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DOE OSTI2024

Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis

Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue ‘The evolution of plant metabolism’.

Life Sciences & Biomedicine - Other Topics↗

DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗

DOE OSTI2026

Small-𝑥 Factorization in the Target Fragmentation Region

We consider the differential cross-section for single-inclusive jet production with transverse momentum 𝑃 ⊥ in deep inelastic scattering at small Bjorken 𝑥 Bj , mediated by a virtual photon with virtuality 𝑄 2 . Unlike most studies at small 𝑥, which focus on particle production in the current fragmentation region, we investigate the kinematic regime where the jet is produced in the target fragmentation hemisphere of the Breit frame, and with 𝑃 ⊥ ≪ 𝑄. For a longitudinally polarized photon, we demonstrate that this cross section is not power suppressed in 𝑃 ⊥ /𝑄 and we derive a factorized expression in terms of extended quark and gluon jet fracture functions. Our formula, valid at next-to-leading order in 𝛼 𝑠 at small 𝑥, is akin to the Altarelli-Martinelli identity for the longitudinal DIS structure function. Numerical estimates show that the extended quark jet fracture function is the most sensitive to saturation effects in large nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Factorization and Resummation for the Near-Side Energy-Energy Correlators

By utilizing the dihadron fragmentation formalism, we extend the previous factorization of near-side energy-energy correlators (EECs) in the collinear limit and derive an all order resummation in the Fourier transform 𝑏 𝑇 -space. A perfect matching is obtained when we compare to the fixed-order results. We further demonstrate the resummation effects for the EECs in 𝑒 + ⁢𝑒 − annihilation and show that they will significantly improve the theoretical predictions at small angles.

Guo, Yuxun [University of California, Berkeley, CA↗

DOE OSTI2025

Factorization and resummation of QED radiative corrections for neutron beta decay

Details of the two-loop analysis of long-distance QED radiative corrections to neutron beta decay are presented. Explicit expressions are given for hard, jet, and soft functions appearing in the factorization formula that describes the limit of small electron mass and large electron energy. Numerical enhancements from the infrared region are resummed using renormalization group methods. Power corrections, cancellation of singularities in the small-mass expansion, renormalization scheme dependence, and bound-state effects are also discussed. These results provide the most precise determination of long-distance radiative corrections to neutron beta decay and impact the determination of |𝑉 𝑢⁢𝑑 | from the measured neutron lifetime and thus set a target for uncertainty reductions in the experimental and short-distance inputs.

Beta decay↗

DOE OSTI2025

Nernst power factor and figure of merit in the compensated semimetal ScSb

Recently, topological semimetals have emerged as strong candidates for solid-state thermomagnetic refrigerators due to their enhanced Nernst effect. This enhancement arises from the combined contributions of the Berry-curvature-induced anomalous Nernst coefficient associated with topological bands and the normal Nernst effect resulting from synergistic electron-hole compensation. Generally, these two effects are intertwined in topological semimetals, making it challenging to evaluate them independently. Here, we report the observation of a high Nernst effect in the electron-hole compensated semimetal ScSb with topologically trivial electronic band structures. Remarkably, we find a high maximum Nernst power factor of 𝑃⁢𝐹 𝑁 ∼ 35 × 10 −4 W m −1 K −2 in ScSb. The Nernst thermopower (𝑆 𝑥⁢𝑦 ) exhibits a peak of ∼ 47 µ⁢V/K at 12 K and 14 T, yielding a Nernst figure of merit (𝑧 𝑁 ) of ∼ 28 × 10 −4 K −1 . Notably, despite its trivial electronic band structure, both the 𝑃⁢𝐹 𝑁 and 𝑧 𝑁 values of ScSb are comparable to those observed in topological semimetals with Dirac band dispersions. In conclusion, the origin of the large Nernst signal in ScSb is explained by compensated electron and hole carriers, through Hall resistivity measurements, angle-resolved photoemission spectroscopy, and density functional theory calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Nucleon axial-vector form factor and radius from radiatively corrected antineutrino scattering data

The nucleon axial-vector form factor, 𝐺 𝐴 , is critical to determine the electroweak interactions of leptons with nucleons. Important examples of processes influenced by 𝐺 𝐴 are elastic (anti)neutrino-nucleon scattering and muon capture by the proton. Sparse experimental data results in a large uncertainty on the momentum dependence of 𝐺 𝐴 and has motivated the consideration of new experimental probes and first-principles lattice quantum chromodynamics (QCD) evaluations. The comparison of new and precise theoretical predictions for 𝐺 𝐴 with future experimental data necessitates the application of radiative corrections to experimentally observable processes. We apply these corrections in the extraction of 𝐺 𝐴 and the associated axial-vector radius from the recent MINERvA antineutrino-hydrogen data, compare the effects from radiative corrections to other uncertainties in neutrino scattering experiments, and discuss the comparison of lattice QCD evaluations to experimental measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Niobium coaxial cavities with internal quality factors exceeding 1.4 × 10 9 for circuit quantum electrodynamics

Group-V materials such as niobium and tantalum have become popular choices for extending the performance of circuit quantum electrodynamics (cQED) platforms, allowing for quantum processors and memories with reduced error rates and more modes. The complex surface chemistry of niobium, however, makes identifying the main modes of decoherence difficult at millikelvin temperatures and single-photon powers. We use niobium coaxial quarter-wave cavities to study the impact of etch chemistry, prolonged atmospheric exposure, and the significance of cavity conditions prior to and during cooldown—in particular, niobium hydride evolution—on single-photon coherence. We demonstrate cavities with quality factors Q int ≳ 1.4 × 10 9 in the single-photon regime, a 15-fold improvement over aluminum cavities of the same geometry. We rigorously quantify the sensitivity of our fabrication process to various loss mechanisms and demonstrate a two- to fourfold reduction in the two-level system loss tangent and a three- to fivefold improvement in the residual resistance over traditional buffered chemical polishing etching techniques. Finally, we demonstrate transmon integration and coherent cavity control while maintaining a cavity coherence of 11.3 ms. The accessibility of our method, which can be easily replicated in academic laboratory settings, together with the demonstration of its performance, mark an advancement in three-dimensional cQED.

Oriani, Andrew E. [Chicago U., EFI; Chicago U.] (O↗

DOE OSTI2024

Absorptive corrections to the electromagnetic form factor in high-energy elastic proton-proton scattering

Recently, it was noted that absorptive corrections to the electromagnetic form factor in high-energy proton-proton scattering are important for the theoretical interpretation of the p ↑ p and p ↑ A analyzing power A N ( t ) measurements with the Hydrogen Jet Target polarimeter (HJET) at RHIC. Here, a concise expression for the absorptive correction was derived within the eikonal approach. The resulting analysis reveals a systematic bias, nearly independent of the beam energy, in the experimental determination of the real-to-imaginary ratio ρ when absorption effects are overlooked in the data analysis. Quantification of this bias, as ρ meas = ρ + ( 0.036 ± 0.016 ) bias , was achieved using a Regge fit applied to available proton-proton measurements of ρ meas ( s ) and σ tot meas ( s ) . Considering the potential impact of such an effect on the experimentally determined A N ( t ) , one may enhance consistency between the HJET and STAR measurements of the hadronic spin-flip amplitude. While the sign of the bias in the value of ρ aligns with the anticipated effective increase in the proton charge radius in p p scattering due to absorption, it amplifies the observed discrepancy between σ tot meas and ρ meas values at s = 13 TeV as measured in the TOTEM experiment. Evaluation (using published TOTEM data) of the measured proton-proton d σ / d t dependence on the absorptive corrections indicated that possible soft photon corrections to the hadronic amplitude slope may be essential for such data analysis. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Jet Definition and Transverse-Momentum–Dependent Factorization in Semi-inclusive Deep-Inelastic Scattering

Using the color dipole picture of deep inelastic scattering (DIS) and the color glass condensate effective theory, we study semi-inclusive jet production in DIS at small x in the limit where the photon virtuality Q 2 is much larger than the transverse momentum squared P$^{2}_{⊥}$ of the produced jet. In this limit, the cross section is dominated by aligned jet configurations, that is, quark–antiquark pairs in which one of the fermions—the would-be struck quark in the Breit frame—carries most of the longitudinal momentum of the virtual photon. We show that physically meaningful jet definitions in DIS are such that the effective axis of the jet sourced by the struck quark is controlled by its virtuality rather than by its transverse momentum. For such jet definitions, we show that the next-to-leading order cross section admits factorization in terms of the (sea) quark transverse momentum dependent distribution, which in turn satisfies a universal Dokshitzer-Gribov-Lipatov-Altarelli-Parisi and Sudakov evolution.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Pion and kaon PDFs from lattice QCD via large momentum effective theory and short-distance factorization

In this paper, we present a first-principles lattice-QCD calculation of the unpolarized quark PDF for the pion and the kaon. The lattice data rely on matrix elements calculated for boosted mesons coupled to non-local operators containing a Wilson line. The calculations on this lattice ensemble correspond to two degenerate light, a strange, and a charm quark (𝑁 𝑓 = 2 + 1 + 1), using maximally twisted mass fermions with a clover term. The lattice volume is 32 3 × 64, with a lattice spacing of 0.0934 fm, and a pion mass of 260 MeV. Matrix elements are calculated for hadron boosts of |𝑃 3 | = 0, 0.41, 0.83, 1.25, 1.66, and 2.07 GeV. To match lattice QCD results to their light-cone counterparts, we employ two complementary frameworks: the large-momentum effective theory (LaMET) and the short-distance factorization (SDF). Using these approaches in parallel, we also test the lattice data to identify methodology-driven systematics. Results are presented for the standard quark PDFs, as well as the valence sector. Beyond obtaining the PDFs, we also explore the possibility of extracting information on SU(3) flavor-symmetry-breaking effects. For LaMET, we also parametrize the momentum dependence to obtain the infinite-momentum PDFs. Since the present calculation is performed on a single ensemble at a pion mass of 260 MeV and fixed lattice spacing, the uncertainties reported are statistical only, and systematic uncertainties remain to be addressed in future multi-ensemble studies.

Miller, Joshua [Temple University, Philadelphia, P↗

DOE OSTI2024

Impact of Reordering on the LU Factorization Performance of Bordered Block-Diagonal Sparse Matrix

Power engineers rely on computer-based simulation tools to assess grid performance and ensure security. At the core of these tools are solvers for sparse linear equations. When transformed into a bordered block-diagonal (BBD) structure, part of the sparse linear equation solving can be parallelized. This work focuses on using the Schur-complement-based method for LU factorization on BBD matrices, specifically, Jacobian matrices from large-scale systems. Our findings show that the natural ordering method outperforms the default ordering method in computational performance for each block of the BBD matrix. This observation is validated using synthetic 25k-bus and 70k-bus cases, showing a speedup of up to 38% when using natural ordering without permutation. Additionally, the impact of the number of partitions is studied, and the result shows that computational performance improves with more, smaller partitions in the BBD matrices.

BBD matrix↗

DOE OSTI2024

Automatic Loss Factor Modeling and Attribution on Unlabeled PV Energy Data

We present a novel approach for modeling the loss factors of photovoltaic power generation systems (PV systems). This method is a white-box machine learning model built on convex optimization that is fast, interpretable, and auditable. It takes as an input the measured daily energy produced by the system, over a multi-year period, and returns a multiplicative decomposition model of the daily energy signal and full attribution of the total energy loss to each feature. The methods section of this paper has two major components: (1) the description of the signal decomposition (SD) model, expressed in the SD framework, and (2) the attribution of total energy losses via Shapley values. We validate the method on synthetic and open-source data sets and compare to similar methods from the literature.

artificial intelligence↗

DOE OSTI2025

A Two-Stage Approach for PV Inverter Engagement in Power Factor Correction and Voltage Regulation

The rapid integration of distributed energy resources, like solar photovoltaics (PVs), can lead to overvolt-age challenges due to reverse power flow and a noticeable decrease in power factor at the substation interface. While existing literature extensively explores utilizing smart inverter capabilities for reactive power flexibility using a volt-var curve (VVC), obtaining time-varying operating points of such curves in real-time is challenging due to computational demands and communication requirements. Similarly, employing optimization-based approaches for reactive power control and active voltage regulation in large-scale distribution feeders is difficult due to the complexity of the problem and the challenges in effectively engaging customer-owned resources. This paper proposes a two-stage strategy to harness smart inverters for reactive power support. The first stage formulates short-term planning by optimally designing VVCs (on a daily or hourly basis) for large-scale solar PVs based on projected system needs and communicating optimal curves to smart inverters in advance. Subsequently, the second stage employs a transactive-based method to involve customer-owned PVs for reactive power support, effectively enhancing overall system performance and addressing real-time demands. In conclusion, the efficacy of this approach will be demonstrated using real-world distribution circuits provided by Vermont Electric Power Company (VELCO) and Vermont Electric Cooperative (VEC).

Poudel, Shiva [Pacific Northwest National Laborato↗

DOE OSTI2024

Algorithms for Non-Negative Matrix Factorization on Noisy Data With Negative Values

Non-negative matrix factorization (NMF) is a dimensionality reduction technique that has shown promise for analyzing noisy data, especially astronomical data. For these datasets, the observed data may contain negative values due to noise even when the true underlying physical signal is strictly positive. Prior NMF work has not treated negative data in a statistically consistent manner, which becomes problematic for low signal-to-noise data with many negative values. In this paper we present two algorithms, Shift-NMF and Nearly-NMF, that can handle both the noisiness of the input data and also any introduced negativity. Both of these algorithms use the negative data space without clipping or masking and recover non-negative signals without any introduced positive offset that occurs when clipping or masking negative data. We demonstrate this numerically on both simple and more realistic examples, and prove that both algorithms have monotonically decreasing update rules.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Apple Bitter Rot: Biology, Ecology, Omics, Virulence Factors, and Management of Causal Colletotrichum Species

ABSTRACT Apple bitter rot is caused by various Colletotrichum spp. that threaten apple production globally resulting in millions of dollars in damage annually. The fungus causes a decline in fruit quality and yield, eventually rotting the fruit and rendering it inedible. The pathogen is difficult to keep out of orchards because of its broad host range and transmissibility by rain splash and insects. Once the disease manifests, pathogen identification is difficult due to evolving taxonomy and similar morphology between species. Current management strategies are threatened by an increase in fungicide resistance and regulations on many multisite fungicides, leading to a pressing need for new management options for control. This review aims to summarise the most current knowledge regarding the biology, virulence factors, ecology, omics and emerging management strategies for Colletotrichum species that cause apple bitter rot. Taxonomy Colletotrichum species—Domain Eukaryota, Kingdom Fungi, Phylum Ascomycota, Class Sordariomycetes, Order Glomerellales, Family Glomerellaceae, Genus Colletotrichum . Biology Hemibiotrophic pathogen with a wide host range that establishes a biotrophic interaction where it penetrates host plants using appressoria followed by a switch to necrotrophy causing rot symptoms. Toxins Cercosporin, colletotrichins, colletotric acid, ferricrocin. Host Range The host range varies by species but largely occurs on dicotyledonous plants and is less prevalent on monocots as well as gymnosperms, ferns, mosses and animals (e.g., insects). Disease Symptoms Symptoms often manifest as flat to sunken necrotic areas on fruit. Lesions on leaves and fruit can have concentric rings with abundant pathogen sporulation. Disease Control Colletotrichum spp. are primarily managed by single‐site quinone outside inhibitor (Qol), methyl benzimidazole carbamate (MBC), demethylation inhibitor (DMI) fungicides, and multisite dithiocarbamate and phthalimide fungicides. Susceptibility may vary with species, strain specificity, or geographic region. Other management options include clean stock production, cultural practices, resistance breeding, and biological control through the introduction of protective or competing microorganisms.

Boeckman, Nathanial J. [Plant Pathology Laboratory↗