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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Recent proteomic advancements have revealed widespread Nε-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance in bacteria. The spontaneous, non-specific nature of this modification in prokaryotes obscures its biological role, necessitating prokaryotic specific in vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles and regulation dynamics of acetyl-lysine in vivo with the precise incorporation of a suite of non-canonical amino acids, including acetyl-lysine analogs. However, its use has been largely restricted to E. coli strains due to challenges associated with implementation and optimization of the technology in more diverse bacterial strains. Here, we present a bacterial host-agnostic, readily optimizable GCE platform designed to site-specifically incorporate non-canonical amino acids into target proteins within living bacteria. We further demonstrate the versatility of this technology by showcasing, for the first time, the successful incorporation of acetyl-lysine in a non- E. coli bacterium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Transport-based initial conditions for heavy-ion collisions at finite densities

Here, we employ the SMASH transport model to provide event-by-event initial conditions for the energy-momentum tensor and conserved charge currents in hydrodynamic simulations of relativistic heavy-ion collisions. We study the fluctuations and dynamical evolution of three conserved charge currents (net baryon, net electric charges, and net strangeness) with a four-dimensional lattice-QCD-based equation of state, NEOS-4D, in the hydrodynamic phase. Out-of-equilibrium corrections at the particlization are generalized to finite densities to ensure the conservation of energy, momentum, and the three types of charges. These theoretical developments are integrated within the X-SCAPE code as a unified framework for studying the nuclear matter properties in the Beam Energy Scan program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Ameliorating the Courant-Friedrichs-Lewy condition in spherical coordinates: A double FFT filter method for general relativistic MHD in dynamical spacetimes

Numerical simulations of merging compact objects and their remnants form the theoretical foundation for gravitational wave and multimessenger astronomy. While Cartesian-coordinate-based adaptive mesh refinement is commonly used for simulations, spherical-like coordinates are more suitable for nearly spherical remnants and azimuthal flows due to lower numerical dissipation in the evolution of fluid angular momentum, as well as requiring fewer numbers of computational cells. However, the use of spherical coordinates to numerically solve hyperbolic partial differential equations can result in severe Courant-Friedrichs-Lewy (CFL) stability condition time step limitations, which can make simulations prohibitively expensive. This paper addresses this issue for the numerical solution of coupled spacetime and general relativistic magnetohydrodynamics evolutions by introducing a double fast Fourier transform (FFT) filter and implementing it within the fully message passing interface (mpi)-parallelized sphericalnr framework in the einstein toolkit. In conclusion, we demonstrate the effectiveness and robustness of the filtering algorithm by applying it to a number of challenging code tests, and show that it passes these tests effectively, demonstrating convergence while also increasing the time step significantly compared to unfiltered simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Micropinch formation dynamics in X pinches

High temporal resolution x-ray streak camera studies of micropinch formation in Cu hybrid x pinches reveal key plasma conditions. Analysis of Ne-like Cu lines indicate an average electron temperature of about 200 eV and 4.5×10 28 m -3 electron density. Here, the spectra suggest that the electron temperature jumps to about 1 keV, inferred from the continuum and the postcontinuum line emission that includes Li-like Cu lines. There is no sign of a rapid temperature change or a substantial surge in radiation emission during the 200 ps precontinuum x-ray burst, suggesting that the radiative collapse process does not play a major role in micropinch formation. Two-dimensional extended Magnetohydrodynamic (MHD) simulations, coupled to a collisional-radiative spectral analysis code, suggest the significance of the rapid radial implosion of high-temperature, low-density plasma, the axial outflow, and the dynamic plasma pressure in micropinch formation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Unprecedented cloud resolution in a GPU-enabled full-physics atmospheric climate simulation on OLCF’s summit supercomputer

Clouds represent a key uncertainty in future climate projection. While explicit cloud resolution remains beyond our computational grasp for global climate, we can incorporate important cloud effects through a computational middle ground called the Multi-scale Modeling Framework (MMF), also known as Super Parameterization. This algorithmic approach embeds high-resolution Cloud Resolving Models (CRMs) to represent moist convective processes within each grid column in a Global Climate Model (GCM). The MMF code requires no parallel data transfers and provides a self-contained target for acceleration. This study investigates the performance of the Energy Exascale Earth System Model-MMF (E3SM-MMF) code on the OLCF Summit supercomputer at an unprecedented scale of simulation. Hundreds of kernels in the roughly 10K lines of code in the E3SM-MMF CRM were ported to GPUs with OpenACC directives. A high-resolution benchmark using 4600 nodes on Summit demonstrates the computational capability of the GPU-enabled E3SM-MMF code in a full physics climate simulation.

58 GEOSCIENCES↗
DOE OSTI2023

Recent Developments in the R-Matrix Code SAMMY [Slides]

This presentation covers recent developments in the R-Matrix Code SAMMY. The presentation starts with a discussion around SAMMY releases. Secondly it provides updates in the program flow. The presentation concludes with goals and achievements in the modernization efforts.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Status Report on Fast Flux Test Facility Mechanistic Fuel Failure Experiment Analysis with BISON for Post Irradiation Examination Support

The renewed interest in metallic U-Zr nuclear fuel alloy has led to a drive for deeper understanding of the mechanisms driving the phenomena observed under irradiation conditions. The Department of Energy Advanced Fuel Campaign has developed infrastructure to support metallic fuel development, including Post Irradiation Examination (PIE) of legacy Fast Flux Test Facility (FFTF) Mechanistic Fuel Failure (MFF) experiments. The PIE performed on legacy FFTF MFF experiments gives insight on metallic fuel performance and can address the lack of knowledge and scarcity of reliable data identified in several studies over recent years. Unfortunately, PIE efforts can cost significant time and resources which can impede the progress of metallic U-Zr fuel development. Metallic U-Zr fuel performance modeling can be used to inform PIE efforts on regions of interest for relevant investigations and can help understand phenomena observed in PIE. This report demonstrates the current progress of FFTF MFF fuel performance simulations using the BISON fuel performance code and discusses the support provided by simulation to PIE efforts. Progress in temperature, profilometry, fission gas release, plenum pressure, and zirconium redistribution simulation results have been demonstrated.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

MassIVE MSV000100641 - Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli: Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.

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Alexander, William G. [Oak Ridge National Laborato↗
DOE OSTI2023

MSTor 2023 : A new version of the computer code for multistructural torsional anharmonicity, now with automatic torsional identification using redundant internal coordinates

The MSTor program is a computer program for calculating partition functions and thermodynamic functions of complex gas-phase molecules with multiple torsions; the multi-structural approximation with torsional anharmonicity (MS-T) can be used based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic (MS-LH) approximation or multi-structural local quasiharmonic (MS-LQ) approximation or by the dual-level MS-T method. Furthermore, the program package includes eight utility codes that can be used as stand-alone programs to help the user to generate the input files for the code or to generate comparison results. The 2023 version of MSTor includes a new capability, namely automatic identification of torsional modes with redundant internal coordinates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A code-to-code benchmark for magneto-convection in a horizontal duct

Liquid metals and magnetic fields are used in many technical applications such as metallurgy, crystal growth and nuclear fusion reactors. When an electrically conducting fluid moves in a magnetic environment, electric currents and electromagnetic forces are generated that affect velocity and pressure losses in the flow. These magnetohydrodynamic (MHD) interactions have to be investigated to optimize the engineering processes. The characteristics of MHD flows depend on the geometrical configuration, the strength of the applied magnetic field, the electrical properties of fluid and structural materials and the thermal conditions. In the so-called blankets for fusion reactors, where liquid metals are used to breed the plasma fuel component tritium and to extract the generated heat, magneto-convective flows play a crucial role in determining heat and mass transfer. Therefore, the availability of numerical codes to simulate this type of flow is mandatory and their validation is a necessary step to guarantee the reliability of the results. For that reason, a benchmark problem has been defined to simulate liquid metal flows in a horizontal rectangular duct heated from below and exposed to a non-uniform magnetic field. Results obtained by five research groups using different codes are compared.

benchmark↗
DOE OSTI2025

ZTF SN Ia DR2: Improved SN Ia colors through expanded dimensionality with SALT3+

Context. Type Ia supernovae (SNe Ia) are a key probe in modern cosmology, as they can be used to measure luminosity distances at gigaparsec scales. Models of their light curves are used to project heterogeneous observed data onto a common basis for analysis. Aims. The SALT model currently used for SN Ia cosmology describes SNe as having two sources of variability, accounted for by a color parameter c , and a “stretch” parameter x 1 . We extend the model to include an additional parameter we label x 2 , to investigate the cosmological impact of currently unaddressed light-curve variability. Methods. We constructed a new SALT model, that we dub “SALT3+”. This model was trained by an improved version of the SALTshaker code, using training data combining a selection of the second data release of cosmological SNe Ia from the Zwicky Transient Facility and the existing SALT3 training compilation. Results. We find additional, coherent variability in supernova light curves beyond SALT3. Most of this variation can be described as phase-dependent variation in g − r and r − i color curves, correlated with a boost in the height of the secondary maximum in i -band. These behaviors correlate with spectral differences, particularly in line velocity. We find that fits with the existing SALT3 model tend to address this excess variation with the color parameter, leading to less informative measurements of supernova color. We find that neglecting the new parameter in light-curve fits leads to a trend in Hubble residuals with x 2 of 0.039 ± 0.005 mag, representing a potential systematic uncertainty. However, we find no evidence of a bias in current cosmological measurements. Conclusions. We conclude that extended SN Ia light-curve models promise mild improvement in the accuracy of color measurements, and corresponding cosmological precision. However, models with more parameters are unlikely to substantially affect current cosmological results.

Kenworthy, W. D. (ORCID:0000000251535983)↗
DOE OSTI2023

Nanoparticle Catalyst Formation and Subsequent Sintering: Size-Distribution Fundamental Understanding and Catalyst Control via Mechanism-Enabled Population Balance Modeling (Final Report)

The challenge of elucidating the chemical mechanisms by which nano- and other particles form, and then using those mechanisms to understand, analyze, and ideally predict particle-size and particle-size distributions, was undertaken. Thanks to multi-year, longer-term DOE support each of these challenges was successfully met. The community is now able to both predict, and control in cases where the underlying mechanism of particle formation has been determined, the key PS and PSD that are, in turn, critical properties that strongly influence the catalytic and other physical properties of nano- and larger particles across nature.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Nuclear Data Sheets for A=203

Evaluated nuclear structure and decay data for all nuclei with mass number A=203 ( 203 Os, 203 Ir, 203 Pt, 203 Au, 203 Hg, 203 Tl, 203 Pb, 203 Bi, 203 Po, 203 At, 203 Rn, 203 Fr, 203 Ra) are presented. All available experimental data are compiled and evaluated, and best values for level and γ-ray energies, quantum numbers, lifetimes, γ-ray intensities and transition probabilities, as well as other nuclear properties, are recommended. Inconsistencies and discrepancies that exist in the literature are discussed. A number of computer codes (https://www-nds.iaea.org/public/ensdf_pgm/index.htm) developed by members of the NSDD network were used during the evaluation process. For example, the reported absolute γ-ray emission probabilities and their uncertainties were determined using the GABS code. Here, the γ-ray transition probabilities were determined using the RULER code and the corresponding uncertainties were estimated by means of a Monte-Carlo approach. This work supersedes the earlier evaluation by F.G. Kondev (2005Ko20), published in Nuclear Data Sheets 105, 1 (2005).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Nuclear Data Sheets for A=201

Evaluated nuclear structure and decay data for all nuclei with mass number A=201 ( 201 Os, 201 Ir, 201 Pt, 201 Au, 201 Hg, 201 Tl, 201 Pb, 201 Bi, 201 Po, 201 At, 201 Rn, 201 Fr, 201 Ra) are presented. All available experimental data are compiled and evaluated, and best values for level and γ-ray energies, quantum numbers, lifetimes, γ-ray intensities and transition probabilities, as well as other nuclear properties, are recommended. Inconsistencies and discrepancies that exist in the literature are discussed. A number of computer codes (https://wwwnds.iaea.org/public/ensdf pgm/index.htm) developed by members of the NSDD network were used during the evaluation process. For example, the reported absolute γ-ray emission probabilities and their uncertainties in various decay data sets were determined using the GABS code. The γ-ray transition probabilities were determined using the RULER code and the corresponding uncertainties were determined using a Monte-Carlo approach. In conclusion, this work supersedes the earlier evaluation by F.G. Kondev (2007Ko06), published in Nuclear Data Sheets 108, 365 (2007).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Toward exascale whole-device modeling of fusion devices: Porting the GENE gyrokinetic microturbulence code to GPU

GENE solves the five-dimensional gyrokinetic equations to simulate the development and evolution of plasma microturbulence in magnetic fusion devices. The plasma model used is close to first principles and computationally very expensive to solve in the relevant physical regimes. In order to use the emerging computational capabilities to gain new physics insights, several new numerical and computational developments are required. Here, we focus on the fact that it is crucial to efficiently utilize GPUs (graphics processing units) that provide the vast majority of the computational power on such systems. In this paper, we describe the various porting approaches considered and given the constraints of the GENE code and its development model, justify the decisions made, and describe the path taken in porting GENE to GPUs. We introduce a novel library called gtensor that was developed along the way to support the process. Performance results are presented for the ported code, which in a single node of the Summit supercomputer achieves a speed-up of almost 15× compared to running on central processing unit (CPU) only. Typical GPU kernels are memory-bound, achieving about 90% of peak. Our analysis shows that there is still room for improvement if we can refactor/fuse kernels to achieve higher arithmetic intensity. We also performed a weak parallel scalability study, which shows that the code runs well on a massively parallel system, but communication costs start becoming a significant bottleneck.

Germaschewski, K. (ORCID:0000000284956354)↗
DOE OSTI2025

Genome sequences of four novel Endozoicomonas strains associated with a tropical octocoral in a long-term aquarium facility

ABSTRACT We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.

Marques, Matilde (ORCID:0000000194430893)↗