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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Global Transformations for Legacy Parallel Applications via Structural Analysis and Rewriting

Performance and scalability optimization of large HPC applications is currently a labor-intensive, manual process with very low productivity. Major difficulties come from the disaggregated environment for HPC application development: the compiler is only involved in local decisions (core or multithreaded domain), while a library-based, communication-oriented programming model realizes whole-machine parallelism. Realizing any major global change in such a disaggregated environment is very difficult and involves changing large portions of the source code. We present semi-automated techniques, based on structural analysis and rewriting, for performing global transformations on an HPC application source code. We present two case studies using the Self-Consistent Field (SCF) standalone benchmark as well as the Coupled Cluster (CCSD) module (2.9 million lines of Fortran code), a key module of the NWChem computational chemistry application. We demonstrate how structural rewriting techniques can be used to automate transformations that affect multiple sections of the application's source code. We show that the transformations can be applied in a systematic fashion across the source code bases with minimal manual effort. These transformations improve the scalability of the SCF benchmark by more than two orders of magnitude and the performance of the full CCSD module by a factor of 4.0.

legacy parallel applications↗
DOE OSTI2018

Green’s Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems

In this paper we present an efficient implementation for the analytical energy- dependent coupled cluster Green’s function with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of real molecular systems. Due to its algebraic structure, the presented method is highly scalable, and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band, but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where many-body effect becomes significant and single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing our GFCCSD results with experimental results as well as the theoretical results from other methods. It turns out GFCCSD method is able to provide qualitative or semi-quantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main states, larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher order many-body terms to be included in the GFCC implementation.

electronic structure theory↗
DOE OSTI2019

A map of the inorganic ternary metal nitrides

Exploratory synthesis in new chemical spaces is the essence of solid-state chemistry. However, uncharted chemical spaces can be difficult to navigate, especially when materials synthesis is challenging. Nitrides represent one such space, where stringent synthesis constraints have limited the exploration of this important class of functional materials. Here, we employ a suite of computational materials discovery and informatics tools to construct a large stability map of the inorganic ternary metal nitrides. Our map clusters the ternary nitrides into chemical families with distinct stability and metastability, and highlights hundreds of promising new ternary nitride spaces for experimental investigation - from which we experimentally realized seven new Zn- and Mg-based ternary nitrides. As a result, by extracting the mixed metallicity, ionicity and covalency of solid-state bonding from the density functional theory (DFT)-computed electron density, we reveal the complex interplay between chemistry, composition and electronic structure in governing large-scale stability trends in ternary nitride materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

The free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation quantum chemical approach at four temperatures between T = 300 and 450 K. The free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system’s potential energy. The latter free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation free energies agree very well with available experimental data. CJM was supported by the US Department of Energy,Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

McGrath, Matthew↗
DOE OSTI2015

Sensitivity of CoSi{sub 2} precipitation in silicon to extra-low dopant concentrations. II. First-principles calculations

The paper is the second part of the study on the influence of very low dopant content in silicon on CoSi{sub 2} precipitation during high-temperature cobalt ion implantation into transmission electron microscope samples. It deals with the computational justification of various assumptions used in Paper I when rationalizing the kinetics of cobalt clustering in ion-implanted intrinsic silicon (both undoped and containing low concentrations of phosphorus atoms). In particular, it is proven that divacancies are efficient nucleation centers for the new Co-Si phase. It is shown that the capture of vacancies and divacancies on phosphorus atoms increases their lifetime in silicon matrix, but practically does not affect the mechanism of their interaction with interstitial cobalt atoms. Finally, it is demonstrated that the mobility of phosphorus interstitials at temperatures of our experiment is orders of magnitude higher than might be expected from the published literature data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Cluster perturbation theory X: A parallel implementation of Lagrangian perturbation series for the coupled cluster singles and doubles ground-state energy through fifth order

We describe an efficient implementation of cluster perturbation and Møller-Plesset Lagrangian energy series through fifth order that target the coupled cluster singles and doubles energy utilizing the resolution of the identity approximation. We illustrate the computational performance of the implementation by performing ground state energy calculations on systems with up to 1200 basis functions using a single node and by comparison to conventional CCSD calculations. We further show that our hybrid MPI/OMP parallel implementation that also utilizes graphical processing units can be used to obtain fifth order energies on systems with almost 1200 basis functions with a 90 minute "time to solution" running on Frontier at Oak Ridge National Laboratory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

dCache on Steroids - Delegated Storage Solutions

For over a decade, dCache.org has delivered a robust software used at more than 80 Universities and research institutes around the world, allowing these sites to provide reliable storage services for the WLCG experiments as well as many other scientific communities. The flexible architecture of dCache allows running it in a wide variety of configurations and platforms - from a SoC based all-in-one Raspberry-Pi up to hundreds of nodes in a multipetabyte installation. Due to lack of managed storage at the time, dCache implemented data placement, replication and data integrity directly. Today, many alternatives are available: S3, GlusterFS, CEPH and others. While such solutions position themselves as scalable storage systems, they cannot be used by many scientific communities out of the box. The absence of community-accepted authentication and authorization mechanisms, the use of product specific protocols and the lack of namespace are some of the reasons that prevent wide-scale adoption of these alternatives. Most of these limitations are already solved by dCache. By delegating low-level storage management functionality to the above-mentioned new systems and providing the missing layer through dCache, we provide a solution which combines the benefits of both worlds - industry standard storage building blocks with the access protocols and authentication required by scientific communities. In this paper, we focus on CEPH, a popular software for clustered storage that supports file, block and object interfaces. CEPH is often used in modern computing centers, for example as a backend to OpenStack services. We will show prototypes of dCache running with a CEPH backend and discuss the benefits and limitations of such an approach. As a result, we will also outline the roadmap for supporting ‘delegated storage’ within the dCache releases.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2025

Boosting H I -Galaxy Cross-Clustering Signal through Higher-Order Cross-Correlations

After reionization, neutral hydrogen (${\rm H\, \small {I}}$) traces the large-scale structure (LSS) of the Universe, enabling ${\rm H\, \small {I}}$ intensity mapping (IM) to capture the LSS in 3D and constrain key cosmological parameters. We present a new framework utilizing higher-order cross-correlations to study ${\rm H\, \small {I}}$ clustering around galaxies, tested using real-space data from the IllustrisTNG300 simulation. This approach computes the joint distributions of k-nearest neighbor (kNN) optical galaxies and the ${\rm H\, \small {I}}$ brightness temperature field smoothed at relevant scales (the kNN-field framework), providing sensitivity to all higher-order cross-correlations, unlike two-point statistics. To simulate ${\rm H\, \small {I}}$ data from actual surveys, we add random thermal noise and apply a simple foreground cleaning model, filtering out Fourier modes of the brightness temperature field with k ∥ < k min,∥ . Under current levels of thermal noise and foreground cleaning, typical of a Canadian Hydrogen Intensity Mapping Experiment (CHIME)-like survey, the ${\rm H\, \small {I}}$-galaxy cross-correlation signal in our simulations, using the kNN-field framework, is detectable at >30σ across r = [3, 12] h –1 Mpc. In contrast, the detectability of the standard two-point correlation function (2PCF) over the same scales depends strongly on the foreground filter: a sharp k ∥ filter can spuriously boost detection to 8σ due to position-space ringing, whereas a less sharp filter yields no detection. Nonetheless, we conclude that kNN-field cross-correlations are robustly detectable across a broad range of foreground filtering and thermal noise conditions, suggesting their potential for enhanced constraining power over 2PCFs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Ionization potential of radium monofluoride

The ionization potential (IP) of radium monofluoride (RaF) was measured to be 4.969(2)[10] eV, revealing a relativistic enhancement in the series of alkaline earth monofluorides. The results are in agreement with a relativistic coupled-cluster prediction of 4.981(7) eV, incorporating up to quantum electrodynamics corrections. Using the same computational methodology, an improved calculation for the dissociation energy (𝐷 0 ) of 5.54(5) eV is presented. This confirms that RaF joins the group of diatomic molecules for which 𝐷 0 > IP, paving the way for precision control and interrogation of its Rydberg states.

Wilkins, S. G. [Massachusetts Inst. of Technology ↗
DOE OSTI2021

Abelian SU(N) 1 chiral spin liquids on the square lattice

In the physics of the Fractional Quantum Hall (FQH) effect, a zoo of Abelian topological phases can be obtained by varying the magnetic field. Aiming to reach the same phenomenology in spin-like systems, in this work we propose a family of SU(N)-symmetric models in the fundamental representation, on the square lattice with short-range interactions restricted to triangular units, a natural generalization for arbitrary N of an SU(3) model studied previously where time-reversal symmetry is broken explicitly. Guided by the recent discovery of SU(2) 1 and SU(3) 1 chiral spin liquids (CSL) on similar models we search for topological SU(N) 1 CSL in some range of the Hamiltonian parameters via a combination of complementary numerical methods such as exact diagonaliza- tions (ED), infinite density matrix renormalization group (iDMRG) and infinite Projected Entangled Pair State (iPEPS). Extensive ED on small (periodic and open) clusters up to N = 10 and an innovative SU(N)-symmetric version of iDMRG to compute entanglement spectra on (infinitely-long) cylinders in all topological sectors pro- vide unambiguous signatures of the SU(N) 1 character of the chiral liquids. An SU(4)-symmetric chiral PEPS, constructed in a manner similar to its SU(2) and SU(3) analogs, is shown to give a good variational ansatz of the N = 4 ground state, with chiral edge modes originating from the PEPS holographic bulk-edge correspondence. Finally, we discuss the possible observation of such Abelian CSL in ultracold atom setups where the possibility of varying N provides a tuning parameter similar to the magnetic field in the physics of the FQH effect.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2016

Kinetics of Aggregation with Choice

Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tails of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Identifying Entangled Physics Relationships Through Sparse Matrix Decomposition to Inform Plasma Fusion Design

We report a sustainable burn platform through inertial confinement fusion (ICF) has been an ongoing challenge for over 50 years. Mitigating engineering limitations and improving the current design involves an understanding of the complex coupling of physical processes. While sophisticated simulation codes are used to model ICF implosions, these tools contain necessary numerical approximation but miss physical processes that limit predictive capability. Identification of relationships between controllable design inputs to ICF experiments and measurable outcomes (e.g., neutron yield, neutron velocity, areal density) from performed experiments can help guide the future design of experiments and development of simulation codes, to potentially improve the accuracy of the computational models used to simulate ICF experiments. We use sparse matrix decomposition methods to identify clusters of a few related design variables. Sparse principal component analysis (SPCA) identifies groupings that are related to the physical origin of the variables (laser, hohlraum, and capsule). A variable importance analysis finds that in addition to variables highly correlated with neutron yield, such as picket power and laser energy, variables that represent a dramatic change of the ICF design, such as number of pulse steps, are also very important. The obtained sparse components are then used to train a random forest (RF) regression surrogate for predicting total yield. The RF performance on the training and testing data compares with the performance of the RF trained using all the design variables considered. This work is intended to inform design changes in future ICF experiments by augmenting the expert intuition and simulation results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Background - Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. Results - We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. Conclusions - Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Using Apptainer in a Pilot-based Distributed Workload

GlideinWMS is a pilot and pressure-based workload manager for distributed scientific computing. Many experiments like CMS and Fermilab’s Neutrino experiments use it to provision elastic clusters for their analysis and simulations, split into close to a million concurrent jobs. Most user jobs require containers, and the pilots use Apptainer to set up the desired platform. For the pilots that run as regular batch jobs, Apptainer is safer, lighter, and easier to use than other containerization solutions. Many images used by the pilots are expanded SIF images distributed via the CernVM-FS: this combination is very efficient. At Fermilab, for example, we store on GitHub Dockerfiles that mimic the platform in the worker nodes of local clusters. GitHub workflows build and push the images to Docker Hub, and a service periodically pulls and converts them to the expanded SIF images in the CernVM-FS, so the scientists can find a familiar environment everywhere. Apptainer has also been used to run services inside the pilot jobs, like benchmarks that characterize the worker node being used, or a Triton Inference Server that allows sharing a GPU with all the jobs that run in parallel on a node.

Mambelli, Marco [Fermilab] (ORCID:0000000294892681↗
NASA NTRS1988

Be-10 and Al-26 contents of eucrites - Implications for production rates and exposure ages

This paper presents the Be-10 contents of 20 and the Al-26 contents of nine eucrites. Most have Be-10 production rates between 16 and 26 dpm/kg. The average value of 21.8 dpm/kg agrees to within 10 percent with the value expected and does not support the suggestion that the eucrites received an unusually low flux of cosmic rays during the last few million years. Measured Be-10 and Al-26 contents are consistent with semiempirical calculations of nuclear production rates. The Al-26 contents provide a basis for computing shielding-corrected Ar-38 exposure ages of eucrites which show little evidence for clustering. Relatively more eucrites than diogenites are younger than 20 Ma.

Aylmer, D.↗