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DOE OSTI2022

A DE1 BINDING FACTOR 1–GLABRA2 module regulates rhamnogalacturonan I biosynthesis in Arabidopsis seed coat mucilage

Abstract The mucilage surrounding hydrated Arabidopsis thaliana seeds is a specialized extracellular matrix composed mainly of the pectic polysaccharide rhamnogalacturonan I (RG-I). Although, several genes responsible for RG-I biosynthesis have been identified, the transcriptional regulatory mechanisms controlling RG-I production remain largely unknown. Here we report that the trihelix transcription factor DE1 BINDING FACTOR 1 (DF1) is a key regulator of mucilage RG-I biosynthesis. RG-I biosynthesis is significantly reduced in loss-of-function mutants of DF1. DF1 physically interacts with GLABRA2 (GL2) and both proteins transcriptionally regulate the expression of the RG-I biosynthesis genes MUCILAGE MODIFIED 4 (MUM4) and GALACTURONOSYLTRANSFERASE-LIKE5 (GATL5). Through chromatin immunoprecipitation-quantitative PCR and transcriptional activation assays, we uncover a cooperative mechanism of the DF1–GL2 module in activating MUM4 and GATL5 expression, in which DF1 binds to the promoters of MUM4 and GATL5 through interacting with GL2 and facilitates the transcriptional activity of GL2. The expression of DF1 and GL2 is directly regulated by TRANSPARENT TESTA GLABRA2 (TTG2) and, in turn, DF1 directly represses the expression of TTG2. Taken together, our data reveal that the transcriptional regulation of mucilage RG-I biosynthesis involves a regulatory module, comprising DF1, GL2, and TTG2.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize

Abstract Understanding gene regulatory networks is essential to elucidate developmental processes and environmental responses. Here, we studied regulation of a maize (Zea mays) transcription factor gene using designer transcription activator-like effectors (dTALes), which are synthetic Type III TALes of the bacterial genus Xanthomonas and serve as inducers of disease susceptibility gene transcription in host cells. The maize pathogen Xanthomonas vasicola pv. vasculorum was used to introduce 2 independent dTALes into maize cells to induced expression of the gene glossy3 (gl3), which encodes a MYB transcription factor involved in biosynthesis of cuticular wax. RNA-seq analysis of leaf samples identified, in addition to gl3, 146 genes altered in expression by the 2 dTALes. Nine of the 10 genes known to be involved in cuticular wax biosynthesis were upregulated by at least 1 of the 2 dTALes. A gene previously unknown to be associated with gl3, Zm00001d017418, which encodes aldehyde dehydrogenase, was also expressed in a dTALe-dependent manner. A chemically induced mutant and a CRISPR-Cas9 mutant of Zm00001d017418 both exhibited glossy leaf phenotypes, indicating that Zm00001d017418 is involved in biosynthesis of cuticular waxes. Bacterial protein delivery of dTALes proved to be a straightforward and practical approach for the analysis and discovery of pathway-specific genes in maize.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Reassessment of Resuspension Factor Following Radionuclide Dispersal: Toward a General-purpose Rate Constant

A recent analysis of historical radionuclide resuspension datasets confirmed the general applicability of the Anspaugh and modified Anspaugh models of resuspension factors following both controlled and disastrous releases. While observations appear to have larger variance earlier in time, previous studies equally weighted the data for statistical fit calculations; this could induce a positive skewing of resuspension coefficients in the early time-period. A refitting is performed using a relative instrumental weighting of the observations. Measurements within a 3-d window are grouped into singular sample sets to construct standard deviations. The resulting best-fit equations produce tamer exponentials, which give decreased integrated resuspension factor values relative to those reported by Anspaugh. As expected, the fits attenuate greater error among the data at earlier time. In conclusion, the reevaluation provides a sharper contrast between the empirical models and reaffirms their deficiencies in the short-lived timeframe wherein the dynamics of particulate dispersion dominate the resuspension process.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2026

ϕ → 3 π and ϕ π 0 transition form factor from Khuri-Treiman equations

This work studies the ϕ → 3 π decay and the ϕ → π 0 γ * transition form factor, utilizing the Khuri-Treiman formalism to account for analyticity, crossing, and unitarity. Using once-subtracted dispersion relations, we perform a simultaneous fit to the ϕ → 3 π Dalitz plot distribution and the ϕ → π 0 γ * measurements from the KLOE collaboration, finding good agreement with these experimental data. These results reaffirm the applicability of the Khuri-Treiman approach in the analysis of three-body decays. An interesting result is that the subtraction constant appearing in the equations is similar to a sum rule expectation, in contrast to analogous studies of ω → 3 π decays and ω → π 0 γ * , which shows significant deviations. Our results also provide a reasonable description of the trend of the transition form factor data from in the e + e − → ϕ π 0 scattering region. These intriguing theoretical differences between the decays of ϕ and ω could encourage further experimental measurements to assess the discrepancies and refine the theoretical predictions.

Lorenzo, A. G. [Instituto de Física Corpuscular; U↗

DOE OSTI2025

Rosenbluth-like separation of the $J/ψ$ near-threshold photoproduction: An access to the gluon gravitational form factors at high t

Here, we perform analysis of the near-threshold $J/\psi $ photoproduction data off the proton based on two theoretical approaches, GPD \cite{Guo3} and holographic \cite{Zahed2}, that represent the differential cross sections as powers of the skewness parameter with coefficients that depend only on the momentum transfer $t$. This allows to separate kinematically the corresponding coefficient functions, in much the same way as this is done for the electric and magnetic form factors using the Rosenbluth separation. We examine the independence of the extracted functions with the photon beam energy. These functions, under additional assumptions, are related to the proton's gluon Gravitational Form Factors (gGFFs). We compare the extracted functions with lattice calculations of the gGFFs in the region of $0.5<|t|<2$~GeV$^{2}$, where they overlap. Such analysis demonstrates the possibility of extracting some combinations of the gGFFs from the data at high $t$, complementary to the lattice calculations available in the low $t$ region. However, higher statistics are needed to more accurately check the predicted scaling behavior of the data and compare with the lattice results, thus testing and comparing the theoretical assumptions used in the GPD and holographic models.

Pentchev, Lubomir [Thomas Jefferson National Accel↗

DOE OSTI2025

Transverse-momentum-dependent pion structures from lattice QCD: Collins-Soper kernel, soft factor, TMDWF, and TMDPDF

We present the first lattice quantum chromodynamics (QCD) calculation of the pion valence-quark transverse-momentum-dependent parton distribution function (TMDPDF) within the framework of large-momentum effective theory (LaMET). Using correlators fixed in the Coulomb gauge (CG), we computed the quasi-TMD beam function for a pion with a mass of 300 MeV, a fine lattice spacing of 𝑎 =0.06 fm, and multiple large momenta up to 3 GeV. The intrinsic soft functions in the CG approach are extracted from form factors with large momentum transfer, and as a byproduct, we also obtain the corresponding Collins-Soper (CS) kernel. Our determinations of both the soft function and the CS kernel agree with perturbation theory at small transverse separations (𝑏 ⊥ ) between the quarks. At larger 𝑏 ⊥ , the CS kernel remains consistent with recent results obtained using both CG and gauge-invariant TMD correlators in the literature. By combining next-to-leading logarithmic factorization of the quasi-TMD beam function and the soft function, we obtain an 𝑥-dependent pion valence-quark TMDPDF for transverse separations 𝑏 ⊥ ≳1 fm. Interestingly, we find that the 𝑏 ⊥ dependence of the phenomenological parametrizations of TMDPDF for moderate values of 𝑥 are in reasonable agreement with our QCD determinations. In addition, we present results for the transverse-momentum-dependent wave function for a heavier pion with 670 MeV mass.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Fast and accurate calculation of EXAFS Debye-Waller factors in U⁢O2 using the dynamical matrix method

Theoretical modeling of bonding dynamics in metal oxides is required for predicting their thermal conductivity, catalytic activity, and mechanical properties. A primary challenge is the scarcity of experimental methods for validating theoretical predictions of these atomic-scale dynamics. This work presents a workflow that uses experimental extended x-ray absorption fine structure (EXAFS) data collected at high temperatures to validate an interatomic force field for uranium dioxide (UO2), an important model material. The validated force field is then used to drive computationally intensive molecular dynamics (MD) simulations and as input for the much faster dynamical matrix Debye-Waller (DMDW) method. The predicted values of the Debye-Waller factors from the DMDW calculations are in good agreement with those obtained from the MD simulations, with residual pair-specific differences attributable to quantum zero-point motion at low temperatures and lattice anharmonicity at high temperatures. We further show that theoretical EXAFS spectra constructed directly from DMDW-derived Debye-Waller factors reproduce the experimental data (at relatively low temperatures) with accuracy comparable to full MD-EXAFS, providing an additional validation of the choice of the potential. This study establishes a validated, rapid computational pathway for modeling bond dynamics, naturally incorporating quantum nuclear\\\\r\\\\nstatistics absent in classical simulations, which are essential for the mechanistic understanding of complex oxide materials.

58 GEOSCIENCES↗

DOE OSTI2022

Decomposition of high-rank factorized unitary coupled-cluster operators using ancilla and multiqubit controlled low-rank counterparts

The factorized form of the unitary coupled-cluster (UCC) approximation is one of the most promising methodologies to prepare trial states for strongly correlated systems within the variational quantum eigensolver framework. The factorized form of the UCC Ansatz can be systematically applied to a reference state to generate the desired entanglement. The difficulty associated with such an approach is the requirement of simultaneously entangling a growing number of qubits, which quickly exceeds the hardware limitations of today's quantum machines. In particular, while circuits for singles and double excitations can be performed on current hardware, higher-rank excitations require too many gate operations. In this work, we propose a set of schemes that trade off using extra qubits for a reduced gate depth to decompose high-rank UCC excitation operators into significantly lower depth circuits. These results will remain useful even when fault-tolerant machines are available to reduce the overall state-preparation circuit depth.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

Further investigation of g factors for the lead monofluoride ground state

We report the results of our theoretical study and analysis of earlier experimental data for the g-factor tensor components of the ground 2 II 1/2 state of the free PbF radical. These values obtained both within the relativistic coupled-cluster method combined with the generalized relativistic effective core potential approach and with our fit of the experimental data from [R. J. Mawhorter, B. S. Murphy, A. L. Baum, T. J. Sears, T. Yang, P. M. Rupasinghe, C. P. McRaven, N. E. Shafer-Ray, L. D. Alphei, and J.-U. Grabow, Phys. Rev. A 84, 022508 (2011); A. L. Baum, B.A. thesis, Pomona College, 2011]. The obtained results agree very well with each other but contradict the previous fit performed in the cited works. Our final prediction for g factors is G ∥ =0.081(5),G ⊥ =–0.27(1).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Relativistic configuration interaction plus linearized-coupled-cluster calculations of U 2 + energies, g factors, transition rates, and lifetimes

In this study, excitation energies, term designations, g factors, transition rates, and lifetimes of U 2+ are determined using a relativistic configuration interaction (CI) + linearized-coupled-cluster (LCC) approach. The CI-LCC energies are compared with CI + many-body-perturbation-theory (MBPT) and available experimental energies. Close agreement has been found with experiment, within hundreds of cm -1 . In addition, lifetimes of higher levels have been calculated for comparison with three experimentally measured lifetimes, and close agreement has been found within the experimental error. CI-LCC calculations constitute a benchmark test of the CI + all-order method in complex relativistic systems such as actinides and their ions with many valence electrons. The theory yields many energy levels, g factors, transition rates, and lifetimes of U 2+ that are not available from experiment. Lastly, the theory can be applied to other multivalence atoms and ions, which would be of interest to many applications.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2019

Leveraging electron-phonon interaction to enhance the thermoelectric power factor in graphene-like semimetals

Electron-phonon interactions (EPIs) are presumably detrimental for thermoelectric performance in semiconductors because they limit carrier mobility. Here we show that enhanced EPIs with strong energy dependence offer an intrinsic pathway to a significant increase in the Seebeck coefficient and the thermoelectric power factor, particularly in the context of two-dimensional (2D) graphene-like Dirac bands. The increase is realized by enabling electron energy filtering through preferential scattering of electron/hole carriers. We prove this concept by implementing first-principles computational methods with explicit treatment of EPIs for a 2D gapless MoS 2 allotrope, which has both massless Dirac bands and a heavy-fermion state that acts as the filter. We determine that the optimal location of the heavy state and hence the onset of the filtering process is at the Dirac point. Our study opens an avenue for attaining ultrahigh power factors via engineering the EPIs in graphene-like semimetals or identifying new compounds that intrinsically possess the featured electronic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Bayesian estimation of the $S$ factor and thermonuclear reaction rate for 16 O(p, γ) 17 F

The 16 O(p, γ) 17 F reaction is the slowest hydrogen-burning process in the CNO mass region. Its thermonuclear rate sensitively impacts predictions of oxygen isotopic ratios in a number of astrophysical sites, including AGB stars. The reaction has been measured several times at low bombarding energies using a variety of techniques. The most recent evaluated experimental rates have a reported uncertainty of about 7.5% below 1 GK. However, the previous rate estimate represents a best guess only and was not based on rigorous statistical methods. We apply a Bayesian model to fit all reliable 16 O(p, γ) 17 F cross section data, and take into account independent contributions of statistical and systematic uncertainties. The nuclear reaction model employed is a single-particle potential model involving a Woods-Saxon potential for generating the radial bound state wave function. The model has three physical parameters, the radius and diffuseness of the Woods-Saxon potential, and the asymptotic normalization coefficients (ANCs) of the final bound state in 17 F. Here, we find that performing the Bayesian S -factor fit using ANCs as scaling parameters has a distinct advantage over adopting spectroscopic factors instead. Based on these results, we present the first statistically rigorous estimation of experimental 16 O(p, γ) 17 F reaction rates, with uncertainties (±4.2%) of about half the previously reported values.

6 ≤ A ≤ 19↗

DOE OSTI2018

Monotonic properties of the shift and penetration factors

Here, we study derivatives of the shift and penetration factors of collision theory with respect to energy, angular momentum, and charge. Definitive results for the signs of these derivatives are found for the repulsive Coulomb case. In particular, we find that the derivative of the shift factor with respect to energy is positive for the repulsive Coulomb case, a long anticipated but heretofore unproven result. In conclusion, these results are closely connected to the properties of the sum of squares of the regular and irregular Coulomb functions; we also present investigations of this quantity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Effective J -factors for Milky Way dwarf spheroidal galaxies with velocity-dependent annihilation

We calculate the effective J-factors, which determine the strength of indirect detection signals from dark matter annihilation, for 25 dwarf spheroidal galaxies (dSphs). We consider several well-motivated assumptions for the relative velocity dependence of the dark matter annihilation cross section: σAv: s -wave (velocity independent), p -wave (σ A v∝v 2 ), d-wave (σ A v∝v 4 ), and Sommerfeld-enhancement in the Coulomb limit (σ A v∝1/v). As a result we provide the largest and most updated sample of J-factors for velocity-dependent annihilation models. For each scenario, we use Fermi-LAT gamma-ray data to constrain the annihilation cross section. Due to the assumptions made in our gamma-ray data analysis, our bounds are comparable to previous bounds on both the p-wave and Sommerfeld-enhanced cross sections using dSphs. Finally, our bounds on the d-wave cross section are the first such bounds using indirect detection data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

All orders factorization and the Coulomb problem

In the limit of large nuclear charge, Z ≫ 1 , or small lepton velocity, β ≪ 1 , Coulomb corrections to nuclear beta decay and related processes are enhanced as Z α / β and become large or even nonperturbative (with α the QED fine structure constant). We provide a constructive demonstration of factorization to all orders in perturbation theory for these processes and compute the all-orders hard and soft functions appearing in the factorization formula. We clarify the relationship between effective field theory amplitudes and historical treatments of beta decay in terms of a Fermi function. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Global fit of electron and neutrino elastic scattering data to determine the strange quark contribution to the vector and axial form factors of the nucleon

We present a global fit of neutral-current elastic (NCE) neutrino-scattering data and parity-violating electron-scattering (PVES) data with the goal of determining the strange quark contribution to the vector and axial form factors of the proton. Previous fits of this form included data from a variety of PVES experiments (PVA4, HAPPEx, G0, SAMPLE) and the NCE neutrino and anti-neutrino data from BNL E734. These fits did not constrain the strangeness contribution to the axial form factor G A s ( Q 2 ) at low Q 2 very well because there was no NCE data for Q 2 < 0.45 GeV 2 . Our new fit includes for the first time MiniBooNE NCE data from both neutrino and antineutrino scattering; this experiment used a hydrocarbon target and so a model of the neutrino interaction with the carbon nucleus was required. Three different nuclear models have been employed: a relativistic Fermi gas model, the superscaling approximation model, and a spectral function model. We find a tremendous improvement in the constraint of G A s ( Q 2 ) at low Q 2 compared to previous work, although more data is needed from NCE measurements that focus on exclusive single-proton final states, for example from MicroBooNE. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Electromagnetic and two-photon transition form factors of the pseudoscalar mesons: An algebraic model computation

We compute electromagnetic and two-photon transition form factors of ground-state pseudoscalar mesons: π , K , η c , η b . To this end, we employ an algebraic model based upon the coupled formalism of Schwinger-Dyson and Bethe-Salpeter equations. Within this approach, the dressed quark propagator and the relevant Bethe-Salpeter amplitude encode the internal structure of the corresponding meson. Electromagnetic properties of the meson are probed via the quark-photon interaction. The algebraic model employed by us unifies the treatment of all ground-state pseudoscalar mesons. Its parameters are carefully fitted performing a global analysis of existing experimental data including the knowledge of the charge radii of the mesons studied. We then compute and predict electromagnetic and two-photon transition form factors for a wide range of probing photon momentum-squared which is of direct relevance to the experimental observations carried out thus far or planned at different hadron physics facilities such as the Thomas Jefferson National Accelerator Facility (JLab) and the forthcoming Electron-Ion Collider. We also present comparisons with other theoretical models and approaches and lattice quantum chromodynamics. Published by the American Physical Society 2024

Higuera-Angulo, I. M. (ORCID:0000000256008875)↗