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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Elongation factor 4 remodels the A-site tRNA on the ribosome

During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. Furthermore, the structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Newton-based optimization for Kullback-Leibler nonnegative tensor factorizations

Tensor factorizations with nonnegativity constraints have found application in analysing data from cyber traffic, social networks, and other areas. We consider application data best described as being generated by a Poisson process (e.g. count data), which leads to sparse tensors that can be modelled by sparse factor matrices. In this paper, we investigate efficient techniques for computing an appropriate canonical polyadic tensor factorization based on the Kullback–Leibler divergence function. We propose novel subproblem solvers within the standard alternating block variable approach. Our new methods exploit structure and reformulate the optimization problem as small independent subproblems. We employ bound-constrained Newton and quasi-Newton methods. Finally, we compare our algorithms against other codes, demonstrating superior speed for high accuracy results and the ability to quickly find sparse solutions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

CI+MBPT calculations of Ar I energies, g factors, and transition line strengths

Excited states of noble gas atoms present certain challenges to atomic theory for several reasons: first, relativistic effects are important and LS coupling is not optimal; second, energy intervals can be quite small, leading to strong mixing of states; third, many-body perturbation theory for hole states does not converge well. Previously, some attempts were made to solve this problem, using for example the all-order coupled-cluster approach and particle-hole configuration-interaction many-body perturbation theory (CI-MBPT) with modified denominators. However, while these approaches were promising, the accuracy was still limited. In this study, we calculate Ar I energies, g factors, and transition amplitudes using ab initio CI-MBPT with eight valence electrons to avoid the problem of slow convergence of MBPT due to strong interaction between 3p and 3s states. We also included in CI many dominant states obtained by double excitations of the ground state configuration. Thus perturbation corrections were needed only for 1s, 2s, 2p core electrons non-included in valence-valence CI, which are quite small. We found that energy, g factors, and electric dipole matrix elements are in reasonable agreement with experiments. It is noteworthy that the theory agreed well with accurately measured g factors. Finally, experimental oscillator strengths have large uncertainty, so in some cases we made a comparison with average values.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Experimental evidence for nonspherical magnetic form factor in Ru 3 +

The Mott insulator ..alpha..-RuCl3 has generated great interest in the community due to its possible field-induced Kitaev quantum spin liquid state. Despite enormous effort spent trying to obtain the form of the low-energy Hamiltonian, there is currently no agreed upon set of parameters which is able to explain all of the data. A key piece of missing information lies in the determination of the magnetic form factor of Ru3+, particularly for a true quantitative treatment of inelastic neutron scattering data. Here we present the experimentally derived magnetic form factor of Ru3+ in the low spin 4d5 state using polarized neutron diffraction within the paramagnetic regime on high-quality single crystals of ..alpha..-RuCl3. We observe strong evidence of an anisotropic form factor, expected of the spin-orbit coupled jeff=12 ground state. We model the static magnetization density in increasing complexity from simple isotropic cases, to a multipolar expansion, and, finally, ab initio calculations of the generalized jeff=12 ground state. Comparison of both single ion models and inclusion of Cl- anions support the presence of hybridization of Ru3+ with the surrounding Cl- ligands.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Proton form factor ratio μ p G E p / G M p from double spin asymmetry

We report the ratio of the electric and magnetic form factor of the proton, $\mu_p G_E^p/G_M^p$, has been measured for elastic electron-proton scattering with polarized beam and target up to four-momentum transfer squared, $Q^2=5.66$ (GeV/c)$^2$ using the double spin asymmetry for target spin orientation aligned nearly perpendicular to the beam momentum direction. This measurement of $\mu_p G_E^p/G_M^p$ agrees with the $Q^2$ dependence of previous recoil polarization data and reconfirms the discrepancy at high $Q^2$ between the Rosenbluth and the polarization-transfer method with a different measurement technique and systematic uncertainties uncorrelated to those of the recoil-polarization measurements. The form factor ratio at $Q^2$=2.06 (GeV/c)$^2$ has been measured as $\mu_p G_E^p/G_M^p = 0.720 \pm 0.176_{stat} \pm 0.039_{sys}$, which is in agreement with an earlier measurement with the polarized target technique at similar kinematics. The form factor ratio at $Q^2$=5.66 (GeV/c)$^2$ has been determined as $\mu_p G_E^p/G_M^p=0.244\pm0.353_{stat}\pm0.013_{sys}$, which represents the highest $Q^2$ reach with the double spin asymmetry with polarized target to date.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Frame dependence of transition form factors in light-front dynamics

We calculate here the transition form factor between vector and pseudoscalar quarkonia in both the timelike and the spacelike region using light-front dynamics. We explore the frame dependence of the form factors for heavy quarkonia with light-front wave functions calculated from the valence Fock sector. This dependence could serve as a measure for the Lorentz symmetry violation arising from the Fock-space truncation. We suggest using frames with minimal longitudinal momentum transfer for calculations in the valence Fock sector, namely, the Drell-Yan frame for the spacelike region and a specific longitudinal frame for the timelike region; at q 2 = 0 these two frames give the same result. We also use the transition form factor in the timelike region to investigate the electromagnetic Dalitz decay ψ A → ψ B l + l - ( l = e , μ ) and predict the effective mass spectrum of the lepton pair.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Nucleon isovector axial form factors

We present results for the isovector axial vector form factors obtained using thirteen 2 + 1 + 1 -flavor highly improved staggered quark (HISQ) ensembles generated by the MILC collaboration. The calculation of nucleon two- and three-point correlation functions has been done using Wilson-clover fermions. In the analysis of these data, we quantify the sensitivity of the results to strategies used for removing excited state contamination and invoke the partially conserved axial current relation between the form factors to choose between them. Our data driven analysis includes removing contributions from multihadron N π states that make significant contributions. Our final results are g A = 1.292 ( 53 ) stat ( 24 ) sys for the axial charge; g S = 1.085 ( 50 ) stat ( 103 ) sys and g T = 0.991 ( 21 ) stat ( 10 ) sys for the scalar and tensor charges; ⟨ r A 2 ⟩ = 0.439 ( 56 ) stat ( 34 ) sys fm 2 for the mean squared axial charge radius, g P * = 9.03 ( 47 ) stat ( 42 ) sys for the induced pseudoscalar charge; and g π N N = 14.14 ( 81 ) stat ( 85 ) sys for the pion-nucleon coupling. We also provide a parametrization of the axial form factor G A ( Q 2 ) over the range 0 ≤ Q 2 ≤ 1 GeV 2 for use in phenomenology and a comparison with other lattice determinations. We find that the various lattice data agree within 10% but are significantly different from the extraction of G A ( Q 2 ) from the ν -deuterium scattering data. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Trace anomaly form factors from lattice QCD

The hadron mass can be obtained through the calculation of the trace of the energy-momentum tensor in the hadron which includes the trace anomaly and sigma terms. The anomaly due to conformal symmetry breaking is believed to be an important ingredient for hadron mass generation and confinement. In this work, we will present the calculation of the glue part of the trace anomaly form factors of the pion up to Q 2 ∼ 4.3 GeV 2 and the nucleon up to Q 2 ∼ 1 GeV 2 . The calculations are performed on a domain wall fermion ensemble with overlap valence quarks at seven valence pion masses varying from ∼ 250 to ∼ 540 MeV , including the unitary point ∼ 340 MeV . We calculate the radius of the glue trace anomaly for the pion and the nucleon from the z expansion. By performing a two-dimensional Fourier transform on the glue trace anomaly form factors in the infinite momentum frame with no energy transfer, we also obtain their spatial distributions for several valence quark masses. The results are qualitatively extrapolated to the physical valence pion mass with systematic errors from the unphysical sea quark mass, discretization effects in the renormalization sum rule, and finite-volume effects to be addressed in the future. We find the pion’s form factor changes sign, as does its spatial distribution, for light quark masses. This explains how the trace anomaly contribution to the pion mass approaches zero toward the chiral limit. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Consistency of the pion form factor and unpolarized transverse momentum dependent parton distributions beyond leading twist in the light-front quark model

We investigate the interplay among the pion’s form factor, transverse momentum dependent distributions (TMDs), and parton distribution functions (PDFs) extending our light-front quark model (LFQM) computation based on the Bakamjian-Thomas construction for the two-point function [1,2] to the three-point and four-point functions. Ensuring the four-momentum conservation at the meson-quark vertex from the Bakamjian-Thomas construction, the meson mass is taken consistently as the corresponding invariant meson mass both in the matrix element and the Lorentz factor in our LFQM computation. We achieve the current-component independence in the physical observables such as the pion form factor and delve into the derivation of unpolarized TMDs and PDFs associated with the forward matrix element. We address the challenges posed by twist-4 TMDs and exhibit the fulfillment of the sum rule. Effectively, our LFQM successfully handles the light-front zero modes and offers insights for broader three-point and four-point functions and related observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Lattice calculation of electric dipole moments and form factors of the nucleon

In this paper, we analyze commonly used expressions for computing the nucleon electric dipole form factors (EDFF) $F_3$ and moments (EDM) on a lattice and find that they lead to spurious contributions from the Pauli form factor $F_2$ due to inadequate definition of these form factors when parity mixing of lattice nucleon fields is involved. Using chirally symmetric domain wall fermions, we calculate the proton and the neutron EDFF induced by the CP-violating quark chromo-EDM interaction using the corrected expression. In addition, we calculate the electric dipole moment of the neutron using a background electric field that respects time translation invariance and boundary conditions, and we find that it decidedly agrees with the new formula but not the old formula for $F_3$. In conclusion, we analyze some selected lattice results for the nucleon EDM and observe that after the correction is applied, they either agree with zero or are substantially reduced in magnitude, thus reconciling their difference from phenomenological estimates of the nucleon EDM.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Structure Factors for Hot Neutron Matter from Ab Initio Lattice Simulations with High-Fidelity Chiral Interactions

We present the first ab initio lattice calculations of spin and density correlations in hot neutron matter using high-fidelity interactions at next-to-next-to-next-to-leading order in chiral effective field theory. These correlations have a large impact on neutrino heating and shock revival in core-collapse supernovae and are encapsulated in functions called structure factors. Unfortunately, calculations of structure factors using high-fidelity chiral interactions were well out of reach using existing computational methods. In this Letter, we solve the problem using a computational approach called the rank-one operator (RO) method. The RO method is a general technique with broad applications to simulations of fermionic many-body systems. It solves the problem of exponential scaling of computational effort when using perturbation theory for higher-body operators and higher-order corrections. Using the RO method, we compute the vector and axial static structure factors for hot neutron matter as a function of temperature and density. Here, the ab initio lattice results are in good agreement with virial expansion calculations at low densities but are more reliable at higher densities. Random phase approximation codes used to estimate neutrino opacity in core-collapse supernovae simulations can now be calibrated with ab initio lattice calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Global Data-Driven Determination of Baryon Transition Form Factors

Hadronic resonances emerge from strong interactions encoding the dynamics of quarks and gluons. The structure of these resonances can be probed by virtual photons parametrized in transition form factors. Here, in this study, twelve N* and Δ transition form factors at the pole are extracted from data with the center-of-mass energy from πN threshold to 1.8 GeV, and the photon virtuality 0 ≤ Q 2 /GeV 2 ≤ 8. For the first time, these results are determined from a simultaneous analysis of more than one state, i.e., ~10 5 π⁢N, η⁢N, and K⁢Λ electroproduction data. In addition, about 5×10 4 data in the hadronic sector as well as photoproduction serve as boundary conditions. For the Δ⁡(1232) and N⁡(1440) states our results are in qualitative agreement with previous studies, while the transition form factors at the poles of some higher excited states are estimated for the first time. Realistic uncertainties are determined by further exploring the parameter space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Efficient structure-factor modeling for crystals with multiple components

Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by an atomic model alone, i.e . using point scatterers. Indeed, entities such as disordered (bulk) solvent, semi-ordered solvent ( e.g. lipid belts in membrane proteins, ligands, ion channels) and disordered polymer loops require other types of modeling than a collection of individual atoms. This results in the model structure factors containing multiple contributions. Most macromolecular applications assume two-component structure factors: one component arising from the atomic model and the second one describing the bulk solvent. A more accurate and detailed modeling of the disordered regions of the crystal will naturally require more than two components in the structure factors, which presents algorithmic and computational challenges. Here an efficient solution of this problem is proposed. All algorithms described in this work have been implemented in the computational crystallography toolbox ( CCTBX ) and are also available within Phenix software. These algorithms are rather general and do not use any assumptions about molecule type or size nor about those of its components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large Scale Tensor Factorization via Parallel Sketches

Tensor factorization methods have recently gained increased popularity. A key feature that renders tensors attractive is the ability to directly model multi-relational data. In this work, we propose ParaSketch, a parallel tensor factorization algorithm that enables massive parallelism, to deal with large tensors. The idea is to compress the large tensor into multiple small tensors, decompose each small tensor in parallel, and combine the results to reconstruct the desired latent factors. Prior art in this direction entails potentially very high complexity in the (Gaussian) compression and final combining stages. Adopting sketching matrices for compression, the proposed method enjoys a dramatic reduction in compression complexity, and features a much lighter combining step. Moreover, theoretical analysis shows that the compressed tensors inherit latent identifiability under mild conditions, hence establishing correctness of the overall approach. Numerical experiments corroborate the theory and demonstrate the effectiveness of the proposed algorithm.

block term decomposition↗
DOE OSTI2022

Key environmental and production factors for understanding variation in switchgrass chemical attributes

Abstract Switchgrass ( Panicum virgatum L.) is a promising feedstock for bioenergy and bioproducts; however, its inherent variability in chemical attributes creates challenges for uniform conversion efficiencies and product quality. It is necessary to understand the range of variation and factors (i.e., field management, environmental) influencing chemical attributes for process improvement and risk assessment. The objectives of this study were to (1) examine the impact of nitrogen fertilizer application rate, year, and location on switchgrass chemical attributes, (2) examine the relationships among chemical attributes, weather and soil data, and (3) develop models to predict chemical attributes using environmental factors. Switchgrass samples from a field study spanning four locations including upland cultivars, one location including a lowland cultivar, and between three and six harvest years were assessed for glucan, xylan, lignin, volatiles, carbon, nitrogen, and ash concentrations. Using variance estimation, location/cultivar, nitrogen application rate, and year explained 65%–96% of the variation for switchgrass chemical attributes. Location/cultivar × year interaction was a significant factor for all chemical attributes indicating environmental‐based influences. Nitrogen rate was less influential. Production variables and environmental conditions occurring during the switchgrass field trials were used to successfully predict chemical attributes using linear regression models. Upland switchgrass results highlight the complexity in plant responses to growing conditions because all production and environmental variables had strong relationships with one or more chemical attributes. Lowland switchgrass was limited to observations of year‐to‐year environmental variability and nitrogen application rate. All explanatory variable categories were important for lowland switchgrass models but stand age and precipitation relationships were particularly strong. The relationships found in this study can be used to understand spatial and temporal variation in switchgrass chemical attributes. The ability to predict chemical attributes critical for conversion processes in a geospatial/temporal manner would provide state‐of‐the‐art knowledge for risk assessment in the bioenergy and bioproducts industry.

09 BIOMASS FUELS↗
DOE OSTI2018

Electron Effective Mass and g Factor in Wide HgTe Quantum Wells

The magnetic-field (0 T < B < 9 T) dependence of the longitudinal and Hall resistances at fixed temperatures (2 K < T < 50 K) for the HgCdTe/HgTe/HgCdTe system with a HgTe quantum well 20.3 nm in width are measured. The activation analysis of the magnetoresistance curves is used as a tool for identifying the mobility gaps between neighboring Landau levels. The activation-energy values obtained from the temperature dependences of the longitudinal resistance in the plateau regions of the quantum Hall effect with the filling factors ν = 1, 2, 3 make it possible to estimate the effective mass and the g factor of electrons in the system under study. Indications concerning the possibility of large values of the g factor (≅ 80) are obtained.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Communication-avoiding symmetric-indefinite factorization

We describe and analyze a novel symmetric triangular factorization algorithm. The algorithm is essentially a block version of Aasen's triangular tridiagonalization. It factors a dense symmetric matrix A as the product A=PLTL T P T where P is a permutation matrix, L is lower triangular, and T is block tridiagonal and banded. The algorithm is the first symmetric-indefinite communication-avoiding factorization: it performs an asymptotically optimal amount of communication in a two-level memory hierarchy for almost any cache-line size. Adaptations of the algorithm to parallel computers are likely to be communication efficient as well; one such adaptation has been recently published. As a result, the current paper describes the algorithm, proves that it is numerically stable, and proves that it is communication optimal.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics

GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Lastly, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.

59 BASIC BIOLOGICAL SCIENCES↗