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At least 469 records · Page 26

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DOE OSTI2026

L'Arlesienne de ROOT

Over many years, ROOT users have repeatedly stumbled over—and loudly rediscovered—the infamous 1 GB limit on individual I/O operations, a constraint that somehow survived long past the era when anyone thought a gigabyte was “a lot.” As experiments embraced ever-larger objects and collections, this limit became an increasingly unavoidable rite of passage. This contribution recounts the sustained, multi-year quest by ROOT I/O developers to finally retire this relic, navigating a maze of legacy APIs, memory-management assumptions, and integer boundaries that seemed determined to preserve the status quo. We describe how internal interfaces were carefully modernized to introduce fully 64-bit–capable code paths without breaking the mountains of existing user code that would definitely have noticed. With the limit now lifted, ROOT can finally handle multi-gigabyte objects in a single read or write operation, even when splitting them into an RNTuple is not an option (we’re looking at you, large RooWorkspaces and giant histograms), liberating users from yet another “fun” debugging adventure and clearing the way for the massive analyses of the HL-LHC and beyond.

Canal, Philippe G. [Fermilab] (ORCID:0000000277487↗

DOE OSTI2026

L'Arlesienne de ROOT

Canal, Philippe G. [Fermilab] (ORCID:0000000277487↗

DOE OSTI2020

Error field correction strategies in preparation to MAST-U operation

In magnetic fusion devices, unwanted non-axisymmetric magnetic field perturbations, known as error fields (EF), can have detrimental effects on plasma stability and confinement. Such EFs may originate from several sources, such as axi-symmetric coil misalignments, coil feeds, 3D structures in the wall surrounding the plasma, presence of ferromagnetic materials near the plasma surface, blanket materials in future devices. To minimize their impact on plasma performance and on the available operational space, it is important to identify the EF sources and develop EF control strategies. MAST Upgrade (MAST-U) is a spherical tokamak which will operate in the near future after a series of enhancements from the previous MAST experiment. To deliver a machine with EF amplitude low enough to allow a high quality experimental programme, systematic analysis of the intrinsic EF sources has been carried out for poloidal eld (P) and divertor (D) coils. To deliver a machine with EF amplitude low enough to allow a high quality experimental programme, systematic analysis of the intrinsic EF sources has been carried out for poloidal field (P) and divertor (D) coils, whose magnetic eld measurements were available when writing this paper. Such measurements reveal that P and D coils are 3D deformed and thus are responsible for intrinsic EFs, with mainly n=1 and n=2 toroidal mode numbers. In preparation to MAST-U operation, both passive and active EF control strategies have been adopted for n=1 and n=2 EFs compensation. Passive EF control consisted of installing finely each D and P coil within MAST-U device so as to minimize the intrinsic n=1 EF amplitude. The optimal coil alignment has been determined based on magnetic eld measurements and the corresponding 3D electro-magnetic modelling, and envisaged coil shift and tilt of 3.2 mm and 0.7 mrad, respectively, in the case of P coil named P4. Conversely, active control will be use during MAST-U operation to reduce the n=2 EF which is associated mainly with P4 and P5, as well. Since these coils have been re-used from the MAST device, studies attempting n=2 EF control, based on MAST plasmas, have been modelled utilizing the MARS-F code to interpret experimental results in MAST and to give hints for future n=2 EF control studies in MAST-U. Here, a model-based control set for n=2 EF control has been identified which would allow for the minimization of rotation braking, of the resonant magnetic field at the q=2 and of the plasma displacement in MAST-U, simultaneously.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii

The genome of Methanocaldococcus (Methanococcus) jannaschii DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated M. jannaschii, creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.org. This reannotation effort has resulted in 652 function assignments with enzyme roles, accounting for a third of the total protein-coding entries for this genome. The updated resource includes 883 reactions, 540 enzymes, and 142 individual pathways. Despite notable progress in computational genomics, more than a third of the genome remains functionally uncharacterized. The publicly available MjCyc pathway-genome database holds great potential for the wider community to conduct research on the biology of methanogenic Archaea.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Persistent mysteries of jet engines, formation, propagation, and particle acceleration: Have they been addressed experimentally?

Here, the physics of astrophysical jets can be divided into three regimes: (i) engine and launch (ii) propagation and collimation, (iii) dissipation and particle acceleration. Since astrophysical jets comprise a huge range of scales and phenomena, practicality dictates that most studies of jets intentionally or inadvertently focus on one of these regimes, and even therein, one body of work may be simply boundary condition for another. We first discuss long standing persistent mysteries that pertain the physics of each of these regimes, independent of the method used to study them. This discussion makes contact with frontiers of plasma astrophysics more generally. While observations theory, and simulations, and have long been the main tools of the trade, what about laboratory experiments? Jet related experiments have offered controlled studies of specific principles, physical processes, and benchmarks for numerical and theoretical calculations. We discuss what has been accomplished on these fronts. Although experiments have indeed helped us to understand certain processes, proof of principle concepts, and benchmarked codes, they have yet to solved an astrophysical jet mystery on their own. A challenge is that experimental tools used for jet-related experiments so far, are typically not machines originally designed for that purpose, or designed with specific astrophysical mysteries in mind. This presents an opportunity for a different way of thinking about the development of future platforms: start with the astrophysical mystery and build an experiment to address it.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

ORNL Contributions to the ENDF/B-VIII.1 Library [Slides]

For uranium and plutonium isotopes, evaluation work is converging to a stable configuration with an overall satisfactory benchmark performance (more information on the validation tests after CSEWG). Strontium evaluation was included in the repository library and successfully tested by processing codes relative to an alternative quantification of the external function. Cerium covariance matrices were updated to address review comments on the magnitude of the uncertainty. For future uncertainty quantification, theoretical observables should be properly decoupled from current measured guidelines. Tests to correctly include LP (from resonance parameters) fitted to measured energy-averaged data are in progress. Current ENDF files contains experimental LP data.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2024

Analysis of the ASME Code Rules for Subsection III-5-HHB (Composite Materials) for Current HTR Design Requirements

This document includes the critical analysis review of the American Society of Mechanical Engineers (ASME) Section III Division 5 Subsection HH Subpart B (HHB), including Mandatory Appendices, that was published in 2023. In the context of this document, reference to “the code” is specific to this subsection unless otherwise specified. A specific composites task group within the ASME Nonmetallic Design and Materials Working Group, with the support of external experts, was established to perform a gap analysis review. The significant findings are summarized here. The committee response with suggested action items are detailed in the body of the report.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Analytic model of electron transport through and over non-linear barriers

Tunneling barriers are an essential component of electron sources, sensors, detectors, and vacuum nanoelectronics, and a pivotal factor in their performance, but the barriers themselves routinely depart from the analytic models used to model their behavior. Here, a new formalism is developed to analytically and accurately model emission through and over barriers associated with depletion layers, nanotip barriers, and MIM structures. The transmission probability for depletion layer and metal-insulator-metal (MIM) and metaloxide-semiconductor (MOS) barriers is accurately modeled as the electron energy exceeds the barrier height using approaches designed for rapid implementation demanded by simulation codes, and extensible to general barriers. The models supersede conventional thermal and field models in depletion and MIM/MOS barrier studies. Thermal-field methods are used to treat the transmission probability, and shape factor methods to treat the tunneling factor. Analytic formulae for current density are obtained. The methods ease device simulation and characterization of current-voltage relations for emerging technologically interesting barriers with better accuracy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Observation of synergy between lower hybrid waves at two frequencies in EAST

Synergistic effects between two frequencies of lower hybrid (LH) waves—operating at 2.45 and 4.6 GHz—were observed in experiment on EAST for the first time. At low density (ne,lin≈2.0×1019 m−3), simultaneous injection of a 65/35 mix of 2.45/4.6 GHz power achieved an lower hybrid current drive efficiency that was 25% higher than what should be expected from the linear combination of the two sources. The experiment was interpreted with time-dependent simulations, using the equilibrium and transport solver TRANSP, coupled with the ray-tracing code GENRAY and the Fokker–Planck solver CQL3D. For each discharge, profiles of current and hard x-rays from simulation and measurement agree within uncertainties. An examination of the electron distribution function indicates that the LH synergy is supported by the increased width of the LH resonance plateau in the simultaneous injection case compared to independent injection.

Choi, W. (ORCID:0000000268912300)↗

DOE OSTI2023

Ray-based cross-beam energy transfer modeling for broadband lasers

Broadband lasers have the potential to mitigate cross-beam energy transfer (CBET) in direct-drive inertial confinement fusion (ICF) experiments. Furthermore, a quantitative assessment of the bandwidth required for CBET mitigation necessitates the development of broadband ray-based CBET models that can be implemented in the radiation-hydrodynamic codes that are used to design ICF experiments. Two different approaches to broadband ray-based CBET modeling (discrete and fixed spectrum) are developed and compared to wave-based calculations. Both approaches give good agreement with wave-based calculations in ICF-relevant configurations. Full-scale 3D calculations show that the bandwidth required for adequate CBET mitigation increases with increasing scale and drive intensity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing

Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m 1 G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m 1 G37 in tRNA Pro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNA Pro bound to either cognate or slippery codons to determine how the m 1 G37 modification prevents mRNA frameshifting. The structures reveal that certain codon–anticodon contexts and the lack of m 1 G37 destabilize interactions of tRNA Pro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m 1 G37 stabilizes the interactions of tRNA Pro with the ribosome in the context of a slippery mRNA codon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

BEYONDPLANCK III. Commander3

We describe the computational infrastructure for end-to-end Bayesian cosmic microwave background (CMB) analysis implemented by the BeyondPlanck Collaboration. The code is called Commander3. It provides a statistically consistent framework for global analysis of CMB and microwave observations and may be useful for a wide range of legacy, current, and future experiments. The paper has three main goals. Firstly, we provide a high-level overview of the existing code base, aiming to guide readers who wish to extend and adapt the code according to their own needs or re-implement it from scratch in a different programming language. Secondly, we discuss some critical computational challenges that arise within any global CMB analysis framework, for instance in-memory compression of time-ordered data, fast Fourier transform optimization, and parallelization and load-balancing. Thirdly, we quantify the CPU and RAM requirements for the current BEYONDPLANCK analysis, finding that a total of 1.5 TB of RAM is required for efficient analysis and that the total cost of a full Gibbs sample for LFI is 170 CPU-hrs, including both low-level processing and high-level component separation, which is well within the capabilities of current low-cost computing facilities. The existing code base is made publicly available under a GNU General Public Library (GPL) license.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A new synthetic correlation electron cyclotron emission diagnostic for validating nonlinear gyrokinetic simulations of electron temperature turbulence

To validate nonlinear gyrokinetic simulations of electron temperature turbulence, the experimental correlation electron cyclotron emission (CECE) measurements are to be compared using a synthetic CECE diagnostic, which generates modeled CECE measurement quantities by implementing realistic measurement parameters (e.g., spatial and wavenumber resolutions, radial location, etc.) to nonlinear gyrokinetic simulations. In this work, we calculate the radial and vertical spatial and wavenumber transfer functions, which are defined by the electron cyclotron emission emissivity radial profile and vertical probing antenna pattern, respectively. These transfer functions are applied to nonlinear gyrokinetic simulations of electron temperature turbulence using the continuum gyrokinetic code. A simultaneous comparison of the experimental electron temperature turbulence power spectrum and root-mean-square (RMS) level, as well as the radial correlation length with the new synthetic CECE diagnostic at a core location ρ ∼ 0.75 in an L-mode DIII-D tokamak plasma, is presented. Here, the preliminary result shows that the synthetic CECE output underestimates the RMS level by ∼42% and overestimates the radial correlation length by ∼40%.

Cyclotron radiation↗

DOE OSTI2025

Simulations of edge and SOL turbulence in diverted negative and positive triangularity plasmas

Optimizing the performance of magnetic confinement fusion devices is critical to achieving an attractive fusion reactor design. Negative triangularity (NT) scenarios have been shown to achieve excellent levels of energy confinement, while avoiding edge localized modes. Modeling turbulent transport in the edge and SOL is key in understanding the impact of NT on turbulence and extrapolating the results to future devices and regimes. Previous gyrokinetic turbulence studies have reported beneficial effects of NT across a broad range of parameters. However, most simulations have focused on the inner plasma region, neglecting the impact of NT on the outermost edge. In this work, we investigate the effect of NT in edge and scrape-off layer simulations, including the magnetic X-point and separatrix. For the first time, we employ a multi-fidelity approach, combining global, non-linear gyrokinetic simulations with drift-reduced fluid simulations, to gain a deeper understanding of the underlying physics at play. First-principles simulations using the GENE-X code demonstrate that in comparable NT and PT geometries, similar profiles are achieved, while the turbulent heat flux is reduced by more than 50% in NT. Comparisons with results from the drift-reduced fluid turbulence code GRILLIX suggest that the turbulence is driven by trapped electron modes. The parallel heat flux width on the divertor targets is reduced in NT, primarily due to a lower spreading factor S.

GENE-X↗

DOE OSTI2020

Genomic analyses implicate noncoding de novo variants in congenital heart disease

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10 -4 ). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10 -5 ). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10 -3 ). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10 -5 ). Overall, our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Hunting for dark matter and new physics with GECCO

We outline the science opportunities in the areas of searches for dark matter and new physics offered by a proposed future MeV gamma-ray telescope, the Galactic Explorer with a Coded Aperture Mask Compton Telescope (GECCO). We point out that such an instrument would play a critical role in opening up a discovery window for particle dark matter with mass in the MeV or sub-MeV range, in disentangling the origin of the mysterious 511 keV line emission in the Galactic Center region, and in potentially discovering Hawking evaporation from light primordial black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

we report a multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗