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DOE OSTI2020

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

ABSTRACT Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Validation of the SCEPTRE Boltzmann-CSD Solver

A new Boltzmann-CSD solver has been developed within the SCEPTRE radiation-transport code, based on the 1st-order form of the transport equation, using discontinuous finite elements in space and energy and discrete ordinates in angle. The Boltzmann-CSD solver has been validated against experimental data for electron energy deposition distributions and for electron emission spectra. Comparison of the calculated results with experimental data shows excellent agreement for many of the test configurations and reasonable agreement for other test configurations. The tests have also been modeled with the ITS Monte Carlo code, which also shows excellent to reasonable agreement with the SCEPTRE results and experimental data. The SCEPTRE Boltzmann-CSD solver relies on electron cross sections generated by the legacy CEPXS code, which currently is limited to electron-only Boltzmann-CSD cross sections. Performing full electron-photon radiation transport with the Boltzmann-CSD solver will require further development in the cross section generating code. For the energy- deposition calculations, neglecting photon transport results in at most about 5% overprediction of the energy deposition for high-energy electrons on high-Z targets, and relatively insignificant difference for the other test configurations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Small-scale validation tests for MFIX-Exa CFD-DEM

This report describes several bench-scale fluidization experiments that can be used to validate the CFD-DEM method as encapsulated in the MFIX-Exa code. The five cases considered are the cold-flow fluidized beds of Müller et al., Link et al. (spout-fluid), and Goldschmidt et al. (bi-disperse), the hot fluidized bed of Patil et al., and the adsorbing fluidized bed of Li et al. and Janssen. In most cases, MFIX-Exa with “standard” or “typical” CFD-DEM settings, the Gidaspow drag model, and the Gunn heat transfer provide a relatively good prediction of the quantities considered: mean void fraction profiles, mean velocity profiles, fluctuating velocity profiles, mean particle temperature and segregation index. These results, with other verification and validation tests reported elsewhere, contribute to a body of work providing confidence and credibility in CFD predictions from the MFIX-Exa code.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Nondestructive and destructive assay for forensics characterization of weapons-grade plutonium produced in LEU irradiated in a thermal neutron spectrum

A post-irradiation examination (PIE) of an enriched uranium sample was performed to advance a nuclear forensics methodology, based on intra-elemental nuclide ratios. The PIE was carried out on a few milligrams of low enriched uranium dioxide (LEUO 2 ) sample, irradiated to a burnup of 1 GWd/MTU. The PIE of the LEUO 2 sample provided the concentration of selected plutonium and fission product nuclides ( 239 Pu, 240 Pu, 241 Pu, 91 Y, 95 Zr, 95 Nb, 103 Ru, 133 Cs, 134 Cs, 135 Cs, 137 Cs, 136 Ba, 138 Ba, 140 Ba, 140 La, 141 Ce, 144 Ce, 149 Sm, 150 Sm, 152 Sm, 153 Eu, and 154 Eu). The PIE supported validation of the MCNP (Monte Carlo N-Particle neutronics simulation code) predicted concentration of these nuclides in the irradiated LEUO 2 sample. This study showed that most of the MCNP predicted nuclide concentrations were within 15% and several within 10% compared to the PIE results. Furthermore, gamma and mass spectrometry of nuclides in irradiated LEUO 2 enabled the determination of uranium burnup and time since irradiation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Application of New Los Alamos OPLIB Opacities in Solar Modeling Using the Mesa Code

The Sun provides the only local laboratory to test our understanding of stellar physics. The production, then, of valid dynamical models of the Sun is critical to how we think about other stars. Despite improvements in modeling methodologies and abundance measurements, solar models continue to reproduce errors in convection zone depth and surface helium abundance compared to helioseismic observations. Using the 1D stellar evolution code MESAstar, this work first evaluates the effect of changes to timestep resolution and mixing length theory on model outputs. A standard test case is then constructed with both GS98 and AGSS09 abundances using OP and OPAL opacities before implementing the new Los Alamos OPLIB opacities. It is shown that, when using GS98 abundances, OPLIB opacities improve agreement with helioseismic inference of the convection zone base radius, R czb , by 1.68-σ and 1.19-σ compared to OP and OPAL, respectively, while worsening agreement with the inferred envelope helium mass fraction, Y surf , by 0.63-σ and 0.98-σ for OP and OPAL.

14 SOLAR ENERGY↗

DOE OSTI2020

CTF Validation and Verification (V.4.2)

Coolant-Boiling in Rod Arrays- Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for Light Water Reactor (LWR) analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of nine conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and has been used and modified by several institutions over the last several decades. COBRA-TF is also used at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently became the PSU RDFMG version of COBRA-TF (CTF). One part of the improvement process includes validating the methods in CTF. This document seeks to provide a certain level of certainty and confidence in the predictive capabilities of the code for the scenarios it was designed to model-rod bundle geometries with operating conditions that are representative of prototypical Pressurized Water Reactor (PWR)s and Boiling Water Reactor (BWR)s in both normal and accident conditions. This is done by modeling a variety of experiments that simulate these scenarios and then presenting a qualitative and quantitative analysis of the results that demonstrates the accuracy to which CTF is capable of capturing specific quantities of interest.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

ASME Code change proposal to implement new universal high temperature constitutive models for Section III, Division 5

This report completes work on a universal high temperature constitutive model suitable for use with the ASME Boiler & Pressure Vessel Code Section III, Division 5 rules for the design by inelastic analysis of Class A nuclear reactor components. The goals of this work are to provide a simple model form that adequately captures the high temperature response of materials and can be applied to any future Code material. Additionally, the report describes an automated process for calibrating a model against test data. The idea is to simplify the effort required to generate a constitutive model for an arbitrary material, provided test data is available. This will accelerate the process of qualifying new Code materials in the future. In addition, the report provides calibrated models and detailed validation comparisons to test data for five currently-qualified or soon-to-be qualified materials: 316H, Grade 91, Alloy 800H, Alloy 617, and Alloy 709. The report surveys the available data for the remaining two ASME Class Materials --- 2.25Cr-1Mo and 304H --- concluding that there is enough data data to generate a model for 2.25Cr-1Mo steel provided some additional sources of non-public data can be included in the test database, but that a dedicated cyclic test campaign would be needed for 304H. Supplemental material includes the full text of an ASME Code change proposal to incorporate the models for the four currently-qualified Class A material, detailed validation comparisons to test data for the five material models, and input files for reference implementations of the constitutive models in the NEML and NEML2 modeling frameworks.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Exploring phage–host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage–host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.

Bacterial Pathogenesis↗

DOE OSTI2022

PICSAR-QED: a Monte Carlo module to simulate strong-field quantum electrodynamics in particle-in-cell codes for exascale architectures

Abstract Physical scenarios where the electromagnetic fields are so strong that quantum electrodynamics (QED) plays a substantial role are one of the frontiers of contemporary plasma physics research. Investigating those scenarios requires state-of-the-art particle-in-cell (PIC) codes able to run on top high-performance computing (HPC) machines and, at the same time, able to simulate strong-field QED processes. This work presents the PICSAR-QED library, an open-source, portable implementation of a Monte Carlo module designed to provide modern PIC codes with the capability to simulate such processes, and optimized for HPC. Detailed tests and benchmarks are carried out to validate the physical models in PICSAR-QED, to study how numerical parameters affect such models, and to demonstrate its capability to run on different architectures (CPUs and GPUs). Its integration with WarpX, a state-of-the-art PIC code designed to deliver scalable performance on upcoming exascale supercomputers, is also discussed and validated against results from the existing literature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

CTF Validation and Verification: Version 4.3

Coolant-Boiling in Rod Arrays- Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) analysis. It uses a two-fluid, three-field (i.e., fluid film, fluid drops, and vapor) modeling approach. Both subchannel and 3D Cartesian forms of nine conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and has been used and modified by several institutions over the last several decades. COBRA-TF is also used at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently became the CTF. One part of the improvement process includes validating the methods in CTF. This document seeks to provide a certain level of certainty and confidence in the predictive capabilities of the code for the scenarios it was designed to model—rod bundle geometries with operating conditions that are representative of prototypical pressurized water reactor (PWR)s and boiling water reactor (BWR)s in both normal and accident conditions. This is done by modeling a variety of experiments that simulate these scenarios and then presenting a qualitative and quantitative analysis of the results that demonstrates the accuracy to which CTF is capable of capturing specific quantities of interest.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

CTF Validation and Verification: Version 4.4

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

OC6 project Phase IV: validation of numerical models for novel floating offshore wind support structures

Abstract. This paper provides a summary of the work done within Phase IV of the Offshore Code Comparison Collaboration, Continued with Correlation and unCertainty (OC6) project, under International Energy Agency Wind Technology Collaboration Programme Task 30. This phase focused on validating the loading on and motion of a novel floating offshore wind system. Numerical models of a 3.6 MW horizontal-axis wind turbine atop the TetraSpar floating support structure were compared using measurement data from a 1:43-Froude-scale test performed in the University of Maine's Alfond Wind–Wave (W2) Ocean Engineering Laboratory. Participants in the project ran a series of simulations, including system equilibrium, surge offsets, free-decay tests, wind-only conditions, wave-only conditions, and a combination of wind and wave conditions. Validation of the models was performed by comparing the aerodynamic loading, floating support structure motion, tower base loading, mooring line tensions, and keel line tensions. The results show a relatively good estimation of the aerodynamic loading and a reasonable estimation of the platform motion and tower base fore–aft bending moment. However, there is a significant dispersion in the dynamic loading for the upwind mooring line. Very good agreement was observed between most of the numerical models and the experiment for the keel line tensions.

17 WIND ENERGY↗

DOE OSTI2024

Development and validation of fully open-source R2S shutdown dose rate capabilities in OpenMC *

We present the first fully open-source capabilities for shutdown dose rate (SDR) calculations of fusion energy facilities based on the Rigorous 2-Step (R2S) methodology. These capabilities have been implemented in the OpenMC Monte Carlo particle transport code, building on its existing capabilities while also leveraging new features that have been added to the code to support SDR calculations, such as decay photon source generation. Each of the individual physics components in the R2S workflow—neutron transport, activation, decay photon source generation, and photon transport—have been verified through code-to-code comparisons with MCNP6.2 and FISPACT-II 4.0. These comparisons generally demonstrate excellent agreement between codes for each of the physics components. The full cell-based R2S workflow was validated by performing a simulation of the first experimental campaign from the Frascati Neutron Generator (FNG) ITER dose rate benchmark problem from the Shielding INtegral Benchmark Archive and Database (SINBAD). For short cooling times, the dose calculated by OpenMC agrees with the experimental measurements within the stated experimental uncertainties. For longer cooling times, an overprediction of the shutdown dose was observed relative to experiment, which is consistent with previous studies in the literature. Altogether, these features constitute a combination of capabilities in a single, open-source codebase to provide the fusion community with a readily-accessible option for SDR calculations and a platform for rapidly analyzing the performance of fusion technology.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Machine Learning-enabled Scalable Performance Prediction of Scientific Codes

Hardware architectures become increasingly complex as the compute capabilities grow to exascale. Here, we present the Analytical Memory Model with Pipelines (AMMP) of the Performance Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware architecture parameters as input and predicts runtime of that code on the target hardware platform, which is defined in the input parameters. PPT-AMMP transforms the code to an (architecture-independent) intermediate representation, then (i) analyzes the basic block structure of the code, (ii) processes architecture-independent virtual memory access patterns that it uses to build memory reuse distance distribution models for each basic block, and (iii) runs detailed basic-block level simulations to determine hardware pipeline usage. PPT-AMMP uses machine learning and regression techniques to build the prediction models based on small instances of the input code, then integrates into a higher-order discrete-event simulation model of PPT running on Simian PDES engine. We validate PPT-AMMP on four standard computational physics benchmarks and present a use case of hardware parameter sensitivity analysis to identify bottleneck hardware resources on different code inputs. We further extend PPT-AMMP to predict the performance of a scientific application code, namely, the radiation transport mini-app SNAP. To this end, we analyze multi-variate regression models that accurately predict the reuse profiles and the basic block counts. We validate predicted SNAP runtimes against actual measured times.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

The Completion of Surrogate Testing for Low-Temperature TEX and a Look Towards the Future

To address the mounting need for below room temperature nuclear data validation, the Low-Temperature Thermal Epithermal eXperiments (LT-TEX) have been designed. Validation of low-temperature neutron cross sections is necessary to verify any operation at temperatures below room temperature which is typically observed in environments far from the equator. For example, a fissile material transportation truck may routinely observe ambient temperatures down to -40°C, which is the lower temperature bound of the normal conditions of transportation defined in the United States Title 10 Code of Federal Regulations §71.71c2. Additionally, sub-room temperature benchmarks can validate newly produced cross sections, that include novel thermal scattering laws, from North Carolina State University.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

A Look Towards the Execution of the Low-Temperature TEX Experimental Campaign

To address the mounting need for below roomtemperature nuclear data validation, the Low-Temperature Thermal Epithermal eXperiments (LT-TEX) have been designed. Validation of low-temperature neutron cross sections is necessary to verify any operation at temperatures below room temperature which is typically observed in environments far from the equator. For example, a fissile material transportation truck may routinely observe ambient temperatures down to -40°C, which is the lower temperature bound of the normal conditions of transportation defined in the United States Title 10 Code of Federal Regulations §71.71c2. Additionally, sub-room temperature benchmarks can validate newly produced cross sections, that include novel thermal scattering laws, from North Carolina State University.

LT-TEX↗

DOE OSTI2023

Nuclear Criticality Safety Integral Experiment Covariance Determination

Integral benchmarks for criticality safety and nuclear data validation require expensive uncertainty quantification studies. Commonly, the uncertainty quantification ignores correlations between experiments that share components. Experiments such as the TEX (Thermal/Epithermal eXperiments) campaigns consist of many shared parts between experiments, such as fuel, which creates a strong correlation in their errors. While these correlations are known to exist, they are often not estimated due to the complexity of such calculations. This paper describes a software package that uses an intuitive method of determining the covariance for each of the experimental components, providing a correlation matrix for each family of parts across the multiple cases examined within a benchmark. The code uses the TEX-HEU campaign as a proof of concept, and we show that the correlations can be calculated with information commonly found in ICSBEP (International Criticality Safety Benchmark Evaluation Project) benchmarks. The estimated covariances are used in χ 2 trending studies to evaluate their impact on nuclear data validation. The covariance determination code can be easily integrated into current benchmark evaluations as well as reevaluating legacy benchmark uncertainties. Uncertainty correlation calculations should become the baseline for criticality safety integral experiment benchmarks and can now be easily calculated with the described software package.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Code for paper "Reconstructing an Implosion with Space-Time Smoothing of Velocimetry Traces"

New diagnostics to obtain high-temporal resolution observation of surface velocity provide a rich collection of data from high-explosive (HE) experiments. Using this data to estimate the temporal evolution of an imploding, HE-driven surface is of great interest for validating simulation of the physical system and for design of future experiments. This is the code for a paper in which we propose a method for using a Gaussian process to estimate the surface position over time and provide uncertainty estimates on that reconstruction accounting for measurement error, uncertainty to sparse spatial sampling velocity data, and robustness to outlying observations. In the paper, the code is applied on data from a hemispherical HE implosion experiment. This code is for release with the paper for peer-review, replicating the results and making the figures from the paper.

Grosskopf, Michael↗