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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times, many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,785 gene families from 993 Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we found that gene family expansion and contraction were significantly linked to trait gain and loss in 45/56 (80%) traits. While 595/739 (81%) significant gene families were associated with only one trait, we also identified several “keystone” gene families that were significantly associated with up to 13/56 (23%) of all traits. Strikingly, most of these families are known to encode metabolic enzymes and transporters, including all members of the industrially relevant MAL tose fermentation loci in the baker’s yeast Saccharomyces cerevisiae. These results indicate that convergent evolution on the gene family level may be more widespread across deeper timescales than previously believed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

The Saccharomycotina fungi have evolved to inhabit a vast diversity of habitats over their 400-million-year evolution. There are, however, only a few known fungal pathogens of plants in this subphylum, primarily belonging to the genera Eremothecium and Geotrichum. We compared the genomes of 12 plant-pathogenic Saccharomycotina strains to 360 plant-associated strains to identify features unique to the phytopathogens. Characterization of the oxylipin synthesis genes, a compound believed to be involved in Eremothecium pathogenicity, did not reveal any differences in gene presence within or between the plant-pathogenic and plant-associated strains. A reverse-ecological approach, however, revealed that plant pathogens lack several metabolic enzymes known to assist other phytopathogens in overcoming plant defenses. This includes L-rhamnose metabolism, formamidase and nitrilase genes. This result suggests that the Saccharomycotina plant pathogens are limited to infecting ripening fruits as they are without the necessary enzymes to degrade common phytohormones and secondary metabolites produced by plants.

Saccharomycotina, fungi, phytopathogen, reverse ec↗
DOE OSTI2023

Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts

Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene–trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Abstract Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Stable hypermutators revealed by the genomic landscape of genes involved in genome stability among yeast species

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing genes involved in DNA repair. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina (phylum Ascomycota) to examine the relationship between reduced gene repertoires broadly associated with genome stability functions (e.g., DNA repair, cell cycle) and elevated evolutionary rates. We identified three distantly related lineages—encompassing 12% of species—that had both the most streamlined sets of genes involved in genome stability (specifically DNA repair) and the highest evolutionary rates in the entire subphylum. Two of these “faster-evolving lineages” (FELs)—a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)—are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of genome stability gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. In the W/S clade, genomic signatures are consistent with a substantial mutational burden, including pronounced A|T bias and endogenous DNA damage. Interestingly, we found that the W/S clade also contains DNA repair genes possibly acquired through horizontal gene transfer, including a photolyase of bacterial origin. These findings highlight how hypermutators can persist across macroevolutionary timescales, potentially linked to the loss of genes related with genome stability, with horizontal gene transfer as a possible avenue for partial functional compensation.

DNA repair↗
DOE OSTI2020

Field-induced transitions in the Kitaev material α - RuCl 3 probed by thermal expansion and magnetostriction

High-resolution thermal expansion and magnetostriction measurements were performed on single crystals of α - RuCl 3 in magnetic fields applied parallel to the Ru-Ru bonds. The length changes were measured in the direction perpendicular to the honeycomb planes. Here, our data show clear thermodynamic characteristics for the field-induced phase transition at the critical field μ 0 H c 1 = 7.8 ( 2 ) T where the antiferromagnetic zigzag order is suppressed. At higher fields, a kink in the magnetostriction coefficient signals an additional transition or crossover around μ 0 H c 2 ≈ 11 T . The extracted Grüneisen ratio shows typical hallmarks for quantum criticality near H c 1 but also displays anomalous behavior above H c 1 . We compare our experimental data with spin-wave calculations employing a minimal Kitaev-Heisenberg model in the semiclassical limit. Most of the salient features are in agreement with each other, however, the peculiar features in the region above H c 1 cannot be accounted for in our semiclassical modeling and hence suggest a genuine quantum nature. We construct a phase diagram for α - RuCl 3 in a magnetic field along the Ru-Ru bonds, displaying a zigzag ordered state below H c 1 , a quantum paramagnetic regime between H c 1 and H c 2 , and a semiclassical partially polarized state above H c 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Magnetoelastic coupling anisotropy in the Kitaev material α-RuCl 3

Here we show that the Kitaev material α-RuCl 3 is among the most prominent candidates to host a quantum spin-liquid state endowed with fractionalized excitations. Recent experimental and theoretical investigations have separately revealed the importance of both the magnetoelastic coupling and the magnetic anisotropy in dependence of the applied magnetic-field direction. In this combined theoretical and experimental research, we investigate the anisotropic magnetic and magnetoelastic properties for magnetic fields applied along the main crystallographic axes as well as for fields canted out of the honeycomb plane. We found that the magnetostriction anisotropy is unusually large compared to the anisotropy of the magnetization, which is related to the strong magnetoelastic $\tilde{Γ}'$-type coupling in our ab-initio derived model. We observed large, nonsymmetric magnetic anisotropy for magnetic fields canted out of the honeycomb ab plane in opposite directions, namely, toward the +c* or -c* axes, respectively. The observed directional anisotropy is explained by considering the relative orientation of the magnetic field with respect to the coaligned RuCl 6 octahedra. Magnetostriction measurements in canted fields support this nonsymmetric magnetic anisotropy; however, these experiments are affected by magnetic torque effects. Comparison of theoretical predictions with experimental findings allow us to recognize the significant contribution of torque effects in experimental setups where α-RuCl 3 is placed in canted magnetic fields.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Comparison of heavy-ion transport simulations: Mean-field dynamics in a box

Within the transport model evaluation project (TMEP) of simulations for heavy-ion collisions, the mean-field response is examined here. Specifically, zero-sound propagation is considered for neutron-proton symmetric matter enclosed in a periodic box, at zero temperature and around normal density. The results of several transport codes belonging to two families (BUU-like and QMD-like) are compared among each other and to exact calculations. For BUU-like codes, employing the test particle method, the results depend on the combination of the number of test particles and the spread of the profile functions that weight integration over space. These parameters can be properly adapted to give a good reproduction of the analytical zero-sound features. QMD-like codes, using molecular dynamics methods, are characterized by large damping effects, attributable to the fluctuations inherent in their phase-space representation. Moreover, for a given nuclear effective interaction, they generally lead to slower density oscillations, as compared to BUU-like codes. The latter problem is mitigated in the more recent lattice formulation of some of the QMD codes. Furthermore, the significance of these results for the description of real heavy-ion collisions is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Comparing pion production in transport simulations of heavy-ion collisions at 270⁢𝐴 MeV under controlled conditions

Within the TMEP, we present a detailed study of the performance of different transport models in Sn+Sn collisions at 270A MeV, and put particular emphasis on the production of pions and Delta resonances, which have been used as probes of the nuclear symmetry energy. We prescribe a common and rather simple physics model, and follow in detail the results of 4 BUU models and 6 QMD models. The nucleonic evolution of the collision and the nucleonic observables in these codes do not completely converge, but the differences among the codes can be understood as being due to several reasons: the basic differences between BUU and QMD models in the representation of the phase-space distributions, computational differences in the mean-field evaluation, and differences in the adopted strategies for the Pauli blocking in the collision integrals. For pionic observables, we find that a higher maximum density leads to an enhanced pion yield and a reduced pi- pi+ yield ratio, while a more effective Pauli blocking generally leads to a slightly suppressed pion yield and an enhanced pi- pi+ yield ratio. We specifically investigate the effect of the Coulomb force, and find that it increases the total pi- pi+ yield ratio but reduces the ratio at high pion energies, although differences in its implementations do not have a dominating role in the differences among the codes. Taking into account only the results of codes that strictly follow the homework specifications, we find a convergence of the codes in the final charged pion yield ratio to a 1 sigma deviation of about 5%. Furthermore, the uncertainty is expected to be reduced to about 1.6% if the same or similar strategies and ingredients, i.e., an improved Pauli blocking and calculation of the non-linear term in the mean-field potential, are similarly used in all codes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Magnetization Process of Atacamite: A Case of Weakly Coupled S = 1/2 Sawtooth Chains

We present a combined experimental and theoretical study of the mineral atacamite Cu 2 Cl(OH) 3 . Density-functional theory yields a Hamiltonian describing anisotropic sawtooth chains with weak 3D connections. Experimentally, we fully characterize the antiferromagnetically ordered state. Here, magnetic order shows a complex evolution with the magnetic field, while, starting at 31.5 T, we observe a plateaulike magnetization at about M sat /2. Based on complementary theoretical approaches, we show that the latter is unrelated to the known magnetization plateau of a sawtooth chain. Instead, we provide evidence that the magnetization process in atacamite is a field-driven canting of a 3D network of weakly coupled sawtooth chains that form giant moments.

1-dimensional spin chains↗
DOE OSTI2020

Complex magnetic properties in the mixed 4 f - 5 d double perovskite iridates X 2 ZnIrO 6 ( X = Nd , Sm , Eu , Gd )

Here in this paper, we report on the synthesis and magnetic properties of a series of double perovskites Ln 2 ZnIrO 6 with Ln = Nd, Sm, Eu, Gd. These compounds present examples of the rare case of double perovskites (general formula A 2 BB'O6) with a magnetic 4ƒ-ion on the A site in combination with the strongly spin-orbit coupled 5d transition-metal ion Ir 4+ on the B sublattice. We discuss the impact of different rare earths on the macroscopic magnetic properties. Gd 2 ZnIrO 6 and Eu 2 ZnIrO 6 show ferrimagnetic or canted antiferromagnetic order below T N = 23 and 12 K, respectively. Sm 2 ZnIrO 6 orders antiferromagnetically at T N = 13 K. Nd 2 ZnIrO 6 exhibits more complex magnetic properties with a strong field dependence ranging from a two-step spin reorientation at μ 0 H = 0.01 T to an antiferromagnetic ground state at intermediate external fields to a spin-flop phase for 0H ≥ 4 T. This unique behavior suggests an interesting interplay between Nd 3+ and Ir 4+ . To further shed light on the relevant magnetic interaction, the zero-field magnetic ground state of Nd 2 ZnIrO 6 is examined via neutron powder diffraction. In general, the magnetic properties of Ln 2 ZnIrO 6 hint towards a substantial contribution of the rare-earth ions and a significant correlation between 5d and 4ƒ magnetism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Off-axis representation of hyperbolic mirror shapes for X-ray beamlines

Mirror-centered, closed-form expressions for hyperbolic surfaces used in X-ray beamlines have been derived. Hyperbolic mirrors create a virtual focus or source point and can be used to lengthen or shorten the effective focal distance of a compound optical system. The derivations here express off-axis segments of a hyperbolic surface in terms of the real and virtual focal distances and the incident glancing angle at the center of the mirror. Conventional mathematical expressions of hyperbolic shapes describe the surfaces in Cartesian or polar coordinates centered on an axis of symmetry, necessitating cumbersome rotation and translation to mirror-centered coordinates. The representation presented here, with zero slope and the origin at the central point, is most convenient for modeling, metrology, aberration correction, and general surface analysis of off-axis configurations. The direct derivation avoids the need for nested coordinate transforms. A series expansion provides a helpful approximation; the coefficients of the implicit equation are also provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Tri-Sectional Approximation of the Shortest Path to Long-Term Voltage Stability Boundary with Distributed Energy Resources

Ensuring long-term voltage stability is critical for reliable operations of power grids. High share of distributed energy resources (DERs) can create complicated system operation modes that may invalidate the traditional long-term voltage stability analysis based on typical operation modes. To address this challenge, this paper investigates how to compute the shortest path to the voltage stability boundary in the DER aggregated load space with large dispersion. Instead of working in the Euclidean space, we establish the analysis and computations on the algebraic power flow manifold to better capture the curvature change of the shortest path along the direction of losing stability. A modified optimal control framework is presented for obtaining the ground-truth of the smooth shortest path on the manifold. To efficiently and accurately solve for the shortest path, we further leverage the geometric features of the power flow manifold and propose a tri-sectional approximation model that is scalable for large-scale systems. Several numerical examples, up to the 1354-bus system, with different DER penetration levels and high dimensional renewable power injection variations are evaluated. The simulation results demonstrate that the tri-sectional approximation achieves high accuracy and efficiency to approximate the shortest path to the voltage stability boundary.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Steam-created grain boundaries for methane C–H activation in palladium catalysts

Defects may display high reactivity because the specific arrangement of atoms differs from crystalline surfaces. We demonstrate that high-temperature steam pretreatment of palladium catalysts provides a 12-fold increase in the mass-specific reaction rate for carbon-hydrogen (C–H) activation in methane oxidation compared with conventional pretreatments. Through a combination of experimental and theoretical methods, we demonstrate that an increase in the grain boundary density through crystal twinning is achieved during the steam pretreatment and oxidation and is responsible for the increased reactivity. The grain boundaries are highly stable during reaction and show specific rates at least two orders of magnitude higher than other sites on the palladium on alumina (Pd/Al 2 O 3 ) catalysts. Theoretical calculations show that strain introduced by the defective structure can enhance C–H bond activation. Introduction of grain boundaries through laser ablation led to further rate increases.

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

Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium

Polycyclic aromatic hydrocarbons (PAHs) contain ≲20% of the carbon in the interstellar medium. They are potentially produced in circumstellar environments (at temperatures ≳1000 kelvin), by (~10 kelvin) interstellar clouds, or by processing of carbon-rich dust grains. We report isotopic properties of PAHs extracted from samples of the asteroid Ryugu and the meteorite Murchison. The doubly- 13 C substituted compositions (Δ2× 13 C values) of the PAHs naphthalene, fluoranthene, and pyrene are 9 to 51‰ higher than values expected for a stochastic distribution of isotopes. The Δ2× 13 C values are higher than expected if the PAHs formed in a circumstellar environment, but consistent with formation in the interstellar medium. By contrast, the PAHs phenanthrene and anthracene in Ryugu samples have Δ2× 13 C values consistent with formation by higher-temperature reactions.

Science & Technology - Other Topics↗
DOE OSTI2024

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. Furthermore, these comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

59 BASIC BIOLOGICAL SCIENCES↗