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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 271 records · Page 15
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DOE OSTI2024

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Thermal and kinematic properties of ejecta in SN1987A revealed by XRISM

We present an analysis of high-resolution spectra from the shock-heated plasmas in SN 1987A, based on an observation using the Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM). The 1.7–10 keV Resolve spectra are accurately represented by a single-component, plane-parallel shock plasma model, with a temperature of $2.84_{-0.08}^{+0.09}$ keV and an ionization parameter of $2.64_{-0.45}^{+0.58}$ × $10^{11}\,\,{\rm s\,\, cm}^{-3}$. The Resolve spectra are also well reproduced by the 3D magneto-hydrodynamic simulation presented by Orlando et al. (2020, A&A, 636, A22) suggesting substantial contribution from the ejecta. The metal abundances obtained with Resolve align with the Large Magellanic Cloud value, indicating that the X-rays in 2024 originate from “non-metal-rich” shock-heated ejecta and the reverse shock has not reached the inner metal-rich region of ejecta. Doppler widths of the atomic lines from Si, S, and Fe correspond to velocities of 1500–1700 km s$^{-1}$, where the thermal broadening effects in this non-metal-rich plasma are negligible. Therefore, the line broadening seen in Resolve spectra is determined by the large bulk motion of ejecta. For reference, we determined a $90\%$ upper limit on non-thermal emission from a pulsar wind nebula at $4.3 \times 10^{-13}$ erg cm$^{-2}$ s$^{-1}$ in the 2–10 keV range, aligning with NuSTAR findings by Greco et al. (2022, ApJ, 931, 132). Additionally, we searched for the $^{44}$Sc K line feature and found a $1\sigma$ upper limit of $1.0 \times 10^{-6}$ photons cm$^{-2}$ s$^{-1}$, which translates to an initial $^{44}$Ti mass of approximately $2 \times 10^{-4}\, M_{\odot }$, consistent with previous X-ray to soft gamma-ray observations (Boggs et al. 2015, Science, 348, 670; Grebenev et al. 2012, Nature, 490, 373; Leising 2006, ApJ, 651, 1019).

ISM: supernova remnants↗
DOE OSTI2024

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Impact of external screening on the valence and core level photoelectron spectra of monolayer W⁢S 2

Transition metal dichalcogenides (TMDs) represent an emerging class of layered materials with applications in microelectronics, optoelectronics, photonics, and catalysis. The confinement of charge carriers within the highly anisotropic, quasi-two-dimensional geometry of one-layer (1L) TMDs leads to reduced, variable dielectric screening, giving rise to a quasiparticle band gap that is highly susceptible to the surrounding dielectric environment. Here, exploiting the contrasting external dielectric environments of gold-supported and suspended 1L W⁢S 2 , we show how the electronic states of W⁢S 2 under the effective and ineffective screening environments align at a junction made within the same sheet of material. Photoelectron spectra point to the close alignment of the charge neutrality levels of W⁢S 2 in both environments, and the breakdown of rigid shifts between the valence states and core levels with the core levels shifting more than twice as much as the valence states. Furthermore, the effectively screened W⁢S 2 exhibits a valence state with the photoemission linewidth twice as large as the ineffectively screened suspended W⁢S 2 , presumably originated from the locally varying W⁢S 2 -Au distance and substrate disorders. Collectively, these findings provide key insights into the electronic behavior of W⁢S 2 and its photoemission process with the electronic states renormalized according to the external screening environments.

Dielectric properties↗
DOE OSTI2026

Practical considerations for measuring global spin density matrix elements of vector mesons in heavy-ion collisions

The STAR Collaboration has reported a significant 𝜙-meson global spin alignment (𝜌 00 ) signal in Au+Au collisions at $\sqrt{s_{NN}}$ ≤ 62 GeV by measuring the polar angle distribution of 𝜙-meson daughters with respect to the orbital angular momentum direction of the collision system. Here, in this paper, a new method is explored for studying vector-meson global spin alignment in heavy-ion collisions by examining the two-dimensional (2D) polar and azimuthal angle distribution. This method allows simultaneous extraction of 𝜌 00 and off-diagonal spin density matrix elements (SDMEs), providing unique access to local quark-antiquark spin correlations and spin hydrodynamics in quark-gluon plasma. The new 2D method also removes potential biases from nonzero off-diagonal SDMEs on 𝜌 00 with the 1D method. A detailed procedure to correct for detector acceptance and resolution effects is also presented and validated by simulation studies.

Wilks, Gavin [University of Illinois, Chicago, IL ↗
DOE OSTI2024

X-ray diagnostics for the cavity-based x-ray free-electron laser project

The success of x-ray free-electron lasers (XFELs) in recent years has greatly advanced many scientific fields. However, most of these XFELs suffer from a low longitudinal coherence and instabilities due to the stochastic start-up process. A cavity-based x-ray free-electron laser (CBXFEL) is a possible future direction in the development of fully coherent and stable x-ray sources. One of the challenges of a CBXFEL is the requirement for the μ⁢m−sized electron bunches to fully overlap in three dimensions with the circulating μ⁢m−sized x-ray pulses in an x-ray cavity tens or hundreds of meters long. We present here the development of an x-ray diagnostics system for accurate alignment of x-ray beams in the CBXFEL cavity. The system was developed within the framework of a CBXFEL research and development collaboration among Argonne National Laboratory, SLAC National Accelerator Laboratory, and Spring-8. All the designed diagnostic components have been fully characterized at the Advanced Photon Source to demonstrate a capability for sub-μ⁢rad angular and μ⁢m spatial alignment of the CBXFEL cavity.

Free-electron lasers↗
DOE OSTI2024

Anomalous temperature-dependent magnetization in the nearly collinear antiferromagnet Y 2 Co 3

Y 2 Co 3 is a newly discovered antiferromagnetic (AFM) compound with distorted kagome layers. Here, previous investigations via bulk magnetization measurements suggested a complex non-collinear magnetic behavior, with magnetic moments primarily anti-aligned along the b axis and some canting towards the ac plane. In this study, we report the magnetic structure of Y 2 Co 3 to be an A-type AFM structure with ferromagnetic (FM) interactions within the distorted kagome plane and an inter-plane antiferromagnetic interaction, as determined by single crystal neutron diffraction. The magnetic moments align along the b axis, with minimal canting towards the c axis, at odds with the previous interpretation of bulk magnetization measurements. The magnetic moments on the two distinct Co sites are (0, -0.68, 0) μB and (0, 1.25, 0.07) μ B . We attribute the previously reported ”non-collinear” behavior to the considerable temperature dependence of itinerant AFM exchange interactions, induced by thermal contraction along the b axis. Additionally, our examination of lattice constants through pressure studies reveals compensating effects on FM and AFM interactions, resulting in negligible pressure dependence of T N .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Temperature-dependent magnetic-field-induced ab -plane Gd spin reorientations in antiferromagnetic domains in a single crystal of the tetragonal A-type antiferromagnet GdRh 2 Si 2

The compound GdRh 2 Si 2 crystallizes in the body-centered tetragonal ThCr 2 Si 2 structure and exhibits A-type antiferromagnetic order below its Néel temperature T N = 107 K where the Gd moments are ferromagnetically aligned in the ab-plane with the moments in adjacent planes aligned antiferromagnetically. Previously, the nonlinear low-field magnetization versus field M ab ( H ∥ [1, 0, 0]) measurements on single crystals were interpreted in terms of a mean-field model. Here, in this work, we reinterpret this nonlinearity more simply in terms of the response of the ordered moments in four noninteracting tetragonal domains to the applied field and find good agreement with our theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Exciton thermalization dynamics in monolayer MoS2: A first-principles Boltzmann equation study

Understanding exciton thermalization is critical for optimizing optoelectronic and photocatalytic processes in many materials. However, it is hard to access the dynamics of such processes experimentally, especially on systems such as monolayer transition metal dichalcogenides, where various low-energy excitations pathways can compete for exciton thermalization. Here, we study exciton dynamics due to exciton-phonon scattering in monolayer MoS2 from a first-principles, interacting Green's function approach, to obtain the relaxation and thermalization of low-energy excitons following different initial excitations at different temperatures. We find that the thermalization occurs on a picosecond time scale at 300 K but can increase by an order of magnitude at 100 K. The long total thermalization time, owing to the nature of its excitonic band structure, is dominated by slow spin-flip scattering processes in monolayer MoS2. In contrast, thermalization of excitons in individual spin-aligned and spin-anti-aligned channels can be achieved within a few hundred fs when exciting higher-energy excitons. We further simulate the intensity spectrum of time-resolved angle-resolved photoemission spectroscopy experiments and anticipate that such calculations may serve as a map to correlate spectroscopic signatures with microscopic exciton dynamics.

Chan, Yang-hao↗
DOE OSTI2025

Tracing cosmic gas in filaments and halos: Low-redshift insights from the kinematic Sunyaev-Zel’dovich effect

In this work, we leverage cosmic microwave background (CMB) data from the Atacama Cosmology Telescope (ACT) and LSS data from the imaging survey conducted by the Dark Energy Spectroscopic Instrument (DESI) to study the distribution of gas around galaxy groups at low redshift, z ≈ 0.3, via the kinematic Sunyaev-Zel'dovich (kSZ) effect. In particular, we perform velocity-weighted stacking on the photometric galaxies from the Bright Galaxy Survey (BGS) to isolate the monopole and quadrupole of the kSZ signal, orienting the stacked images along 2D filaments identified using the Hessian of the projected gravitational potential. We find a 7.2σ detection in the monopole of the signal (i.e., the gas density profile) and a 4σ detection in the quadrupole (m = 2), constituting the first measurement of the alignment between gas distribution and the cosmic web through the kSZ effect. As it is a linear probe of the local gas density, the kSZ has heightened sensitivity to the warm-hot intergalactic medium (WHIM), which is believed to house the majority of the "missing baryons."Mapping out the gas density at low redshifts, as enabled by our measurements, is crucial for weak lensing surveys, for which the impact of baryons on small scales is a major impediment. We compare the anisotropic signal against two hydrodynamical simulations, TNG300-1 and Illustris, which have very different baryonic feedback prescriptions. We find that the anisotropic signal measured in the data is comparable but slightly larger and more extended compared with the simulations. Further, this suggests that there is excess accretion and feedback taking place through the filaments, hinting at the possible presence of spin-filament alignment of the BGS objects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Dark Energy Survey Year 3 results: Simulation-based cosmological inference with wavelet harmonics, scattering transforms, and moments of weak lensing mass maps. II. cosmological results

Here, we present a simulation-based cosmological analysis using a combination of Gaussian and non-Gaussian statistics of the weak lensing mass (convergence) maps from the first three years of the Dark Energy Survey. We implement the following: (1) second and third moments; (2) wavelet phase harmonics; (3) the scattering transform. Our analysis is fully based on simulations, spans a space of seven 𝑤 Cold Dark Matter (𝑤⁢ CDM) cosmological parameters, and forward models the most relevant sources of systematics inherent in the data: masks, noise variations, clustering of the sources, intrinsic alignments, and shear and redshift calibration. We implement a neural network compression of the summary statistics, and we estimate the parameter posteriors using a simulation-based inference approach. Including and combining different non-Gaussian statistics is a powerful tool that strongly improves constraints over Gaussian statistics (in our case, the second moments); in particular, the figure of merit (𝑆 8 , Ω m ) is improved by 70% (Λ ⁢CDM) and 90% (𝑤 ⁢CDM). When all the summary statistics are combined, we achieve a 2% constraint on the amplitude of fluctuations parameter 𝑆 8 ≡ 𝜎 8 ⁢(Ω m /0.3) 0.5 , obtaining 𝑆 8 = 0.794 ±0.017 (Λ⁢ CDM) and 𝑆 8 = 0.817 ±0.021 (𝑤 ⁢CDM), and a ∼10% constraint on Ω m , obtaining Ω m =0.259 ±0.025 (Λ ⁢CDM) and Ω m = 0.273 ±0.029 (𝑤⁢ CDM). In the context of the 𝑤⁢ CDM scenario, these statistics also strengthen the constraints on the parameter 𝑤, obtaining 𝑤 <−0.72. The constraints from different statistics are shown to be internally consistent (with a 𝑝-value>0.1 for all combinations of statistics examined). We compare our results to other weak lensing results from the first three years of the Dark Energy Survey data, finding good consistency; we also compare with results from external datasets, such as planck constraints from the cosmic microwave background, finding statistical agreement, with discrepancies no greater than <2.2⁢𝜎.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Interplay of Nanoscale Strain and Smectic Susceptibility in Kagome Superconductors

Exotic quantum solids can host electronic states that spontaneously break rotational symmetry of the electronic structure, such as electronic nematic phases and unidirectional charge density waves (CDWs). When electrons couple to the lattice, uniaxial strain can be used to anchor and control this electronic directionality. Here, we reveal an unusual impact of strain on unidirectional “smectic” CDW orders in kagome superconductors AV 3⁢ Sb 5 using spectroscopic-imaging scanning tunneling microscopy. We discover local decoupling between the smectic electronic director axis and the direction of anisotropic strain. While the two can generally be aligned along the same direction in regions of a small CDW gap, the tendency for alignment decreases in regions where the CDW gap is the largest. This feature, in turn, suggests nanoscale variations in smectic susceptibility, which we attribute to a combination of local strain and electron correlation strength. Overall, we observe an unusually high decoupling rate between the smectic electronic director of the three-state Potts order and anisotropic strain, revealing weak smectoelastic coupling in the CDW phase of kagome superconductors. This finding is phenomenologically different from the extensively studied nematoelastic coupling in the Ising nematic phase of Ising nematic phase of Fe-based superconductor bulk single crystals, providing a contrasting picture of how strain can control electronic unidirectionality in different families of quantum materials.

Wang, Yidi [Boston College, Chestnut Hill, MA (Uni↗
DOE OSTI2025

Polarization of the 𝜙 meson in the hadronic phase with nucleon scatterings and a viscous hydrodynamic background

We extend our previous work on the spin alignment of the ϕ vector meson in the hadronic phase of the quark gluon plasma, by including effects of nucleon scatterings. The emission rates are calculated in a realistic hydrodynamic background simulated with the code FLUIDuM , for different beam energies. We find that all the effects taken into account cannot explain the out-of-plane spin alignment of the ϕ meson observed experimentally.

Polarization phenomena↗
DOE OSTI2024

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Techno-Economic Analysis for the Addition of a Thermal Energy Storage System to a Central Plant

Increasing energy demand and rising peak loads present significant challenges for energy management in commercial and institutional settings. As climate change drives greater cooling needs, central plants must navigate the complex tradeoffs between operational efficiency, cost control, and grid stability. Thermal energy storage (TES) systems offer a viable solution by shifting energy consumption from peak to off-peak periods, thereby reducing peak demand, lowering utility expenses, and improving grid resilience. However, the success of TES implementation hinges on appropriate system sizing, effective control strategies, and alignment with local utility rate structures. This article presents a techno-economic analysis of integrating a chilled water TES system into the central plant at California State University, Dominguez Hills. Drawing on historical load profiles and utility tariffs, we assess three TES sizing approaches and their corresponding control strategies from both energy and economic perspectives. This article utilizes a model-based approach to assess the impact of TES sizing and control strategies on the techno-economic feasibility of integrating TES into an existing central plant. The models employed for this analysis were calibrated using 4 years of historical data. Here, the results demonstrated that utility tariffs and the campus's operational profiles dictate the most feasible sizing and control methods. The findings offer valuable insights for institutions and commercial building managers exploring sustainable energy solutions. By demonstrating how optimized TES strategies can improve operational efficiency while achieving financial savings, this study highlights the potential for TES to align performance with cost effectiveness in real-world applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Rapid Commissioning of Large Machine Tools Using Finite Element-Based Correction of Geometric Errors

Large computer numerical control (CNC) machine tools derive their stiffness from monolithic cast iron bases or weldments that are sometimes integral to machine motion systems like box ways or guideways. However, the sheer size of castings and even floor flatness deviations result in dimensional errors in these systems, which manifest as machine motion errors. Typical geometric alignment processes rely on an iterative approach, where measurements are taken to assess alignment (straightness, squareness, and parallelism), followed by adjustment of the machine supports (fixators or leveling pads), which can take weeks even for an experienced operator. Conversely, a novel method is proposed to shorten the correction time by eliminating the trial-and-error process in favor of a more deterministic approach guided by a finite element (FE) method. A feasibility study is conducted on a CNC polymer hybrid machine, with a steel weldment frame, supported by six leveling pads. An FE model of the frame is utilized to obtain recommended leveling pad adjustments, based on measurement of machine errors taken using a laser tracker. After a single adjustment cycle, measurements reveal that geometric errors of the machine tool are reduced from 2.22 mm of flatness deviation to 0.32 mm, achieving an 85.6% reduction. Furthermore, the entire process including measurement, adjustment, and assessment is completed in just 6 h by two operators who are not professional service engineers. In conclusion, this methodology demonstrates feasibility for scaling up, especially to large, high-precision CNC machine tools with bases mounted by fixators, offering the capability for bidirectional adjustment.

42 ENGINEERING↗
DOE OSTI2026

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages

Bacteriophage auxiliary metabolic genes (AMGs) alter host metabolism by hijacking reactions, but previous studies mostly inferred their roles from annotations, ignoring system-wide impacts and phage production. Here we integrate AMGs and phage assembly into a genome-scale metabolic model of Prochloroccocus marinus MED4 infected by P-HM2. We show that 17 directly hijacked reactions substantially affect more than 30% of the reactions in MED4 metabolism, including carbon fixation, photosynthesis, and nucleotide synthesis, distinguishing these AMGs as either phage aligned—shifting feasible reaction velocities in accordance with maximal phage production—or phage antialigned. Pareto optimization reveals that phage-aligned reactions alter phage-host growth trade-offs, while phage-antialigned reactions do not. We experimentally validate our predictions of system-level AMG impacts by measuring the N-dependent effect of P-HM2 cp12 expression on growth in a model relative of the genetically intractable MED4, Synechococcus elongatus. We also show that AMGs’ indirect impacts are synergistically and antagonistically coupled, providing systems-level insight into AMG perturbations and highlighting how nontrivial cascading effects shape host metabolism.

Rozum, Jordan C. [Pacific Northwest National Labor↗
DOE OSTI2025

Elastic Bayesian Model Calibration

Functional data are ubiquitous in scientific modeling. For instance, quantities of interest are modeled as functions of time, space, energy, density, etc. Uncertainty quantification methods for computer models with functional response have resulted in tools for emulation, sensitivity analysis, and calibration that are widely used. However, many of these tools do not perform well when the computer model’s parameters control both the amplitude variation of the functional output and its alignment (or phase variation). This paper introduces a framework for Bayesian model calibration when the model responses are misaligned functional data. The approach generates two types of data out of the misaligned functional responses: (1) aligned functions so that the amplitude variation is isolated and (2) warping functions that isolate the phase variation. These two types of data are created for the computer simulation data (both of which may be emulated) and the experimental data. The calibration approach uses both types so that it seeks to match both the amplitude and phase of the experimental data. The framework is careful to respect constraints that arise, especially when modeling phase variation, and is framed in a way that it can be done with readily available calibration software. In conclusion, we demonstrate the techniques on two simulated data examples and on two dynamic material science problems: a strength model calibration using flyer plate experiments and an equation of state model calibration using experiments performed on the Sandia National Laboratories’ Z-machine.

97 MATHEMATICS AND COMPUTING↗