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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

LibERI—A portable and performant multi-GPU accelerated library for electron repulsion integrals via OpenMP offloading and standard language parallelism

A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.g., Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low and high contraction s, p, and d functions using the rotated-axis and Rys quadrature methods. GPU codes are factorized based on previous developments with two layers of integral screening and quartet presorting. In this work, the density screening is moved to the GPU to enhance the computational efficacy for large molecular systems. Here, the L-shells in the Pople basis set are also separated into pure S and P shells to increase the ERI homogeneity and reduce atomic operations and the memory footprint. LibERI is compatible with any quantum chemistry drivers supporting the MolSSI Driver Interface. Benchmark calculations of LibERI interfaced with the GAMESS software package were carried out on various GPU architectures and molecular systems. The results show that the LibERI performance is comparable to other state-of-the-art GPU-accelerated codes (e.g., TeraChem and GMSHPC) and, in some cases, outperforms conventionally developed ERI CUDA kernels (e.g., QUICK) while fully maintaining portability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of edge-localized electron cyclotron current drive on edge-localized mode suppression by resonant magnetic perturbations in DIII-D

Abstract According to recent DIII-D experiments (Logan et al 2024 Nucl. Fusion 64 014003), injecting edge localized electron cyclotron current drive (ECCD) in the counter-plasma-current (counter- I p ) direction reduces the n = 3 resonant magnetic perturbation (RMP) current threshold for edge-localized mode (ELM) suppression, while co- I p ECCD during the suppressed ELM phase causes a back transition to ELMing. This paper presents nonlinear two-fluid simulations on the ECCD manipulation of edge magnetic islands induced by RMP using the TM1 code. In the presence of a magnetic island chain at the pedestal-top, co- I p ECCD is found to decrease the island width and restore the initially degraded pedestal pressure when its radial deposition location is close to the rational surface of the island. With a sufficiently strong co- I p ECCD current, the RMP-driven magnetic island can be healed, and the pedestal pressure fully recovers to its initial ELMing state. On the contrary, counter- I p ECCD is found to increase the island width and further reduce the pedestal pressure to levels significantly below the peeling-ballooning-mode limited height, leading to even stationary ELM suppression. These simulations align with the results from DIII-D experiments. However, when multiple magnetic island chains are present at the pedestal-top, the ECCD current experiences substantial broadening, and its effects on the island width and pedestal pressure become negligible. Further simulations reveal that counter- I p ECCD enhances RMP penetration by lowering the penetration threshold, with the degree of reduction proportional to the amplitude of ECCD current. For the ∼1 MW ECCD in DIII-D, the predicted decrease in the RMP penetration threshold for ELM suppression is approximately 20%, consistent with experimental observations. These simulations indicate that edge-localized ECCD can be used to either facilitate RMP-driven ELM suppression or optimize the confinement degradation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Homological Invariants of Pauli Stabilizer Codes

Abstract We study translationally invariant Pauli stabilizer codes with qudits of arbitrary, not necessarily uniform, dimensions. Using homological methods, we define a series of invariants called charge modules. We describe their properties and physical meaning. The most complete results are obtained for codes whose charge modules have Krull dimension zero. This condition is interpreted as mobility of excitations. We show that it is always satisfied for translation invariant 2D codes with unique ground state in infinite volume, which was previously known only in the case of uniform, prime qudit dimension. For codes all of whose excitations are mobile we construct a p-dimensional excitation and a $$(D-p-1)$$ ( D - p - 1 ) -form symmetry for every element of thep-th charge module. Moreover, we define a braiding pairing between charge modules in complementary degrees. We discuss examples which illustrate how charge modules and braiding can be computed in practice.

Physics↗
DOE OSTI2020

SNPeffect: identifying functional roles of SNPs using metabolic networks

Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1989

NASA Lewis Stirling engine computer code evaluation

In support of the U.S. Department of Energy's Stirling Engine Highway Vehicle Systems program, the NASA Lewis Stirling engine performance code was evaluated by comparing code predictions without engine-specific calibration factors to GPU-3, P-40, and RE-1000 Stirling engine test data. The error in predicting power output was -11 percent for the P-40 and 12 percent for the Re-1000 at design conditions and 16 percent for the GPU-3 at near-design conditions (2000 rpm engine speed versus 3000 rpm at design). The efficiency and heat input predictions showed better agreement with engine test data than did the power predictions. Concerning all data points, the error in predicting the GPU-3 brake power was significantly larger than for the other engines and was mainly a result of inaccuracy in predicting the pressure phase angle. Analysis into this pressure phase angle prediction error suggested that improvements to the cylinder hysteresis loss model could have a significant effect on overall Stirling engine performance predictions.

Sullivan, Timothy J.↗
NASA NTRS1990

SATCOM antenna siting study on a P-3C using the NEC-BSC V3.1

The location of a UHF SATCOM antenna on a P-3C aircraft is studied using the NEC-Basic Scattering Code V3.1 (NEC-BSC3). The NEC-BSC3 is a computer code based on the uniform theory of diffraction. The code is first validated for this application using scale model measurements. In general, the comparisons are good except in 10 degree regions near the nose and tail of the aircraft. Patterns for various antenna locations are analyzed to achieve a prescripted performance.

Bensman, D.↗
DOE OSTI2021

pKPDB: a protein data bank extension database of p Ka and pI theoretical values

Abstract Summary pKa values of ionizable residues and isoelectric points of proteins provide valuable local and global insights about their structure and function. These properties can be estimated with reasonably good accuracy using Poisson–Boltzmann and Monte Carlo calculations at a considerable computational cost (from some minutes to several hours). pKPDB is a database of over 12 M theoretical pKa values calculated over 120k protein structures deposited in the Protein Data Bank. By providing precomputed pKa and pI values, users can retrieve results instantaneously for their protein(s) of interest while also saving countless hours and resources that would be spent on repeated calculations. Furthermore, there is an ever-growing imbalance between experimental pKa and pI values and the number of resolved structures. This database will complement the experimental and computational data already available and can also provide crucial information regarding buried residues that are under-represented in experimental measurements. Availability and implementation Gzipped csv files containing p Ka and isoelectric point values can be downloaded from https://pypka.org/pKPDB. To query a single PDB code please use the PypKa free server at https://pypka.org. The pKPDB source code can be found at https://github.com/mms-fcul/pKPDB. Supplementary information Supplementary data are available at Bioinformatics online.

Reis, Pedro B. P. S. (ORCID:0000000335636239)↗
NASA NTRS1994

Acoustic waves in M dwarfs: Maintaining a corona

We use a time-dependent hydrodynamics code to follow the propagation of acoustic waves into the corona of an M dwarf star. An important qualitative difference between M dwarfs and stars such as the Sun is that the acoustic spectrum in M dwarfs is expected to peak at periods close to the acoustic cutoff P(sub A): this allows more effective penetration of waves into the corona. In our code, radiative losses in the photosphere, chromosphere, and corona are computed using Rosseland mean opacities, Mg II kappa and Ly alpha emission, and optically thin emissivities respectively. We find that acoustic heating can maintain a corona with a temperature of order 0.7-1 x 10(exp 6) K and a surface X-ray flux as large as 10(exp 5)ergs/sq cm/s. In a recent survey of X-rays from M dwarfs, some (20%-30%) of the stars lie at or below this limiting X-ray flux: we suggest that such stars may be candidates for acoustically maintained coronae.

Mullan, D. J.↗
DOE OSTI2024

Thermonuclear 28 P(p, γ ) 29 S reaction rate and astrophysical implication in ONe nova explosion

An accurate 28 P(p, γ) 29 S reaction rate is crucial to defining the nucleosynthesis products of explosive hydrogen burning in ONe novae. Using the recently released nuclear mass of 29 S, together with a shell model and a direct capture calculation, we reanalyzed the 28 P(p, γ) 29 S thermonuclear reaction rate and its astrophysical implication. We focus on improving the astrophysical rate for 28 P(p, γ) 29 S based on the newest nuclear mass data. Our goal is to explore the impact of the new rate and associated uncertainties on the nova nucleosynthesis. We evaluated this reaction rate via the sum of the isolated resonance contribution instead of the previously used Hauser-Feshbach statistical model. The corresponding rate uncertainty at different energies was derived using a Monte Carlo method. Nova nucleosynthesis is computed with the 1D hydrodynamic code SHIVA. The contribution from the capture on the first excited state at 105.64 keV in 28 P is taken into account for the first time. We find that the capture rate on the first excited state in 28 P is up to more than 12 times larger than the ground-state capture rate in the temperature region of 2.5 × 10 7 K to 4 × 10 8 K, resulting in the total 28 P(p, γ) 29 S reaction rate being enhanced by a factor of up to 1.4 at ~1 × 10 9 K. In addition, the rate uncertainty has been quantified for the first time. It is found that the new rate is smaller than the previous statistical model rates, but it still agrees with them within uncertainties for nova temperatures. The statistical model appears to be roughly valid for the rate estimation of this reaction in the nova nucleosynthesis scenario. Using the 1D hydrodynamic code SHIVA, we performed the nucleosynthesis calculations in a nova explosion to investigate the impact of the new rates of 28 P(p, γ) 29 S. Our calculations show that the nova abundance pattern is only marginally affected if we use our new rates with respect to the same simulations but statistical model rates. Finally, the isotopes whose abundance is most influenced by the present 28 P(p, γ) 29 S uncertainty are 28 Si, 33,34 S, 35,37 Cl, and 36 Ar, with relative abundance changes at the level of only 3% to 4%.

Astronomy & Astrophysics↗
DOE OSTI2021

Investigation of secondary γ -ray angular distributions using the N 15 ( p , α 1 γ ) C * 12 reaction

The observation of secondary γ-rays provides an alternative method of measuring cross sections that populate excited final states in nuclear reactions. The angular distributions of these γ-rays also provide information on the underlying reaction mechanism. Despite a large amount of data of this type in the literature, publicly available R-matrix codes do not have the ability to calculate these types of angular distributions. In this report, the mathematical formalism derived in Brune and deBoer is implemented in the R-matrix code AZURE2 and calculations are compared with previous data from the literature for the 15 N( p, α1γ ) 12 C* reaction. In addition, new measurements, made at the University of Notre Dame Nuclear Science Laboratory using the Hybrid Array of Gamma Ray Detectors (HAGRiD), are reported that span an energy range from E p = 0.88 to 4.0 MeV. Excellent agreement between data and the phenomenological fit is obtained up to the limit of the previous fit at E p = 2.0 MeV and the R-matrix fit is extended from E x ≈ 13.5 up to E x ≈ 15.3 MeV, where 15 N+p and 12 C+α reactions are fit simultaneously for the first time. An excellent reproduction of the 15 N( p, α1γ ) 12 C* and 12 C(α, α) 12 C data is achieved, but inconsistencies and difficulty in fitting other data is encountered and discussed.

6 ≤ A ≤ 19↗
DOE OSTI2022

Validation of ray-based cross-beam energy transfer models

Ray-based cross-beam energy transfer (CBET) models have become a common feature of the radiation-hydrodynamic codes used to simulate inertial confinement fusion experiments. Here, these models are necessary for achieving better agreement with experimental measurements, but their detailed implementation can vary widely between the codes and often rely on artificial multipliers. To address this, a series of 2D and 3D test cases has been developed with validated solutions from wave-based calculations. Comparisons of various ray-based CBET models to the wave-based calculations highlight the essential physics that is required for accurate ray-based CBET modeling. Quantitative comparison metrics and/or field data from the wave-based calculations have been made available for use in the validation of other ray-based CBET codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Axially-deformed solution of the Skyrme-Hartree-Fock-Bogoliubov equations using the transformed harmonic oscillator basis (IV) HFBTHO (v4.0): A new version of the program

We describe the new version 4.0 of the code HFBTHO that solves the nuclear Hartree-Fock-Bogoliubov problem by using the deformed harmonic oscillator basis in cylindrical coordinates. In the new version, we have implemented the restoration of rotational, particle number, and reflection symmetry for even-even nuclei. The restoration of rotational symmetry does not require using bases closed under rotation. Furthermore, we added the SeaLL1 functional and improved the calculation of the Coulomb potential. Finally, we refactored the code to facilitate maintenance and future developments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Fission product yields from the 238 U ( n,f ) reaction at E n = 4.6 MeV

Here, we present cumulative fission product yields from the 238 U (n, f) reaction at an incident energy of 4.6 MeV for fission products with half-lives from less than one second to several hours. We employed direct γ-ray spectroscopy to measure unseparated fission products with a conventional neutron activation analysis and a cyclic activation technique using the RApid Belt-driven Irradiated Target Transfer System (RABITTS). Yields were determined for 78 isotopes and isomers, covering the mass range 84 ≤ A ≤ 148 and the charge range from 33(As) ≤ Z ≤ 58(Ce). Our experimental cumulative yields are compared to the literature and evaluated data at E n ≈0.5 MeV from ENDF/B-VIII.0 and JEFF-3.3 libraries and with theoretical models using the GEF and FREYA codes at E n =4.6 MeV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1983

Stability analysis of Centaur-in-Shuttle composite corrugated adapters

This paper evaluates analytically the structural integrity of discretely-loaded, graphite-epoxy, corrugated adapters for the Centaur-in-Shuttle, where combined compression and shear are the critical loads involved. With normal build-ups in the thickness at load introduction boundaries, the structural integrity for both compression and shear buckling was little (or not al all) affected by the discrete load introductions. The analytical tool employed was the STAGSC computer code, and both bifurction buckling and nonlinear collapse options were used; the latter option was limited to shear since postbuckling strength in compression for plate-type structures is governed by crippling strengths, which is not attainable by existing computer codes.

Spier, E. E.↗