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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 OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗
DOE OSTI2020

A Group of O-Acetyltransferases Catalyze Xyloglucan Backbone Acetylation and Can Alter Xyloglucan Xylosylation Pattern and Plant Growth When Expressed in Arabidopsis

Abstract Xyloglucan is a major hemicellulose in plant cell walls and exists in two distinct types, XXXG and XXGG. While the XXXG-type xyloglucan from dicot species only contains O-acetyl groups on side-chain galactose (Gal) residues, the XXGG-type xyloglucan from Poaceae (grasses) and Solanaceae bears O-acetyl groups on backbone glucosyl (Glc) residues. Although O-acetyltransferases responsible for xyloglucan Gal acetylation have been characterized, the biochemical mechanism underlying xyloglucan backbone acetylation remains to be elucidated. In this study, we showed that recombinant proteins of a group of DUF231 members from rice and tomato were capable of transferring acetyl groups onto O-6 of Glc residues in cello-oligomer acceptors, indicating that they are xyloglucan backbone 6-O-acetyltransferases (XyBATs). We further demonstrated that XyBAT-acetylated cellohexaose oligomers could be readily xylosylated by AtXXT1 (Arabidopsis xyloglucan xylosyltransferase 1) to generate acetylated, xylosylated cello-oligomers, whereas AtXXT1-xylosylated cellohexaose oligomers were much less effectively acetylated by XyBATs. Heterologous expression of a rice XyBAT in Arabidopsis led to a severe reduction in cell expansion and plant growth and a drastic alteration in xyloglucan xylosylation pattern with the formation of acetylated XXGG-type units, including XGG, XGGG, XXGG, XXGG,XXGGG and XXGGG (G denotes acetylated Glc). In addition, recombinant proteins of two Arabidopsis XyBAT homologs also exhibited O-acetyltransferase activity toward cellohexaose, suggesting their possible role in mediating xyloglucan backbone acetylation in vivo. Our findings provide new insights into the biochemical mechanism underlying xyloglucan backbone acetylation and indicate the importance of maintaining the regular xyloglucan xylosylation pattern in cell wall function.

Cell Biology↗
DOE OSTI2022

Tonoplast Sucrose Trafficking Modulates Starch Utilization and Water Deficit Behavior in Poplar Leaves

Leaf osmotic adjustment by the active accrual of compatible organic solutes (e.g. sucrose) contributes to drought tolerance throughout the plant kingdom. In Populus tremula x alba, PtaSUT4 encodes a tonoplast sucrose–proton symporter, whose downregulation by chronic mild drought or transgenic manipulation is known to increase leaf sucrose and turgor. While this may constitute a single drought tolerance mechanism, we now report that other adjustments which can occur during a worsening water deficit are damped when PtaSUT4 is constitutively downregulated. Specifically, we report that starch use and leaf relative water content (RWC) dynamics were compromised when plants with constitutively downregulated PtaSUT4 were subjected to a water deficit. Leaf RWC decreased more in wild-type and vector control lines than in transgenic PtaSUT4-RNAi (RNA-interference) or CRISPR (clustered regularly interspersed short palindromic repeats) knockout (KO) lines. The control line RWC decrease was accompanied by increased PtaSUT4 transcript levels and a mobilization of sucrose from the mesophyll-enriched leaf lamina into the midvein. The findings suggest that changes in SUT4 expression can increase turgor or decrease RWC as different tolerance mechanisms to reduced water availability. Evidence is presented that PtaSUT4-mediated sucrose partitioning between the vacuole and the cytosol is important not only for overall sucrose abundance and turgor, but also for reactive oxygen species (ROS) and antioxidant dynamics. Interestingly, the reduced capacity for accelerated starch breakdown under worsening water-deficit conditions was correlated with reduced ROS in the RNAi and KO lines. A role for PtaSUT4 in the orchestration of ROS, antioxidant, starch utilization and RWC dynamics during water stress and its importance in trees especially, with their high hydraulic resistances, is considered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID ( http://isolate.fusariumdb.org/blast.php ) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

Plant Sciences↗
DOE OSTI2022

Sparsifying priors for Bayesian uncertainty quantification in model discovery

We propose a probabilistic model discovery method for identifying ordinary differential equations governing the dynamics of observed multivariate data. Our method is based on the sparse identification of nonlinear dynamics (SINDy) framework, where models are expressed as sparse linear combinations of pre-specified candidate functions. Promoting parsimony through sparsity leads to interpretable models that generalize to unknown data. Instead of targeting point estimates of the SINDy coefficients, we estimate these coefficients via sparse Bayesian inference. The resulting method, uncertainty quantification SINDy (UQ-SINDy), quantifies not only the uncertainty in the values of the SINDy coefficients due to observation errors and limited data, but also the probability of inclusion of each candidate function in the linear combination. UQ-SINDy promotes robustness against observation noise and limited data, interpretability (in terms of model selection and inclusion probabilities) and generalization capacity for out-of-sample forecast. Sparse inference for UQ-SINDy employs Markov chain Monte Carlo, and we explore two sparsifying priors: the spike and slab prior, and the regularized horseshoe prior. UQ-SINDy is shown to discover accurate models in the presence of noise and with orders-of-magnitude less data than current model discovery methods, thus providing a transformative method for real-world applications which have limited data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Kinematics and dynamics of disclination lines in three-dimensional nematics

An exact kinematic law for the motion of disclination lines in nematic liquid crystals as a function of the tensor order parameter Q is derived. Unlike other order parameter fields that become singular at their respective defect cores, the tensor order parameter remains regular. Following earlier experimental and theoretical work, the disclination core is defined to be the line where the uniaxial and biaxial order parameters are equal, or equivalently, where the two largest eigenvalues of Q cross. This allows an exact expression relating the velocity of the line to spatial and temporal derivatives of Q on the line, to be specified by a dynamical model for the evolution of the nematic. By introducing a linear core approximation for Q, analytical results are given for several prototypical configurations, including line interactions and motion, loop annihilation, and the response to external fields and shear flows. Behaviour that follows from topological constraints or defect geometry is highlighted. Finally, the analytic results are shown to be in agreement with three-dimensional numerical calculations based on a singular Maier–Saupe free energy that allows for anisotropic elasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Precise mapping of new group I introns in tRNA genes

Bacterial tRNA have been found interrupted at various positions in the anticodon loop by group I introns, in four types. The primary bioinformatic tool for group I intron discovery is a covariance model that can identify conserved features in the catalytic core and can sometimes identify the typical uridine residue at the -1 position, preceding the 5-prime splice site, but cannot identify the typical guanidine residue at the omega position, preceding the 3-prime splice site, to achieve precise mapping. One approach to complete the automation of group I intron mapping is to focus instead on the exons, which is enabled by the regularity of tRNAs. We develop a software module, within a larger package (tFind) aimed at mapping bacterial tRNA and tmRNA genes precisely, that expands this list of four known classes of intron-interrupted tRNAs to 21 cases. A new covariance model for these introns is presented. The wobble base pair formed by the -1 uridine is considered a determinant of the 5-prime splice site, yet one reasonably large new type bears a cytidine nucleotide at that position.

Williams, Kelly P.↗
DOE OSTI2025

Second-order renormalized Hamiltonian of Yukawa theory

Using the renormalization group procedure for effective particles we calculate the effective Hamiltonians in the theory of a fermion field coupled to a scalar field via the Yukawa interaction. The theory is renormalized by the addition of counterterms. Necessary counterterms are determined by computing matrix elements of the effective Hamiltonian. All calculations are performed up to the second order in the expansion in powers of the coupling constant. Renormalized effective Hamiltonians are well-defined symmetric forms acting in the Fock space as opposed to the renormalized bare Hamiltonian, which is not well defined without regularization. We introduce computational techniques that should streamline higher-order calculations and may be of independent interest.

Ab initio calculations↗
DOE OSTI2026

Quantum critical collapse abhors a naked singularity

Classical critical collapse yields naked singularities from smooth initial data, challenging cosmic censorship, and shaping the spectrum of primordial black holes. We show that one-loop vacuum polarization near the threshold qualitatively changes this outcome by dressing the singularity with a horizon within a controlled semiclassical regime. In analytically tractable Einstein-scalar critical spacetimes, a one-loop $s$-wave treatment linearized around self-similar backgrounds shows that regularity uniquely selects an asymptotically Minkowskian, vacuum-polarization state. Its renormalized stress tensor carries a universal quantum growing mode that competes with the classical unstable mode, shifts the critical point, and generates a trapped surface along with a finite mass gap at the new threshold, thereby enforcing horizon formation even under arbitrary fine-tuning. In primordial collapse, the threshold shift enters exponentially into the formation fraction, while the mass gap truncates the low-mass tail, suggesting potentially important consequences for the predicted mass spectrum. Furthermore, these results provide a self-consistent semiclassical treatment of critical collapse and yield sharp predictions within the one-loop, near-critical, linearized regime.

Anomalies↗
DOE OSTI2026

Quantum Ising model on (2+1)-dimensional anti–de Sitter space using tensor networks

We study the quantum Ising model on (2+1)-dimensional anti-de Sitter space using matrix product states (MPS) and matrix product operators (MPOs). We explore the bulk phase diagram of the theory on regular tessellations of hyperbolic space with coordination number seven and find disordered and ordered phases separated by a phase transition. We find that the boundary-boundary spin correlation function exhibits power law scaling deep in the disordered phase of the Ising model consistent with holography. At the critical point, we find the boundary entanglement entropy scales logarithmically with subsystem size but away from this, we see a linear scaling. In comparison, the full system exhibits a volume law scaling, which is expected in chaotic and/or highly connected systems. We also measure out of time ordered correlators (OTOCs) to explore the scrambling behavior of the theory.

Quantum spin models↗
DOE OSTI2025

Beyond fragmented dopant dynamics in quantum spin lattices: Robust localization and non-Gaussian diffusion

The motion of dopants in magnetic spin lattices has received tremendous attention for at least four decades due to its connection to high-temperature superconductivity. Despite these efforts, we lack a complete understanding of their behavior, especially out of the equilibrium and at nonzero temperatures. In this paper, we take a significant step towards a much deeper understanding based on state-of-the-art matrix-product-state calculations. In particular, we investigate the nonequilibrium dynamics of a dopant in two-leg 𝑡−𝐽 ladders with antiferromagnetic XXZ spin interactions. In the Ising limit, we find that the dopant is localized for all investigated nonzero temperatures due to an emergent disordered potential, with a localization length controlled by the underlying correlation length of the spin lattice, which increases exponentially with decreasing temperature. The dopant, hereby, only delocalizes asymptotically in the zero temperature limit. This greatly generalizes the localization effect discovered recently in Hilbert space fragmented models [Phys. Rev. Res. 6, 023325 (2024), SciPost Phys. Core 7, 054 (2024)]. In the presence of spin-exchange processes at rate 𝛼, the dopant diffuses with a diffusion coefficient, 𝐷 ℎ , depending nonmonotonically on 𝛼. It initially increases linearly as 𝐷 ℎ ∝ 𝛼 for 𝛼 ≪ 1 before dropping off as 𝛼 −1 for 𝛼 > 1. Moreover, we show that the underlying spin dynamics at infinite temperature behaves qualitatively the same, albeit with important quantitative differences. We substantiate these findings by showing that the dynamics features self-similar scaling behavior, which strongly deviates from the Gaussian behavior of regular diffusion, especially for weak spin exchange. Finally, we show that the diffusion coefficient 𝐷 ℎ follows an Arrhenius relation at high temperatures, whereby it is exponentially suppressed upon cooling.

Anomalous diffusion↗
DOE OSTI2025

Kinematic Flow and the Emergence of Time

Perhaps the most basic question we can ask about cosmological correlations is how their strength changes as we smoothly vary kinematic parameters. The answer is encoded in differential equations that govern this evolution in kinematic space. In this Letter, we introduce a new perspective on these differential equations. We show that, in the simplified setting of conformally coupled scalars in power-law Friedmann-Robertson-Walker spacetimes, the equations for arbitrary tree-level processes can be obtained from a small number of simple combinatorial rules. While this “kinematic flow” is defined purely in terms of boundary data, it reflects the physics of bulk time evolution. The unexpected regularity of the equations suggests the existence of an autonomously defined mathematical structure from which cosmological correlations and the time evolution of the associated spacetime emerge.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Flavor diagonal nucleon charges using clover fermions on MILC HISQ ensembles

We present lattice results for the flavor diagonal charges of the proton from the analysis of eight ensembles generated using 2+1+1-flavors of highly improved staggered quarks by the MILC Collaboration. The calculation includes all the needed connected and disconnected contributions to nucleon three-point function. For extracting matrix elements using fits to the spectral decomposition of these correlation functions, two strategies to remove excited state contributions are employed and compared. To renormalize these charges, the 2+1-flavor mixing matrix is calculated in the regularization independent symmetric momentum subtraction intermediate scheme on the lattice. The final results are presented in the $\overline{MS}$ scheme at scale 2 GeV. The axial charges for the proton are $𝑔$$^{𝑢}_{𝐴}$ = 0.781⁢(25), $𝑔$$^{𝑑}_{𝐴}$ =−0.440⁢(39), and $𝑔$$^{𝑠}_{𝐴}$ = −0.055⁢(9); the tensor charges are $𝑔$$^{𝑢}_{𝑇}$ = 0.782⁢(28), $𝑔$$^{𝑑}_{𝑇}$ = −0.195⁢(16), and $𝑔$$^{𝑠}_{𝑇}$ = −0.0016⁢(12); and the scalar charges are $𝑔$$^{𝑢}_{𝑆}$ = 9.39⁢(88), $𝑔$$^{𝑑}_{𝑆}$ = 8.84⁢(93), and $𝑔$$^{𝑠}_{𝑆}$ = 0.37⁢(14). Results for the neutron are given by the 𝑢 ↔ 𝑑 interchange. Results for the sigma terms are 𝜎 𝜋⁢𝑁 | standard = 42⁢(6) MeV from a “standard” analysis and 𝜎 𝜋⁢𝑁 | 𝑁⁢𝜋 = 61⁢(6) MeV from an “𝑁⁢𝜋” analysis that includes the contributions of multihadron 𝑁⁢𝜋 excited states as motivated by chiral perturbation theory. Our preferred value 𝜎 𝜋⁢𝑁 | 𝑁⁢𝜋 is consistent with the phenomenological extraction from 𝜋 −𝑁 scattering data. The strangeness content of the proton, for which the standard analysis is appropriate, is 𝜎 𝑠 | standard = 35⁢(13) MeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Correlated purification for restoring 𝑁-representability in quantum simulation

Experimentally measured reduced density matrices (RDMs) often violate constraints that ensure they represent N-electron states—known as N-representability conditions—because of statistical and hardware noise. In this work, we present a correlated purification framework based on semidefinite programming to restore the accuracy of a noisy, unphysical two-electron RDM (2-RDM). The method performs a bi-objective optimization that minimizes both the many-electron energy and the nuclear norm of the correction to the measured 2-RDM. The nuclear norm, often employed in matrix completion, promotes low-rank corrections, while the energy term acts as a regularization term that can improve the purity of the ground state. While the method is particularly effective for ground states, it can also be applied to excited and nonstationary states by decreasing the weight of the energy relative to the error norm. In an application to fermionic shadow tomography of large hydrogen chains, correlated purification yields substantial reductions in both energy and 2-RDM error, achieving chemical accuracy across dissociation curves. This framework provides a robust strategy for tomography in many-body quantum simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Coherence-Induced Deep Thermalization Transition in Random Permutation Quantum Dynamics

We report a phase transition in the projected ensemble—the collection of postmeasurement wave functions of a local subsystem obtained by measuring its complement. The transition emerges in systems undergoing random permutation dynamics, a type of quantum time evolution wherein computational basis states are shuffled without creating superpositions. It separates a phase exhibiting deep thermalization, where the projected ensemble is distributed over Hilbert space in a maximally entropic fashion (Haar random), from a phase where it is minimally entropic (“classical bit-string ensemble”). Crucially, this deep thermalization transition is invisible to the subsystem’s density matrix, which always exhibits thermalization to infinite temperature across the phase diagram. Through a combination of analytical arguments and numerical simulations, we show that the transition is tuned by the total amount of injected by the input state and the measurement basis, and is exhibited robustly across different microscopic models. Our findings represent a novel form of ergodicity-breaking universality in quantum many-body dynamics, characterized not by a failure of regular thermalization, but rather by a failure of deep thermalization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Lattice calculation of short-range contributions to neutrinoless double-beta decay 𝜋 − → 𝜋 + ⁢𝑒⁢𝑒 at physical pion mass

Neutrinoless double-beta (0⁢𝜈⁢𝛽⁢𝛽) decays provide an excellent probe for determining whether neutrinos are Dirac or Majorana fermions. The short-range matrix elements associated with the 𝜋 − → 𝜋 + ⁢𝑒⁢𝑒 process contribute at leading order in the 0⁢𝜈⁢𝛽⁢𝛽 decay channel 𝑛⁢𝑛 → 𝑝⁢𝑝⁢𝑒⁢𝑒 through pion exchange between nucleons. However, current lattice calculations show notable discrepancies in predicting these short-range contributions. To address this issue, we perform a lattice QCD calculation of the 𝜋 − → 𝜋 + ⁢𝑒⁢𝑒 matrix elements using domain wall fermion ensembles at the physical pion mass generated by the RBC/UKQCD Collaboration. To mitigate contamination from around-the-world effects, we develop a new method to reconstruct and subtract them directly from lattice data. We then perform nonperturbative renormalization in the regularization-independent symmetric momentum-subtraction scheme (RI/SMOM), using the (𝛾 𝜇 , 𝛾 𝜇 ) and ($\not{𝑞}$, $\not{𝑞}$) projectors. Compared with previous studies, this work reduces the uncertainties in the matrix elements and provides an independent cross-check that helps to reconcile the discrepancies among previous lattice calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗