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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗
DOE OSTI2025

ACES-GNN: can graph neural network learn to explain activity cliffs?

Graph Neural Networks (GNNs) have revolutionized molecular property prediction by leveraging graph-based representations, yet their opaque decision-making processes hinder broader adoption in drug discovery. This study introduces the Activity-Cliff-Explanation-Supervised GNN (ACES-GNN) framework, designed to simultaneously improve predictive accuracy and interpretability by integrating explanation supervision for activity cliffs (ACs) into GNN training. ACs, defined by structurally similar molecules with significant potency differences, pose challenges for traditional models due to their reliance on shared structural features. By aligning model attributions with chemist-friendly interpretations, the ACES-GNN framework bridges the gap between prediction and explanation. Validated across 30 pharmacological targets, ACES-GNN consistently enhances both predictive accuracy and attribution quality for ACs compared to unsupervised GNNs. Our results demonstrate a positive correlation between improved predictions and accurate explanations, offering a robust and adaptable framework to better understand and interpret ACs. This work underscores the potential of explanation-guided learning to advance interpretable artificial intelligence in molecular modeling and drug discovery.

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

Heavy boron doping in superconducting carbon materials

Here we examine physical properties of heavily boron-doped sp 3 -hybridized carbon allotropes: cubic diamond, hexagonal diamond, and body centered tetragonal C 4 . The structural similarity between cubic diamond and hexagonal diamond leads to similar responses to substitutional boron doping. On the other hand, body centered tetragonal C 4 exhibits distinct structural and electronic properties because of its characteristic structure. Our study also shows that the superconducting transition temperatures up to 60 K are possible in heavily doped carbon materials despite their various atomistic structures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structures of five salt forms of disulfonated monoazo dyes

The structures of five s -block metal salt forms of three disulfonated monoazo dyes are presented. These are poly[di-μ-aqua-diaqua[μ 4 -3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)]disodium(I)], [Na 2 (C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (I), catena -poly[[tetraaquacalcium(II)]-μ-3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)], [Ca(C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (II), catena -poly[[[diaquacalcium(II)]-μ-2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] dihydrate], {[Na(C 12 H 10 N 3 O 6 S 2 )(H 2 O) 2 ]·2H 2 O} n , (III), hexaaquamagnesium bis[2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] octahydrate, [Mg(H 2 O) 6 ](C 12 H 10 N 3 O 6 S 2 ) 2 ·8H 2 O, (IV), and poly[[{μ 2 -4-[2-(4-amino-2-methyl-5-methoxyphenyl)diazen-1-yl]benzene-1,3-disulfonato}di-μ-aqua-diaquabarium(II)] dihydrate], {[Ba(C 14 H 13 N 3 O 7 S 2 )(H 2 O) 4 ]·2H 2 O} n , (V). Compound (III) is that obtained on crystallizing the commercial dyestuff Acid Yellow 9 [74543-21-8]. The Mg species is a solvent-separated ion-pair structure and the others are all coordination polymers with bonds from the metal atoms to sulfonate groups. Compound (I) is a three-dimensional coordination polymer, (V) is a two-dimensional coordination polymer and both (II) and (III) are one-dimensional coordination polymers. The coordination behaviour of the azo ligands and the water ligands, the dimensionality of the coordination polymers and the overall packing motifs of these five structures are contrasted to those of monosulfonate monoazo congers. It is found that (I) and (II) adopt similar structural types to those of monosulfonate species but that the other three structures do not.

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

Three-Dimensional Site Effects at Mortandad Canyon, NM: I. Validation against ambient noise recordings of topography effects

Observations from large earthquakes have shown that the presence of a strong topographic relief can significantly aggravate the catastrophic consequences of strong seismic motions. Structures on the tops of hills, ridges, and canyons, for example, have suffered systematically greater damage than similar structures at the hill bases or on level ground. Various earthquake recordings have confirmed the macroseismic observations, indicating systematic amplification of seismic motion over convex topographies, deamplification over concave topographic features, and complex amplification and deamplification patterns on hill slopes that result in significant differential motion. Despite the documented evidence of their role in elevating seismic risk, however, topography effects are not accounted for in the majority of seismic code provisions and microzonation studies, which are based instead on models of flat earth surface.

58 GEOSCIENCES↗
NASA NTRS1979

Monte Carlo simulation of lunar megaregolith and implications

A realistic Monte Carlo model closely simulating the evolution of the lunar megaregolith over a large area of 67 million sq. km of the front surface of the moon is presented. Craters larger than 100 km in diameter observed over the entire surface of the moon and those less than 100 km lying in the referenced area are included in the simulation. A total of 21,664 craters are processed. The model predicts the average thickness of the megaregolith to be about 1.9-2.0 km. Curves for the variation of the regolith thickness across the simulated area are given and show that about 50% of the area is covered with regolith less than 1 km thick. The model produces crater structures similar to the ones observed in the lunar highlands, it partially supports the layering theory for crater structures that the variations in strength and density of target materials may be responsible for the observed differences in the morphologies of lunar craters, and rules out the possibility that all craters when formed are bowl-shaped with a fixed depth/diameter ratio characteristic of small craters.

Aggarwal, H. R.↗
DOE OSTI2020

Structural characterization of sugarcane lignins extracted from different protic ionic liquid pretreatments

Previous studies based on protic ionic liquids have shown them to be effective for extracting lignins from biomass. Moreover, ILs synthesized with amine cations can promote the insertion of nitrogen into lignin, favoring its valorization for industrial applications. Here, lignins extracted from sugarcane bagasse by eight different PILs were analyzed. Several techniques of characterization were employed (2D HSQC NMR, 31P NMR, GPC, Py-GC/MS, TGA, FTIR, and elemental analysis), seeking a deeper understanding of lignin structure post-PILS treatment. In particular, lignin obtained with acetate and lactate anions with monoethanolamonium cations showed similar structural compositions. Lignins obtained from ethylenediamonium cation combined anions acetate and lactate exhibited relatively higher molecular weights compared to the other lignins studied. The elemental analysis of these lignins further revealed the presence of nitrogen in their structures, suggesting that amination occurred. In this work we used PILs not yet reported in the literature for this purpose, and consequently obtained lignins with specific structures. Overall, our results demonstrated that depending on the PILs used, lignins with distinct properties could be obtained which might be used for value-added applications. This work covered new advances in elucidation of lignin chemical structure and opened a new path for lignin valorization.

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

The kagomé metals RbTi 3 Bi 5 and CsTi 3 Bi 5

Abstract The kagomé metals RbTi 3 Bi 5 and CsTi 3 Bi 5 were synthesized both as polycrystalline powders by heating the elements in an argon atmosphere and as single crystals grown using a self-flux method. The compounds crystallize in the hexagonal crystal system isotypically to KV 3 Sb 5 ( P 6/ mmm , Z = 1, CsTi 3 Bi 5 : a = 5.7873(1), c = 9.2062(1) Å; RbTi 3 Bi 5 : a = 5.773(1), c = 9.065(1) Å). The titanium atoms form a kagomé net with bismuth atoms in the hexagons as well as above and below the triangles. The alkali metal atoms are coordinated by 12 bismuth atoms and form AlB 2 -like slabs between the kagomé layers. Magnetic susceptibility measurements with CsTi 3 Bi 5 and RbTi 3 Bi 5 single crystals reveal Pauli-paramagnetism and traces of superconductivity caused by CsBi 2 /RbBi 2 impurities. Magnetotransport measurements reveal conventional Fermi liquid behavior and quantum oscillations indicative of a single dominant orbit at low temperature. DFT calculations show the characteristic metallic kagomé band structure similar to that of CsV 3 Sb 5 with reduced band filling. A symmetry analysis of the band structure does not reveal an obvious and unique signature of a nontrivial topology.

Chemistry↗
DOE OSTI2026

Neural Scaling Laws of Deep ReLU and Deep Operator Network: A Theoretical Study

Neural scaling laws play a pivotal role in the performance of deep neural networks and have been observed in a wide range of tasks. However, a complete theoretical framework for understanding these scaling laws remains underdeveloped. In this paper, we explore the neural scaling laws for deep operator networks, which involve learning mappings between function spaces, with a focus on the Chen and Chen style architecture. These approaches, which include the popular Deep Operator Network (DeepONet), approximate the output functions using a linear combination of learnable basis functions and coefficients that depend on the input functions. We establish a theoretical framework to quantify the neural scaling laws by analyzing its approximation and generalization errors. We articulate the relationship between the approximation and generalization errors of deep operator networks and key factors such as network model size and training data size. Moreover, we address cases where input functions exhibit low-dimensional structures, allowing us to derive tighter error bounds. These results also hold for deep ReLU networks and other similar structures. Our results offer a partial explanation of the neural scaling laws in operator learning and provide a theoretical foundation for their applications.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1977

Spatial variations in tropical ozone - The influence of meridional transport and planetary waves in the stratosphere

The backscatter ultraviolet instrument on the Atmosphere Explorer-E satellite has acquired a large body of stratospheric and total ozone data in the tropical region. The latitudinal variation of the ozone mixing ratio on constant pressure surfaces shows the transition from chemical domination to transport control between 5 and 10 mb. Spectral analysis of the longitudinal O3 structure reveals large wavenumber 1 and 2 patterns, although considerable activity in wavenumbers 5 through 7 sometimes appears. Longitudinal structure increases with decreasing pressure between 30 and 5 mb. The spatial variability near 5 mb must reflect similar structure in the odd nitrogen distribution which provides the major loss mechanism for ozone at this level.

Frederick, J. E.↗
NASA NTRS1990

Fault propagation folds induced by gravitational failure and slumping of the Central Costa Rica volcanic range - Implications for large terrestrial and Martian volcanic edifices

Maps are presented that describe the compressional tectonic structures found at the base of the Central Costa Rica volcanic range (CCRVR), which comprise thrust faults and related fault propagation folds, only partly covered by syntectonic and posttectonic volcanoclastic deposits. Evidence is presented that these structures formed by gravitational failure and lumping of the flanks of the volcanic range. It is suggested that similar structures may be found at the toe of the southern flank of Kilauea volcano, Hawaii, and along the perimeter scarp of the Olympus Mons volcano on Mars.

Borgia, Andrea↗
NASA NTRS1998

Changing patterns of localization of the tobacco mosaic virus movement protein and replicase to the endoplasmic reticulum and microtubules during infection

Tobacco mosaic virus (TMV) derivatives that encode movement protein (MP) as a fusion to the green fluorescent protein (MP:GFP) were used in combination with antibody staining to identify host cell components to which MP and replicase accumulate in cells of infected Nicotiana benthamiana leaves and in infected BY-2 protoplasts. MP:GFP and replicase colocalized to the endoplasmic reticulum (ER; especially the cortical ER) and were present in large, irregularly shaped, ER-derived structures that may represent "viral factories." The ER-derived structures required an intact cytoskeleton, and microtubules appeared to redistribute MP:GFP from these sites during late stages of infection. In leaves, MP:GFP accumulated in plasmodesmata, whereas in protoplasts, the MP:GFP was targeted to distinct, punctate sites near the plasma membrane. Treating protoplasts with cytochalasin D and brefeldin A at the time of inoculation prevented the accumulation of MP:GFP at these sites. It is proposed that the punctate sites anchor the cortical ER to plasma membrane and are related to sites at which plasmodesmata form in walled cells. Hairlike structures containing MP:GFP appeared on the surface of some of the infected protoplasts and are reminiscent of similar structures induced by other plant viruses. We present a model that postulates the role of the ER and cytoskeleton in targeting the MP and viral ribonucleoprotein from sites of virus synthesis to the plasmodesmata through which infection is spread.

NASA Discipline Plant Biology↗
NASA NTRS1984

Identification and control of structures in space

The derivation of the equations of motion for the Spacecraft Control Laboratory Experiment (SCOLE) is reported and the equations of motion of a similar structure orbiting the earth are also derived. The structure is assumed to undergo large rigid-body maneuvers and small elastic deformations. A perturbation approach is proposed whereby the quantities defining the rigid-body maneuver are assumed to be relatively large, with the elastic deformations and deviations from the rigid-body maneuver being relatively small. The perturbation equations have the form of linear equations with time-dependent coefficients. An active control technique can then be formulated to permit maneuvering of the spacecraft and simultaneously suppressing the elastic vibration.

Meirovitch, L.↗
DOE OSTI2025

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗
DOE OSTI2021

High-resolution crystal structure of the Borreliella burgdorferi PlzA protein in complex with c-di-GMP: new insights into the interaction of c-di-GMP with the novel xPilZ domain

ABSTRACT In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Here, we present the crystal structure of PlzA in complex with c-di-GMP (1.6 Å resolution). This is the first structure of a xPilz domain in complex with c-di-GMP to be determined. PlzA has a two-domain structure, where each domain comprises topologically equivalent PilZ domains with minimal sequence identity but remarkable structural similarity. The c-di-GMP binding site is formed by the linker connecting the two domains. While the structure of apo PlzA could not be determined, previous fluorescence resonance energy transfer data suggest that apo and holo forms of the protein are structurally distinct. The information obtained from this study will facilitate ongoing efforts to identify the molecular mechanisms of PlzA-mediated regulation in ticks and mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold ; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.

Bragagnolo, Nicholas↗
NASA NTRS1981

Vibration of prestressed periodic lattice structures

Equations are developed for vibration of general lattice structures that have repetitive geometry. The method of solution is an extension of a previous paper for buckling of similar structures. The theory is based on representing each member of the structure with the exact dynamic stiffness matrix and taking advantage of the repetitive geometry to obtain an eigenvalue problem involving the degrees-of-freedom at a single node in the lattice. Results are given for shell-and beam-like lattice structures and for rings stiffened with tension cables and a central mast. The variation of frequency with external loading and the effect of local member vibration on overall modes is shown.

Anderson, M. S.↗
NASA NTRS1984

The Possibility of Detection and Measurement of Cloud Structure in the Atmosphere of Uranus

Historical data concerning variability of surface brightness of the visible cloud deck are reviewed. The data do not rule out low contrast small cloud structures of the type measured in the Saturnian Voyager wind measurements. Convective models in which methane can condense suggest similar structure may be present at the level of the visible cloud deck in Uranus' atmosphere. Horizontal space and time scales derived from dynamical considerations lie within the accessible range of the wide and narrow angle Voyager cameras. Therefore, Voyager 2 may obtain significant dynamical information about the Uranian atmosphere.

Beebe, R.↗