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At least 775 records · Page 43

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of a Reference Model for Molten-Salt-Cooled Pebble-Bed Reactor Using SAM

To support the development and utilization of the SAM code for fluoride-salt-cooled high-temperature pebble-bed reactor (PB-FHR) safety analysis and licensing, an effort was devoted to developing reference models for PB-FHR primary loop and the reactor cavity cooling system (RCCS). A reference standard problem of a prototypical reactor design is foundational to NRC and industry to verify the adequacy of computer codes and evaluation models for a specific reactor type. The SAM code was enhanced for the reference PB-FHR model development, including a 1D-3D flow coupling scheme and conjugate heat transfer between porous media and solid structures. The reference FHR primary loop model was developed based on the UC Berkeley Mk1 FHR design with additional design features from the Kairos Power’s KP-FHR core. The PB-FHR core is modeled by a two-dimensional porous medium while the rest of the primary loop is represented by a SAM one-dimensional model. A SAM one-dimensional primary loop model was also developed for comparison using a single channel approach for the reactor core. Furthermore, the water-based NSTF cavity was modeled using SAM multi-dimensional flow module, to assist in evaluating SAM capabilities of modeling the emergency heat removal systems relying on RCCS concepts.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Data and code from: Selective oxidation of 3-hydroxypropionic acid to malonic acid over Pd/C: Mechanistic and kinetic study

Malonic acid (MA) is a high-value dicarboxylic acid with strong industrial demand, yet its current production heavily relies on petrochemical feedstocks. Here, we report the first systematic study for the sustainable production of MA via oxidation of 3-hydroxypropionic acid (3-HP) with a Pd/Carbon catalyst. The effects of oxidant type (O2 and H2O2), pH, and temperature on the reaction chemistry were comprehensively evaluated. Guided by experimental observation and DFT-calculated thermochemical energetics, reaction networks for 3-HP oxidation with both oxidants are proposed and validated through kinetic modeling. MA was identified as the primary oxidation product, while further oxidation yields acetic acid and oxalic acid. The kinetic model validated the network, displaying excellent agreement (R2 > 0.95). Kinetic observations also enabled a direct comparison between O2 and H2O2 and revealed their distinct behaviors. The model was further developed into a temperature-time map, providing insight into conditions that maximize MA production. Malonic acid selectivity of 56.9 % and yield of 50.5 % were achieved at 3 bar oxygen, equimolar NaOH:3-HP ratio, and 50 °C.

3-Hydroxypropionic Acid↗

Validation of 3D MHD simulations of Ne/D 2 mixed shattered pellet injection in JET

Nonlinear 3D magnetohydrodynamic (MHD) modeling of shattered pellet injection (SPI) in JET tokamak plasmas is performed with the JOREK code. The study focuses on the validation of simulation result with respect to experimental observations, addressing in particular figures of merit for the efficiency of the SPI, as a technique to mitigate thermal loads by injecting radiative impurities like neon during the thermal quench (TQ) phase of disruptions. A set of JET pulses with neon/deuterium atomic mixture ratio in the shattered pellet varying from 10% to 100% provides the experimental data to be compared with. Simulations using different models for the ablation of solid fragments and the radiation of neon impurities are considered. Synthetic diagnostics are employed for a direct quantitative comparison with key JET diagnostic systems providing in particular radiation, electron temperature and density, and magnetic measurements. 3D radiation structures from MHD simulations are analyzed to estimate the toroidal asymmetry of radiation, which is difficult to measure in JET due to the presence of only two toroidally displaced multi-channel bolometry systems. JOREK simulations show that, before the TQ, the bulk of the radiation is concentrated in a toroidal region enclosing the radiating fragments that is missed by both multi-channel bolometers, suggesting a possible underestimation of the total radiation by such diagnostic systems in the pre-TQ phase. On the other hand, JOREK predicts that during the TQ the radiation becomes more toroidally symmetric, with positive implications for the heat load to plasma facing components.

JOREK↗

Verification of the ENDF/B-VII.1 Based MC 2 -3 Library Rev.1

The MC 2 -3 code, developed by Argonne National Laboratory under the DOE-NE NEAMS program, is a multigroup cross section generation code for fast reactor applications. Last year, the ENDF/B-VII.0 (E70) MC 2 -3 library, which has been extensively used, verified, and validated over a long period, was intensively reverified and updated to support the commercial grade dedication (CGD) requirement of the TerraPower Natrium project. This year, the ENDF/B-VII.1 (E71) MC 2 -3 library, the preliminary version of which was generated several years ago, was regenerated and rigorously verified to support the Natrium project as well as the completion of verification of the E71 library. The E71 library was verified using the process developed during the verification of the E70 library, including comparisons of cross sections with the NJOY-generated cross sections, comparisons of the resolved resonance cross sections with those using the PEDNF library, and comparison of total cross sections with the sum of partial cross sections. Additional verifications were conducted to ensure that the benchmark problem solutions with the E71 library are reasonable compared to the corresponding Monte Carlo solutions. Furthermore, the E71 gamma library was generated, which includes data for prompt gamma, delayed gamma, and delayed beta as well as neutron and gamma heating. The gamma library was verified at the level of individual isotopes. The EBR-II core solutions from MC 2 -3/ DIF3D and MCNP were compared, demonstrating that those solutions in terms of k-effective and assembly powers were in good agreement.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Graphite Oxidation Studies Irradiated Graphite, GIF Summary, ASME Task Force, ASTM Activities

Introduction Comparison of Graphite Oxidation Rates for Irradiated and Unirradiated NBG-25 (Rebecca Smith and Austin Matthews, INL) Annealing effect over range of oxidation temperatures Irradiation effect (~6.5 dpa) over range of oxidation temperatures Dose dependency of irradiation effect Generation IV International Forum High Level Deliverable Summary of DOE ART Historic Oxidation Research (Cristian Contescu, ORNL) Publications issued over the last ~10 years Acute and chronic oxidation ASME Graphite Oxidation Task Force (C. Contescu, Paul Ryan, ORNL, Joe Bass, A. Matthews, R. Smith, INL) Collaborative effort headed by ORNL and engaging INL and others Initial review of relevant oxidation discussion in ASME code ASTM Activities (C. Contescu) Virtual Meetings New and Revised Standards

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Assessment of UTP A 2133 Mn as a Matching Filler Metal for Alloy 800H in Section III, Division 5 Applications

Six alloys are qualified in the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code (BPVC) for elevated-temperature nuclear components. Due to reactor design alloy restrictions and motivation to improve operational efficiency and plant lifetimes, it is necessary to maximize the usefulness of qualified alloys. One of these alloys is Alloy 800H, which is qualified for a maximum temperature of 760°C and a maximum 300,000-hour service life. However, the welding filler metals qualified to join Alloy 800H have stress rupture factors that reduce the allowable weldment strength by factors as low as 0.59 times the Alloy 800H base metal. In an effort to improve the weldment creep-rupture performance, or to increase the stress reduction factor, non-code qualified filler metals are under investigation by the Department of Energy?s Advanced Reactor Technologies program. For this investigation, UTP A 2133 Mn filler metal (Fe-Cr-Ni-Mn-Nb) was used to join 0.5 in. thick Alloy 800H plate to demonstrate passing an ASME BPVC Section IX weld qualification. The multi-pass, pulsed GTAW process showed successful weld qualification results, and additional property measurements were conducted to compare previous analyses of Alloy 82 and Alloy 617 filler metals. Future work will evaluate the cross-weld creep-rupture performance of the UTP A 2133 Mn in comparison to Alloy 82 and Alloy 617 filler metals.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Quantitative Performance Assessment of Proxy Apps and Parents (ECP Proxy App Project Milestone ADCD-504-9)

This report presents highlights of these efforts. Section 2 describes work that has been done to compare the performance of proxy applications on AMD MI60 vs. Nvidia V100 GPUs. So far only a small set of ECP proxies are running on AMD GPUs, but we will continue to expand this analysis as additional proxies become available. We find that although the MI60 and V100 have nearly the same measured memory bandwidth, memory bound proxy app kernels perform 20-30% worse on the MI60. Further work is needed to refine these comparisons to determine whether the root cause is due to differences in the hardware, software stack, platform specific optimization, or some combination of the three. Section 3 describes our continuing effort to find methods to accurately assess the similarity of proxies and parents. We have recently seen very encouraging results using a cosine similarity metric. This technique uses the angle between two vectors of hardware performance counters to characterize the similarity (or difference) between two applications or proxies. We show not only that several widely used proxies are highly similar to their parents, but also that they differ from non-related codes. We also show that cosine similarity can be used to identify gaps and redundancies in suites and even to gain insight into the effects of architectural differences between platforms. Our work on assessing the Exascale toolchain is ongoing. Our successes with performance measurement tools are evident from the data provided in this report. However, our assessments across the broader tool chain are still too incomplete to provide a meaningful report at this time. We will continue to assess tools and work with vendors and third party developers as issues are identified.

97 MATHEMATICS AND COMPUTING↗

Higher-order space-charge stability in anisotropic beams: Vlasov-Poisson derivation, refined dispersion relations, and stability charts

The Hofmann stability chart is used to screen working points in space-charge-dominated linacs. We identify two errors in its published higher-order dispersion relations: missing $(1\mp2\hatη^2/α)$ factors in the third-order $S^4$ coupling residues, and a sign error in the stated isotropic reduction of the fourth-order relation. Both corrections follow from Hofmann's Vlasov-Poisson equations without fitted parameters. They reproduce coherent tune-shift coefficients in the author's later monograph that the printed forms miss by 24% and 127%. Mode-resolved figures from a published application agree with the corrected relations and reject the printed forms, indicating an inconsistency between the 1998 equations and the calculations underlying those tested figures. We quantify the effect on the non-oscillatory stability chart. Inside the adopted $S^2\le10$ comparison domain, printed and corrected forms disagree on 0.73-2.11% of cells, with no preferred direction. Among excluded cells, disagreement reaches 22%, and the printed relation over-predicts instability at every sampled anisotropy. This concentration may help explain why the errors persisted, although it does not establish their historical cause. For PIP-II, the corrected chart flags four of thirty-two evaluable periods, including one on a third-order odd branch missed by a second-order screen. This count covers non-oscillatory modes only and remains conditional on an unresolved factor-five disagreement between two codes on transverse emittance growth.

Pathak, Abhishek [Fermilab] (ORCID:000000021704208↗

Representativity error scaling of models of the high temperature test facility

Error scaling is a critical step toward the validation of modeling capabilities for high-temperature gas-cooled reactors (HTGRs). Extensive effort is being made to bring HTGRs into the validation basis of numerous thermal-hydraulics codes. Here, this paper demonstrates how systems-level codes can be leveraged to perform error scaling analyses between an experimental facility and a plant-to-be facility. Specifically, we focus on two conduction cooldown experiments from the High Temperature Test Facility (HTTF) and the General Atomics 350 MW th modular high-temperature gas-cooled reactor (MHTGR-350). The error scaling methodology employed in this study is representativity, which in the context of this work was used to quantify how well experiments captured the physics of the plant facility by comparing sensitivity vectors between the two facilities. In addition, two different RELAP5–3D models of the HTTF were included in the comparison to determine if modeling methodologies notably impact the representativity results. The key figures of merit are the maximum block temperature and the coolant outlet temperature. The time-dependent maximum block temperature had a low representativity of below 0.1 for both models across both transients. The coolant outlet temperature had a higher representativity of around 0.6 for both models during the pressurized conduction cooldown, but it was below 0.2 for the depressurized conduction cooldown. Overall, the HTTF experiments were not representative of the transients in the MHTGR-350. However, these results can play a significant role in informing future potential experiments for HTGR systems that iterate on what the HTTF accomplished.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

TRISO fuel performance analysis: Uncertainty quantification toward optimization

Tri-structural isotropic (TRISO) fuel particles are a fuel form being considered for potential use in next-generation nuclear reactors (i.e., high-temperature gas-cooled reactors). Though the TRISO fuel manufacturing process has continually advanced in recent years, particle comparisons still reveal statistical variations and uncertainties in terms of geometric configurations and material properties. Given that the physical processes ongoing in TRISO fuel particles during reactor operation are highly correlated with each other, a small degree of uncertainty in one model may lead to significant uncertainty in another. This makes appropriate uncertainty quantification of TRISO fuel particles essential. However, one may wonder about the extent to which the current version of TRISO particles has been optimized, and whether any room remains for further improvements. This paper quantifies TRISO fuel performance model uncertainties that stem from geometric and material data. For this analysis, the BISON code was used, and the Advanced Gas Reactor (AGR)-2 experiment served as a reference case. A total of 10 5 calculations was performed for the uncertainty and optimization analysis, altering the geometric and material data within their uncertainty range. Lastly, the optimization potential of TRISO particles is evaluated from a fuel performance perspective.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Resonant Slow Extraction Simulation using Bmad

Simulations of slow extraction and transport of charged particle beams from synchrotrons requires careful modeling and experimentation. In this paper, we outline how the Bmad modeling software was adapted and developed to run third-integer resonant extraction simulations of beams at Brookhaven National Laboratory’s Booster synchrotron. Further, we show experimental comparisons of the slowly extracted beams transferred to the NASA Space Radiation Laboratory (NSRL) transport line. In this process, beam passes through a stripping foil element at the extraction point, which, along with stripping remaining electrons from the beam ions, acts as a scatterer to modify the phase space, moving to a more Gaussian-like distribution. This modification to the beam helps generate a uniform beam at the beam line’s target location; which is necessary for the variety of experiments performed at the facility. During this work, beam energy loss and multiple scattering by foil routines were built in conjunction with the Bmad code developers and are now integrated into the software.

43 PARTICLE ACCELERATORS↗

High fidelity actuator line data from 9 turbine wind farm simulations using ExaWind

This data was generated with the ExaWind code suite (https://github.com/Exawind) to investigate the performance of different Active Wake Mixing turbine control in a wind farm situated in a stable atmospheric boundary layer. All cases correspond to a 3x3 wind farm in a 10km x 10km domain using a total mesh size that varied between 1.6 X 10^9 to 1.85 X 10^9 grid cells. The simulations were run across 1800-2000 GPUs on Frontier. The case description and data generation process is fully documented in Yalla, G. R., Brown, K., Cheung, L., Houck, D., deVelder, N., and Balaji, J. (2025). "Estimating annual energy production of wake mixing control strategies including comparisons to wake steering." Wind Energy Sciences (https://doi.org/10.5194/wes-2025-250).

17 WIND ENERGY↗

Radiation Shielding Analysis of Linac Extension Area in APS Using FLUKA and PHITS Monte Carlo Radiation Transport Codes

The Linac extension area tunnel can accept 300- to 500-MeV electrons for experiments. Radiations from various normal and accident beam loss scenarios were analyzed with the FLUKA and PHITS Monte Carlo radiation transport codes. In normal beam loss scenarios, the beam was dumped on the horizontal and vertical beam dumps, while the accident scenarios were horizontal and vertical mis-steered beams that can occur due to incorrect beam energy and magnet settings. The extent of beam deviation, which was established using particle tracking studies, was used to define the beam directions in the Monte Carlo transport calculations. Further, a mis-steered condition, where the beam was not intercepted by the dumps, was also analyzed. For the horizontal dump, the PHITS results above the berm were higher for neutrons and somewhat lower for photons, compared to the FLUKA results. Comparison of the secondary particle yields from FLUKA and PHITS from an Al block with dimensions comparable to what was used in the beam dumps showed a 40% higher neutron yield and a 10% lower photon yield. Finally, to ensure compliance with Argonne National Laboratory's shielding policy, the design of the horizontal beam dump was modified, and additional shielding was recommended.

FLUKA↗

Gas-Cooled High-Temperature Pebble-Bed Reactor Reference Plant Model Updates

This work presents the latest improvements to, and investigations performed with, the pebble-bed high-temperature gas-cooled reactor (PB-HTGR) reference plant models for the United States Nuclear Regulatory Commission. These models serve as the foundation for the future development of detailed design evaluation models based on license applications. The reference plant models have been developed with the Comprehensive Reactor Analysis Bundle, or BlueCRAB, which is the code suite proposed for non-light-water reactor systems safety analysis. It incorporates various simulation tools developed by the Nuclear Energy Advanced Modeling and Simulation program, including the Griffin code for reactor physics, the Pronghorn and SAM codes for core thermal fluids, the BISON code for solid conduction and fuel performance, and the SAM code for system analysis. The primary objective of the work that was performed was to assess BlueCRAB’s level of readiness for modeling a PB-HTGR. To do so, we first developed numerical models in BlueCRAB that include the key physics for this technology to ensure an adequate level of fidelity for modeling PB-HTGR core performance and for performing multiphysics simulations for equilibrium core conditions and different accident scenarios. Then we simulated transient scenarios, including depressurized and pressurized loss of forced cooling accidents, over-cooling, and control rod withdrawal events with delayed and prompt supercritical reactivity insertions. The analysis in this report includes comparisons of the 2D thermal fluid porous media models in Pronghorn and SAM, and comparisons of coupled SAM/Griffin/SAM and coupled Pronghorn/Griffin for depressurized and pressurized loss of forced cooling, over-cooling, and control rod withdrawal events. In addition, we compare 3D, 2D, and 0D/PKE neutronic models for the two control rod withdrawal scenarios with coupled Pronghorn/Griffin. The comparisons show that the BlueCRAB models lead to physically intuitive solutions for the scenarios examined. The changes in the various scalar and vector fields, such as neutron flux, power, temperature, density, pressure, and velocity, are within the expected ranges, and their distributions can be explained by the system response of the transients and the geometric and material variations. Several comparisons suggest that the porous media models in Pronghorn and SAM can lead to similar solutions, even though they are based on different methodologies. This work further highlights the need for flexible tools with various levels of fidelity to cover the breadth and depth of needs that may arise in future technical evaluations of the PB-HTGR. We believe that the BlueCRAB capabilities will be a significant asset for confirmatory analyses in order to resolve important safety questions.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Multi-scale fission product release model with comparison to AGR data

TRistructural ISOtropic (TRISO) particle fuel is central to several advanced, high-temperature reactor designs. Each particle consists of a fuel kernel encapsulated by three layers of carbon and ceramics that prevent the release of fission products and ensure physical integrity. Despite outstanding retention properties, fission product release has been observed from intact particles. To better understand and quantify fission product release from TRISO particles, a multiscale, mechanistic model of fission product transport is being developed by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. Previous work focused on silver (Ag) transport and improved Ag release predictions. The work described in this report builds on this experience to better understand cesium (Cs) transport in silicon carbide (SiC), the main barrier to the release of fission products. Atomistic simulations provide bulk and grain boundary (GB) Cs diffusivities in SiC, which are used by phase field simulations in the mesoscale code Marmot to determine the temperature, microstructure, and irradiation-dependent Cs diffusivity at the mesoscale in SiC. This approach attributes the different temperature regimes experimentally observed for Cs diffusivities in SiC to a transition from bulk-dominated diffusivity at high temperatures to a GB-dominated regime at low temperatures, providing new insight. The multiscale, mechanistic effective diffusivity is then implemented in the fuel performance code BISON and further validated by comparing Cs release predictions from Advanced Gas Reactor (AGR)-1 and AGR-2 post-irradiation measurements. The new model improves BISON’s predictability. This document also reports improvements made on Ag transport modeling by accounting for different GB types having different diffusivities. Moreover, this report details preliminary efforts to model palladium (Pd) attack of the SiC at the mesoscale using a phase field approach. Pd attack and its impact on accelerated Ag transport remains a misunderstood phenomenon, and we use the model to demonstrate that the formation of lamellae that has been observed in experiments can be explained by the reaction of Pd with SiC to form alternating layers of graphite and Pd 2 Si. This effort aims to improve our understanding of the reaction and eventually provide a model for BISON to account for Pd penetration and its effects on fission product release.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Validation of realistic Monte Carlo plasma gamma-ray source on JET discharges

A novel modelling methodology has been developed for the creation of a realistic plasma gamma-ray source for Monte Carlo transport simulations in the tokamak JET. The methodology couples the TRANSP code for plasma transport calculations with the MCNP Monte Carlo particle transport code, thus connecting plasma physics with gamma-ray transport. Here, we present the validation of the developed source methodology by comparing calculated gamma-ray spectra with measurements performed at JET. The validation focuses on gamma-ray spectra measured by the tangential gamma-ray spectrometer during two JET three ion RF scenario discharges, performed in the JET 2019 deuterium experimental campaign. For validation the calculated plasma gamma-ray spectrum was combined with the neutron induced prompt gamma-ray background, originating in the vacuum vessel, and scaled to absolute values calculating the total number of plasma gamma-ray and neutron emitting reactions. The comparison between calculated and measured gamma-ray spectra shows good agreement with the shape of the calculated gamma-ray spectra matching that of measurements for both studied discharges. Moreover, the calculated absolute values of the gamma-ray spectra were of the same order of magnitude at the position of the gamma-ray detector located at the end of a long line-of-sight in a biological shield. Finally, the comparison has validated the developed plasma gamma-ray source methodology for MCNP photon transport calculations at JET. The validation provides a basis for the developed plasma gamma-ray source to be used as a support for the development of future tokamaks such as DEMO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SAS4A/SASSYS-1 Verification Testing for Sodium Fast Reactor Applications (Acceptance Testing Report)

SAS4A/SASSYS-1 (SAS) is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal- cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over fifty years and represents a critical investment in safety analysis capabilities for the U.S. Department of Energy. To support demonstration of software pedigree and confirm key functional requirements, this report has been generated to provide detailed verification of the software. Although SAS was developed to support the analysis of any liquid-metal-cooled nuclear reactor, the acceptance testing described in this document focuses on the verification of SAS capabilities as they relate to pool-type Sodium Fast Reactors (SFRs). This report includes documentation of the test problem definition, analytical solution(s), computational solution(s), acceptance criteria, comparisons of analytical/computational solutions, and determination of acceptance of the computational solution(s). Deviations from acceptance criteria are noted.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗