO 2 loss is competitive with CO loss, possibly due to favorable entropy and low activation energy (free energy barrier of 48.9 kcal mol -1 ) for the first reaction step (the analogous value for CO loss is 58.0 kcal mol -1 ). The extent of CO 2 loss is strongly affected by substituents – it either is not observed or is very slow for the other compounds studied here. For example, it is substantially less favorable than CO loss (highest free energy barrier 60.9 kcal mol -1 ) for deprotonated acetovanillone for which the first reaction step for CO 2 loss has a substantially greater free energy barrier (60.6 kcal mol-1) than for vanillin.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗