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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 OSTI2024

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases (FAPs) to catalyse unnatural photoredox radical C–C bond formation by leveraging strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases (RAPs) to facilitate decarboxylative radical cyclisation with excellent chemo-, enantio-, and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of FAPs. An orthogonal set of RAPs was engineered to access all four possible stereoisomers of stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved RAPs allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclisation. The development of stereoselective RAPs provides unnatural C–C bond forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free radical-mediated reactions.

Ju, Shuyun (ORCID:000000020322104X)↗
DOE OSTI2025

Two decades of bacterial ecology and evolution in a freshwater lake

Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. Further, these genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A genomic perspective on fungal diversity and evolution

Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different ‘species’ and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute’s MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, in this study, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.

Mondo, Stephen J. [USDOE Joint Genome Institute (J↗
DOE OSTI2024

Unraveling the electronic structure and magnetic transition evolution across monolayer, bilayer, and multilayer ferromagnetic Fe 3 GeTe 2

Two-dimensional (2D) van der Waals (vdW) magnets have sparked widespread attention due to their potential in spintronic applications as well as in fundamental physics. Ferromagnetic vdW compound Fe 3 GeTe 2 (FGT) and its Ga variants have garnered significant interest due to their itinerant magnetism, correlated states, and high magnetic transition temperature. Experimental studies have demonstrated the tunability of FGT’s Curie temperature, T C , through adjustments in quintuple layer numbers (QL) and carrier concentrations, n. However, the underlying mechanism remains elusive. In this study, we employ molecular beam epitaxy (MBE) to synthesize 2D FGT films down to 1 QL with precise layer control, facilitating an exploration of the band structure and the evolution of itinerant carrier density. Angle-resolved photoemission spectroscopy (ARPES) reveals significant band structure changes at the ultra-thin limit, while first-principles calculations elucidate the band evolution from 1 QL to bulk, largely governed by interlayer coupling. Additionally, we find that n is intrinsically linked to the number of QL and temperature, with a critical value triggering the magnetic phase transition. Our findings underscore the pivotal role of band structure and itinerant electrons in governing magnetic phase transitions in such 2D vdW magnetic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Deep learning forecasts the spatiotemporal evolution of fluid-induced microearthquakes

Microearthquakes generated by subsurface fluid injection record the evolving stress state and permeability of reservoirs. Forecasting their spatiotemporal evolution is therefore critical for applications such as enhanced geothermal systems, carbon dioxide sequestration and other geoengineering applications. Here we propose a transformer neural network model that ingests hydraulic stimulation history and prior microearthquake observations to forecast four key quantities: cumulative microearthquake count, cumulative logarithmic seismic moment, and the 50th- and 95th-percentile extents of the microearthquake cloud. Applied to the EGS Collab Experiment 1 dataset, the model achieves R2 > 0.98 for the 1-s forecast horizon and R2 > 0.88 for the 15-s forecast horizon across all targets, and supplies uncertainty estimates through a learned standard deviation term. These accurate, uncertainty-quantified forecasts enable real-time inference of fracture propagation and permeability evolution, demonstrating the strong potential of deep-learning approaches to improve seismic-risk assessment and guide mitigation strategies in future fluid-injection operations.

Chung, Jaehong↗
DOE OSTI2026

Part-scale evolution of fine-scale microstructural heterogeneity in solid-state additive manufacturing

Current solid-state additive manufacturing methods, refined through costly and time-consuming trial and error, have spurred interest in computational models that replicate material behavior under typical thermomechanical conditions (e.g., strain-rate ~ 102 s−1). These models, however, struggle to capture time-dependent microstructural evolution. In this work, Additive Friction-Stir Deposition (AFSD) is used as a representative case study for part-scale quantification of microstructure evolution at a fine spatial resolution (200 μm) by examining a liquid-nitrogen-cooled stop-action build via energy-dispersive X-ray diffraction coupled with a multi-channel detector. These results inform modeling efforts by linking process asymmetry to stored plastic strain, residual elastic strain, and texture development, and unlike current state-of-the-art characterization methods (e.g., EBSD or neutron diffraction), this approach provides both the spatial resolution and collection efficiency necessary to quantify fine-scale microstructural heterogeneity over large component volumes. As such, this technique provides essential validation data for computational models, e.g., crystal plasticity, enabling future prediction of heterogeneous behavior in AFSD and other additive manufacturing processes.

Franz, Cole [ORNL] (ORCID:0000000213465881)↗
DOE OSTI2025

The Three Hundred Project: Modeling baryon and hot-gas fraction evolution in simulated clusters

The baryon fraction of galaxy clusters, expressed as the ratio between the mass in baryons (including both stars and cold or hot gas) and the total mass, is a powerful tool to provide information on the cosmological parameters, while the hot-gas fraction provides indications on the physics of the intracluster plasma and its interplay with the processes that drive galaxy formation. Using cosmological hydrodynamical simulations of about 300 simulated massive galaxy clusters with a median mass M 500 ≈ 7 × 10 14 M ⊙ at z = 0, we model the relations between total mass and either baryon fraction or the hot gas fractions at overdensities Δ = 2500, 500, and 200 with respect to the cosmic critical density, and their evolution from z ∼ 0 to z ∼ 1.3. We utilized the simulated galaxy clusters from the Three Hundred project, which include star formation and feedback from both supernovae and active galactic nuclei. We fit the simulation results for such scaling relations against three analytic forms (linear, quadratic, and logarithmic in a logarithmic plane) and three forms for the redshift dependence, and we considered as a variable both the inverse of the cosmic scale factor, (1 + z), and the Hubble expansion rate, E(z). We show that power-law dependencies on cluster mass poorly describe the investigated relations. A power law fails to simultaneously capture the flattening of the total baryon and gas fractions at high masses, their drop at low masses, and the transition between these two regimes. The other two functional forms provide a more accurate description of the curvature in mass scaling. The fractions measured within smaller radii exhibit a stronger evolution than those measured within larger radii. From the analysis of these simulations, we evince that as long as we include systems in the mass range herein investigated, the baryon or gas fraction can be accurately related to the total mass through either a parabola or a logarithm in the logarithmic plane. The trends are common to all modern hydro simulations, although the amplitude of the drop at low masses might differ. Being able to observationally determine the gas fraction in groups will thus provide constraints on the baryonic physics.

galaxy clusters↗
DOE OSTI2024

Quantum to classical parton evolution in the QGP

We study the time evolution of the density matrix of a high energy quark in the presence of a dense QCD background that is modeled as a stochastic Gaussian color field. At late times, we find that only the color singlet component of the quark’s reduced density matrix survives the in-medium evolution and that the density matrix becomes asymptotically diagonal in both transverse position and momentum spaces. In addition, we observe an accelerated entropy growth due to the larger phase space being explored by the quark and that the quantum and classical quark entropies converge at late times. We further observe that the quark state loses all memory of the initial condition. Combined with the fact that the reduced density matrix satisfies Boltzmann-diffusion transport, we conclude that the quark reduced density matrix can be interpreted as a classical phase space distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

In situ study of microstructure evolution and α → ω phase transition in annealed and pre-deformed Zr under hydrostatic loading

The detailed study of the effect of the initial microstructure on its evolution under hydrostatic compression before, during, and after the irreversible α → ω phase transformation and during pressure release in Zr using in situ x-ray diffraction is presented. Two samples were studied: one is plastically pre-deformed Zr with saturated hardness and the other is annealed. Phase transformation α → ω initiates at lower pressure for a pre-deformed sample but for a volume fraction of ω Zr, c > 0.7, a larger volume fraction is observed for the annealed sample. This implies that the proportionality between the athermal resistance to the transformation and the yield strength in the continuum phase transformation theory is invalid; an advanced version of the theory is outlined. Phenomenological plasticity theory under hydrostatic loading is outlined in terms of microstructural parameters, and plastic strain is estimated. During transformation, the first rule is suggested, i.e., the average domain size, microstrain, and dislocation density in ω Zr for c < 0.8 are functions of the volume fraction, c of ω Zr only, which are independent of the plastic strain tensor prior to transformation and pressure. The microstructure is not inherited during phase transformation. Surprisingly, for the annealed sample, the final dislocation density and the average microstrain after pressure release in the ω phase are larger than for the severely pre-deformed sample. The results suggest that an extended experimental basis is required for the predictive models for the combined pressure-induced phase transformations and microstructure evolutions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

An efficient surrogate model of secondary electron formation and evolution

This work extends the adjoint-deep learning framework for runaway electron (RE) evolution, developed by McDevitt et al. [Phys. Plasmas 32, 042503 (2025)], to account for large-angle collisions. By incorporating large-angle collisions, the framework allows the avalanche of REs to be captured, an essential component of RE dynamics. This extension is accomplished by using a Rosenbluth–Putvinski approximation to estimate the distribution of secondary electrons generated by large-angle collisions. By evolving both the primary and multiple generations of secondary electrons, the present formulation can capture both the detailed temporal evolution of a RE population beginning from an arbitrary initial momentum space distribution, along with providing approximations to the saturated growth and decay rates of the RE population. Predictions of the adjoint-deep learning framework are verified against a traditional RE solver, with good agreement present across a broad range of parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Phase-field modeling of aging-induced microstructure evolution in pentaerythritol tetranitrate thin films and ramifications for shock initiation

Aging of energetic materials may change performance and affect their safety and reliability, but the relationship between microstructure changes induced by aging and consequent performance changes has not been fully established. This work presents results of phase-field method simulations used to model microstructure evolution of vapor-deposited pentaerythritol tetranitrate (PETN) thin films. Simulated aging is shown to induce grain coarsening and substantial changes of the configuration of porosity in the film: Specifically, we show that porosity tends to concentrate in large pores to a greater degree in aged films, a state that is arrived at by closure or consolidation of small pores. To evaluate the performance of the as-deposited and aged films, we perform two-dimensional hydrocode flyer-film impact simulations that incorporate the phase-field output microstructures directly, permitting us to connect features therein to changes in reactivity, a key metric of energy output for shock initiation. The results demonstrate that declining sensitivity obtained for the simulated aged films can be correlated with the loss of fine-structured pores relatively early in the aging process, while long-term microstructure evolution that gradually alters the shape of large, branching pores is less impactful. Finally, we discuss commonalities and discrepancies between our simulation results and high-throughput initiation experiments on shock initiation of aged PETN thin films.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Evolution of intermittent filaments in the scrape-off layer of NSTX

Filamentary structures naturally arise from background turbulence in the scrape-off layer (SOL) of plasmas, leading to significant particle and heat transport that can degrade overall plasma confinement. This enhanced transport can contribute to unacceptably high heat loads on plasma-facing components. As such, understanding the physics of SOL plasma filaments is critical for predicting and mitigating their effects in future fusion devices. On the National Spherical Torus Experiment (NSTX), plasma filaments—commonly referred to as “blobs”—were investigated using the gas-puff imaging (GPI) diagnostic in the edge and SOL regions. The analysis involved identifying, segmenting, and tracking the characteristic contours of the blobs in each frame of the GPI video sequences. Their evolution was characterized through shape descriptors, velocity, and angular velocity derived from their contour coordinates. The results indicate that as the blob area increases, their shapes become more concave and less circular, suggesting reduced structural stability in larger blobs. This result aligns with previous theoretical results where it was shown that larger blobs are more susceptible to instabilities [Krasheninnikov et al., J. Plasma Phys. 74, 679–717 (2008) and D'Ippolito et al., Phys. Plasmas 18, 060501 (2011)]. A positive correlation was observed between radial velocity and radial position, suggesting radially outward acceleration of the filaments, potentially driven by decreasing viscous drag toward the far SOL. Interestingly, blobs in background SOL turbulence exhibited minimal spinning in contrast to filaments originating from edge localized modes, which show substantial rotation during their paths [Lampert et al., Phys. Plasmas 29, 102502 (2022)]. Statistical analysis of the solidity and total curvature shape descriptors, along with their temporal evolution, revealed relatively broad, near-Gaussian distributions. This suggests that blob morphology is strongly influenced by stochastic turbulent processes in the surrounding plasma environment. Blob parameters were also compared with bulk plasma and radial profile measurements. Notable trends were found between blob rotation and poloidal velocity with collisionality and line-integrated density. These findings contribute to a deeper understanding of blob dynamics and provide valuable insights for refining SOL turbulence models.

Covariance and correlation↗
DOE OSTI2026

Hierarchical-embedding autoencoder with a predictor as efficient architecture for learning time-evolution in multi-scale turbulent flows

We introduce a scale-aware, data-driven deep learning modeling framework for accurately predicting the time evolution of multi-scale turbulent plasma and liquid flows. The approach is motivated by the idea of scale separation. Structures of vastly different length scales emerge in these systems, and interactions between these structures occur only locally. To exploit this structure, the flow state is transformed by a hierarchical, fully convolutional autoencoder, not into a single embedding layer as in conventional convolutional surrogate models, but into a series of embedding layers. A stepwise training strategy ensures that fine-scale features are encoded on a high-resolution grid, while larger structures are represented on progressively coarser layers. The time evolution predictor advances all embedding layers in sync, capturing local interactions between features at the same scale as well as between all scales. This approach enables efficient modeling of multi-scale systems since negligible interactions between distant, small-scale structures do not need to be directly modeled. Our hierarchical-embedding autoencoder with a predictor framework is evaluated on canonical examples of multi-scale turbulence: two-dimensional Kolmogorov flow and Hasegawa–Wakatani plasma turbulence. In both cases, the proposed framework significantly improves predictive accuracy relative to conventional convolutional network architectures. A significant improvement in prediction accuracy was observed for crucial statistical characteristics of the Hasegawa–Wakatani plasma as well as for individual trajectories of the Kolmogorov flow turbulence. Importantly, the model's rollout for the Hasegawa–Wakatani problem demonstrates a four-order-of-magnitude speedup compared to traditional numerical solvers.

Khrabry, Alexander I. [Princeton Univ., NJ (United↗
DOE OSTI2026

Time-resolved interferometric measurements of plasma density evolution in laser-driven capacitor-coil targets

Laser-driven capacitor-coil targets provide a compact platform for generating strong magnetic fields and are widely used in magnetized high-energy-density (HED) plasma experiments. In addition to magnetic-field generation, these targets also produce plasma in the coil region, which can influence the subject physical processes and interact with secondary targets or external plasmas in their applications. However, direct, time-resolved measurements of the plasma density surrounding the coil remain limited. Here, we report interferometric measurements of the plasma density evolution in laser-driven capacitor-coil targets irradiated by the University of Osaka LFEX laser. Two-dimensional electron density maps reveal two distinct plasma sources loading the coil region: plasma generated in the coil itself and plasma produced by laser ablation of the target plates. These results provide quantitative information on plasma loading and evolution in capacitor-coil targets and are directly relevant to the design and modeling of magnetized HED plasma experiments.

Zhang, Yang [Princeton University, NJ (United Stat↗
DOE OSTI2025

Structure and evolution of photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis

Thylakoid-free cyanobacteria are thought to preserve ancestral traits of early-evolving organisms capable of oxygenic photosynthesis. However, and until recently, photosynthesis studies in thylakoid-free cyanobacteria were only possible in the model strain Gloeobacter violaceus , limiting our understanding of photosynthesis evolution. Here, we report the isolation, biochemical characterization, cryo-EM structure, and phylogenetic analysis of photosystem I (PSI) from a recently discovered thylakoid-free cyanobacterium, Anthocerotibacter panamensis , a distant relative of the genus Gloeobacter . We find that A. panamensis PSI exhibits a distinct carotenoid composition and has one conserved low-energy chlorophyll site, which was lost in G. violaceus . Furthermore, PSI in thylakoid-free cyanobacteria has changed at the sequence level to a degree comparable to that of other strains, yet its subunit composition and oligomeric form might be identical to that of the most recent common ancestor of cyanobacteria. This study therefore provides a glimpse into the ancient evolution of photosynthesis.

Jiang, Han-Wei (ORCID:0000000234008698)↗
DOE OSTI2024

Imprints of light dark matter on the evolution of cosmic neutrinos

Neutrinos are often considered as a portal to new physics beyond the Standard Model (SM) and might possess phenomenologically interesting interactions with dark matter (DM). Here, this paper examines the cosmological imprints of DM that interacts with and is produced from SM neutrinos at temperatures below the MeV scale. We take a model-independent approach to compute the evolution of DM in this framework and present analytic results which agree well with numerical ones. Both freeze-in and freeze-out regimes are included in our analysis. Furthermore, we demonstrate that the thermal evolution of neutrinos might be substantially affected by their interaction with DM. We highlight two distinctive imprints of such DM on neutrinos: (i) a large, negative contribution to N eff , which is close to the current experimental limits and will readily be probed by future experiments; (ii) spectral distortion of the cosmic neutrino background (CνB) due to DM annihilating into neutrinos, a potentially important effect for the ongoing experimental efforts to detect CνB.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Homologous recombination shapes the architecture and evolution of bacterial genomes

Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

Torrance, Ellis L [University of North Carolina, G↗
DOE OSTI2024

Cytochrome b5 diversity in green lineages preceded the evolution of syringyl lignin biosynthesis

Abstract Lignin production marked a milestone in vascular plant evolution, and the emergence of syringyl (S) lignin is lineage specific. S-lignin biosynthesis in angiosperms, mediated by ferulate 5-hydroxylase (F5H, CYP84A1), has been considered a recent evolutionary event. F5H uniquely requires the cytochrome b5 protein CB5D as an obligatory redox partner for catalysis. However, it remains unclear how CB5D functionality originated and whether it coevolved with F5H. We reveal here the ancient evolution of CB5D-type function supporting F5H-catalyzed S-lignin biosynthesis. CB5D emerged in charophyte algae, the closest relatives of land plants, and is conserved and proliferated in embryophytes, especially in angiosperms, suggesting functional diversification of the CB5 family before terrestrialization. A sequence motif containing acidic amino residues in Helix 5 of the CB5 heme-binding domain contributes to the retention of CB5D function in land plants but not in algae. Notably, CB5s in the S-lignin–producing lycophyte Selaginella lack these residues, resulting in no CB5D-type function. An independently evolved S-lignin biosynthetic F5H (CYP788A1) in Selaginella relies on NADPH-dependent cytochrome P450 reductase as sole redox partner, distinct from angiosperms. These results suggest that angiosperm F5Hs coopted the ancient CB5D, forming a modern cytochrome P450 monooxygenase system for aromatic ring meta-hydroxylation, enabling the reemergence of S-lignin biosynthesis in angiosperms.

59 BASIC BIOLOGICAL SCIENCES↗