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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic “Toomer's Oak,” this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

Quercus virginiana↗
DOE OSTI2020

Repeated horizontal gene transfer of GAL actose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. Furthermore, these findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2021

TOI-431/HIP 26013: a super-Earth and a sub-Neptune transiting a bright, early K dwarf, with a third RV planet

ABSTRACT We present the bright (Vmag = 9.12), multiplanet system TOI-431, characterized with photometry and radial velocities (RVs). We estimate the stellar rotation period to be 30.5 ± 0.7 d using archival photometry and RVs. Transiting Exoplanet Survey Satellite (TESS) objects of Interest (TOI)-431 b is a super-Earth with a period of 0.49 d, a radius of 1.28 ± 0.04 R⊕, a mass of 3.07 ± 0.35 M⊕, and a density of 8.0 ± 1.0 g cm−3; TOI-431 d is a sub-Neptune with a period of 12.46 d, a radius of 3.29 ± 0.09 R⊕, a mass of $9.90^{+1.53}_{-1.49}$ M⊕, and a density of 1.36 ± 0.25 g cm−3. We find a third planet, TOI-431 c, in the High Accuracy Radial velocity Planet Searcher RV data, but it is not seen to transit in the TESS light curves. It has an Msin i of $2.83^{+0.41}_{-0.34}$ M⊕, and a period of 4.85 d. TOI-431 d likely has an extended atmosphere and is one of the most well-suited TESS discoveries for atmospheric characterization, while the super-Earth TOI-431 b may be a stripped core. These planets straddle the radius gap, presenting an interesting case-study for atmospheric evolution, and TOI-431 b is a prime TESS discovery for the study of rocky planet phase curves.

Osborn, Ares↗
DOE OSTI2021

Arabidopsis bZIP11 Is a Susceptibility Factor During Pseudomonas syringae Infection

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2025

𝐴𝑏 initio density-matrix approach to exciton coherence: Phonon scattering, Coulomb interactions, and radiative recombination

Relaxation processes following light excitation in semiconductors are key in materials-based quantum technology applications. These processes are broadly studied in atomically thin transition-metal dichalcogenides, quasi-two-dimensional excitonic semiconductors in which atomistic design allows for tunable excited-state properties, such as relaxation lifetimes and photoinduced coherence. In this work, we present a density-matrix-based approach to compute exciton relaxation within a many-body ab initio perspective. We expand our previously developed Lindblad density-matrix formalism to capture multichannel electron-hole pair relaxation processes, including phonon and Coulomb scattering as well as radiative recombination, and we study their effect on the time-resolved excited-state propagation. Using monolayer MoSe 2 as a prototypical example, we examine many-body effects on the time-dependent dynamics of photoactive excitations, exploring how the electron-hole pair interactions are reflected in variations of the excitation energy, spectral signature, and state coherence. In conclusion, our method supplies a detailed understanding of exciton relaxation mechanisms in realistic materials, offering a previously unexplored pathway to study excited-state dynamics in semiconductors from first principles.

Band structure methods↗
DOE OSTI2020

Interlayer coupling induced quasiparticles

In this work, we present an exact treatment of layered many-body electronic systems in the presence of interlayer coupling within the Schwinger functional derivative approach on the Keldysh contour. Our transparent approach allows us to clarify the definition of interlayer coupling by showing the independent roles hybridization and interactions play in generating new electronic and magnetic excitations. We find interlayer coupling to induce a variety of plasmons, magnons, and excitons, residing within a layer, traversing between layers, or propagating along the interface. Moreover, we predict interfacial excitations, including an electron-hole pairing pathway, facilitated by previously ignored layer nonconserving interactions. Finally, we briefly explore the consequence of interlayer coupling on a bilayer square lattice system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Integrable model of topological SO(5) superfluidity

Assisted by general symmetry arguments and a many-body invariant, we introduce a phase of matter that constitutes a topological SO(5) superfluid. Key to this finding is the realization of an exactly solvable model that displays some similarities with a minimal model of superfluid 3 He. We study its quantum phase diagram and correlations, and find exotic superfluid as well as metallic phases in the repulsive sector. At the critical point separating trivial and nontrivial superfluid phases, our Hamiltonian reduces to the globally SO(5)-symmetric Gaudin model with a degenerate ground manifold that includes quartet states. Most importantly, the exact solution permits uncovering of an interesting non-pair-breaking mechanism for superfluids subject to external magnetic fields. Furthermore, nonintegrable modifications of our model lead to a strong-coupling limit of our metallic phase with a ground-state manifold that shows an extensive entropy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Enhancing T c in a composite superconductor/metal bilayer system: A dynamical cluster approximation study

It has been proposed that the superconducting transition temperature T c of an unconventional superconductor with a large pairing scale but strong phase fluctuations can be enhanced by coupling it to a metal. However, the general efficacy of this approach across different parameter regimes remains an open question. Using the dynamical cluster approximation, we study this question in a system composed of an attractive Hubbard layer in the intermediate coupling regime, where the magnitude of the attractive Coulomb interaction |U| is slightly larger than the bandwidth W, hybridized with a noninteracting metallic layer. We find that while the superconducting transition becomes more mean-field-like with increasing interlayer hopping, the superconducting transition temperature T c exhibits a nonmonotonic dependence on the strength of the hybridization t ⊥ . Furthermore, this behavior arises from a reduction of the effective pairing interaction in the correlated layer that outcompetes the growth in the intrinsic pair-field susceptibility induced by the coupling to the metallic layer. We find that the largest T c inferred here for the composite system is comparable to the maximum value currently estimated for the isolated negative-U Hubbard model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Topological quantum computation on a chiral Kondo chain

We describe the chiral Kondo chain model based on the symplectic Kondo effect and demonstrate that it has a quantum critical ground state populated by non-Abelian anyons. We show that the fusion channel of two arbitrary anyons can be detected by locally coupling the two anyons to an extra single channel of chiral current and measuring the corresponding conductance at a finite frequency. Based on such measurements, we propose that the chiral Kondo chain model with symplectic symmetry can be used for the implementation of measurement-only topological quantum computations, and it possesses several distinct features favorable for such applications. Furthermore, the sources and effects of errors in the proposed system are analyzed and possible material realizations are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Electronic excitation spectra of molecular hydrogen in phase I from quantum Monte Carlo and many-body perturbation methods

Here, we study the electronic excitation spectra in solid molecular hydrogen (phase I) at ambient temperature and 5- to 90-GPa pressures using quantum Monte Carlo methods and many-body perturbation theory. In this range, the system changes from a wide-gap molecular insulator to a semiconductor, altering the nature of the excitations from localized to delocalized. Computed gaps and spectra agree with experiments, proving the ability to predict accurately band gaps of many-body systems in the presence of nuclear quantum and thermal effects.

08 HYDROGEN↗
DOE OSTI2025

Five-point functions and the permutation group 𝑆 5

Five-point functions and five-body wave functions play an important role in many areas of nuclear and particle physics, e.g., in 2 →3 scattering processes, in the five-gluon vertex, or in the study of pentaquarks. In this work we consider the permutation group 𝑆 5 to facilitate the description of such objects. We work out the multiplets transforming under irreducible representations of 𝑆 5 and provide compact formulas allowing one to cast the permutations of an object 𝑓 12345 into combinations with definite permutation symmetry. We also give the explicit expressions for the irreducible multiplet products. We consider several practical applications as examples: We arrange the four-momenta and Lorentz invariants of a five-point function into the multiplet structure, we work out the color tensors of the five-gluon vertex in the multiplet notation, and we discuss applications for five-body wave functions like those of pentaquarks.

Bethe-Salpeter equation↗
DOE OSTI2020

Localized excitons in defective monolayer germanium selenide

Germanium selenide (GeSe) is a van der Waals–bonded layered material with promising optoelectronic properties, which has been experimentally synthesized for two-dimensional (2D) semiconductor applications. In the monolayer, due to reduced dimensionality and, thus, screening environment, perturbations such as the presence of defects have a significant impact on its properties. We apply density functional theory and many-body perturbation theory to understand the electronic and optical properties of GeSe containing a single selenium vacancy in the –2 charge state. We predict that the vacancy results in midgap “trap states” that strongly localize the electron and hole density and lead to sharp, low-energy optical absorption peaks below the predicted pristine optical gap. Analysis of the exciton wave function reveals that the 2D Wannier-Mott exciton of the pristine material monolayer is strongly modified by the presence of the defect. The lowest-energy exciton wave function is highly localized around the defect, with the Bohr radius reduced by a factor of 4 when compared to the pristine material and a dipole moment along the out-of-plane axis due to the defect-induced symmetry breaking. Altogether, these results suggest that the vacancy significantly modifies the excitonic properties of the system, demonstrating the importance of considering defects in the context of material design.

2-dimensional systems↗