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At least 793 records · Page 44

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↗

Machine Learning Moment Closure Models for the Radiative Transfer Equation III: Enforcing Hyperbolicity and Physical Characteristic Speeds

This is the third paper in a series in which we develop machine learning (ML) moment closure models for the radiative transfer equation. In our previous work (Huang et al. in J Comput Phys 453:110941, 2022), we proposed an approach to learn the gradient of the unclosed high order moment, which performs much better than learning the moment itself and the conventional $P_N$ closure. However, while the ML moment closure has better accuracy, it is not able to guarantee hyperbolicity and has issues with long time stability. In our second paper (Huang et al., in: Machine learning moment closure models for the radiative transfer equation II: enforcing global hyperbolicity in gradient based closures, 2021. arXiv:2105.14410), we identified a symmetrizer which leads to conditions that enforce that the gradient based ML closure is symmetrizable hyperbolic and stable over long time. The limitation of this approach is that in practice the highest moment can only be related to four, or fewer, lower moments. In this paper, we propose a new method to enforce the hyperbolicity of the ML closure model. Motivated by the observation that the coefficient matrix of the closure system is a lower Hessenberg matrix, we relate its eigenvalues to the roots of an associated polynomial. Here, we design two new neural network architectures based on this relation. The ML closure model resulting from the first neural network is weakly hyperbolic and guarantees the physical characteristic speeds, i.e., the eigenvalues are bounded by the speed of light. The second model is strictly hyperbolic and does not guarantee the boundedness of the eigenvalues. Several benchmark tests including the Gaussian source problem and the two-material problem show the good accuracy, stability and generalizability of our hyperbolic ML closure model.

97 MATHEMATICS AND COMPUTING↗

BoBa

BoBa is a C++ software library for working with large matrices, tensors, and tensor decompositions. The library provides tools for dense matrix and tensor operations, tensor decompositions, and tensor decomposition methods that support modern CPU and GPU architectures. It includes portable abstractions for linear algebra, tensor algebra, and multidimensional computation. BoBa is intended for scientific computing applications that involve large multidimensional data sets or high dimensional mathematical models. Its capabilities support tasks such as data compression, linear algebra, efficient numerical computation, and the development of scalable algorithms for heterogeneous hardware. Tutorials, tests, and example applications are included to help users learn and apply the library.

Yao, Jin [Lawrence Livermore National Laboratory (↗

Microstructural evolution in shear-punch tests: A comparative study of pure Cu and Cu-Cr alloy

Understanding the mechanisms behind microstructural evolution during shear deformation has been a long-standing area of interest. However, establishing a connection between microstructure, mechanical properties, and extent of shear deformation is challenging and requires refined experimental approaches. Shear-punch testing (SPT) provides a controlled method to introduce shear into small volumes of material that later can be subjected to detailed microstructural characterization. In this study, we utilize an SPT device to induce shear deformation to pure copper and a binary copper-chromium alloy. Electron backscatter diffraction and transmission electron microscopy were used to study the mechanisms of plastic deformation after SPT. Our results indicate that shear deformation of pure Cu produces a dense network of intercepting microshear bands upon sustained deformation. Twin boundaries undergo degradation into high angle grain boundaries due to simultaneous deviation from the axis-angle pair condition of 60° misorientation on [111] direction. The presence of 50% volume Cr particles in the soft Cu matrix fundamentally altered the shear deformation mechanism. Preferential deformation of the Cu matrix led to accelerated shear-induced formation of low and high angle grain boundaries, and subsequent grain refinement. Comparatively, no grain refinement occurred in pure Cu at a strain ~10 times larger (ϵ = 4.73) than that of the copper-chromium case (ϵ = 0.42). Overall, our study sheds light on the microstructural evolution during shear deformation and highlights the significant influence of particle reinforcements on the shear deformation mechanisms of metals.

36 MATERIALS SCIENCE↗

Nuclear data uncertainty propagation applied to the versatile test reactor conceptual design

We report the Versatile Test Reactor (VTR) currently under development is a 300 MWth sodium-cooled fast reactor (SFR) fueled with ternary metal alloy fuel, which aims to accelerate the testing of advanced nuclear fuels, materials, instrumentation, and sensors in high flux environments that are necessary to license the next generation of advanced reactor concepts. To support the VTR design process, uncertainties associated with the nuclear data has been propagated through the reactor core neutronics calculation to global parameters of interest, such as the core multiplication factor, kinetic parameters, and various reactivity feedback coefficients, following the sensitivity based uncertainty propagation approach. By folding the sensitivity coefficients, separately computed by the generalized perturbation theory code PERSENT and Monte Carlo code Serpent 2, with the variance-covariance matrices from COMMARA-2.0, we obtain the reaction-wise, isotope-wise, and overall uncertainties for each response of interest due to nuclear data uncertainty. With Serpent 2, the statistical error of the uncertainty is obtained by propagating the statistical error of the sensitivity coefficients through the same process using a newly developed uncertainty propagation method. From both codes, the overall top uncertainty contributors are found to be the cross section of Fe-56 elastic scattering, Na-23 elastic scattering, and U 238 inelastic scattering. The large contributions of the Fe-56 elastic scattering cross sections to global parameters are due to its relatively large relative uncertainty of 5–10% in nuclear data and the large volume of Fe-containing reflector assemblies in the fairly compact VTR core design. Both codes agreed well for the overall uncertainty estimates of all responses of interest, except the delayed neutron fraction, prompt neutron generation time, and the coolant density feedback coefficient, where Serpent 2 yielded a much larger value than PERSENT due to the large statistical error of sensitivity coefficients. The calculated uncertainties are also compared to those associated with other SFR cores. Another outcome of this study is a variance-covariance matrix of reactivity coefficients, which can be used in the subsequent uncertainty propagation to the system level to investigate the impact of identified uncertainties on system responses in the safety analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials

We report the MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ( C ij ) obtained from any ab-initio density-functional theory (DFT) code. The current version of this package reads the output of VASP, ABINIT, and Quantum Espresso codes (but it can be easily generalized to any other DFT code) and performs the appropriate post-processing of elastic constants as per the requirement of the user. This program can also detect the input structure's crystal symmetry and test the mechanical stability of all crystal classes using the Born-Huang criteria. Various useful material-specific properties such as elastic moduli, longitudinal and transverse elastic wave velocities, Debye temperature, elastic anisotropy, 2D layer modulus, hardness, Pugh's ratio, Cauchy's pressure, Kleinman's parameter, and Lame's coefficients, can be estimated using this program. Another existing feature of this program is to employ the ELATE package (2016) [29] and plot the spatial variation of several elastic properties such as Poisson's ratio, linear compressibility, shear modulus, and Young's modulus in three dimensions. Further, the MechElastic package can plot the equation of state (EOS) curves for energy and pressure for a variety of EOS models such as Murnaghan, Birch, Birch-Murnaghan, and Vinet, by reading the inputted energy/pressure versus volume data obtained via numerical calculations or experiments. This package is particularly useful for the high-throughput analysis of elastic and mechanical properties of materials.

2D materials↗

Towards Improving luminosity using optics tuning and data-driven methods

The results of Run 24 experiments at Relativistic Heavy Ion Collider (RHIC) for improving luminosity using optics tuning are presented in this study. In the first experiment, MADx matching was used to output magnet strengths corresponding to specific s star movements around Interaction Region 8 (IR8). The corresponding Zero Degree Calorimeter (ZDC) signal was measured in place of luminosity, and Bayesian Optimization aids search of optimal movements. It was found that values retrieved from matching were inaccurate, resulting in negative feedback loops. The second experiment focused on calculating accurate s star movements. The matching method was replaced with a linear sensitivity matrix, directly relating optics to power supply, and its null space was used to fit constraints such as hysteresis effects. At the experiment, beam losses were observed at collimators around boundary of IR8, which were fixed for the third experiment. Dynamic mode decomposition was also introduced to improve quality of turn-by-turn (TBT) data as well as accuracy and consistency of optics measurements at IR8. These improvements will be tested in the experiment of next RHIC run for luminosity optimization.

Accelerator Physics↗

BISON TRISO Modeling Advancements and Validation to AGR-1 Data

BISON is a finite element-based nuclear fuel performance code. Among its unique characteristics are its ability to model 1D, 2D, and 3D geometries and its applicability to a wide variety of nuclear fuels. For the last eight years, BISON has included a beginning capability to model tri-structural isotropic (TRISO) fuel. Recently, interest in TRISO fuel has grown, and a significant effort has been made to improve BISON’s capabilities in this area. Capability development has occurred for each material present in TRISO fuel particles: the buffer, inner pyrolytic carbon, silicon carbide, and outer pyrolytic carbon layers, as well as the fuel kernel. New elastic, creep, swelling, thermal expansion, thermal conductivity, and fission gas release (FGR) models are available. New models for the graphite matrix are also now available. Another important addition is the ability to perform statistical failure analysis of large samples of fuel particles. This new capability, which continues to grow, enables evaluation of failure due to pressure or crack formation by analyzing many thousands of particles. This enables realistic calculations of fission product release from the many particles in a TRISO-fueled reactor. These capabilities were checked via regression and verification tests. A large number of code benchmarking problems were also run, showing that BISON’s results closely match those of other software tools. Finally, a significant validation effort was completed in which fission product release, measured as part of the AGR-1 capsule experiments, was compared to BISON outputs. BISON outputs compared very well to the experimental data and to PARFUME results. Interest in BISON’s TRISO capabilities is growing, with the U.S. Nuclear Regulatory Commission (NRC) and Westinghouse Electric Company receiving training during the past year. Multiple other entities have expressed interest in or are actively using BISON. Kairos Power, LLC, has a strong partnership with Idaho National Laboratory (INL) regarding the use of BISON for TRISO analysis. While its capabilities still continue to grow, BISON has already become a powerful tool for TRISO analysis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Role of Cr Content in Microstructure, Creep, and Oxidation Resistance of Alumina-Forming Austenitic Alloys at 850–900 °C

Creep-rupture properties and oxidation behavior of a series of alumina-forming austenitic (AFA) alloys with variations of Cr contents, based on Fe-(13.5-18)Cr-25Ni-4Al-1.5Nb-0.1C in weight percent, have been evaluated at 850–900 °C. The study investigates material responses in the properties and microstructure through compositional modifications in AFA alloys, targeting performance optimization of alloys under high-temperature, corrosive industrial environments. The creep-rupture life of the alloys at 850 °C and 30MPa monotonically decreased with increasing Cr content, which was correlated with changes in secondary phase volume fractions, such as the reduction in B2-NiAl + Laves-Fe2Nb and increase in Sigma-FeCr with Cr content. The oxidation test at 900 °C in a water-vapor containing environment revealed a range of Cr content from 13.9 to 15.7 wt.%, enabling the formation of stable, protective external alumina scale as well as preventing internal oxidation/nitridation for up to total 7000 h exposure. On the other hand, the alloys with >16.7 wt.% Cr formed Sigma precipitates, which caused a reduction in not only Cr but also Al in the austenite matrix, resulting in less oxidation resistance than other alloys. The findings will guide the further optimization of material performance in the AFA alloy series.

36 MATERIALS SCIENCE↗

Self-Assembled TiN-Metal Nanocomposites Integrated on Flexible Mica Substrates towards Flexible Devices

The integration of nanocomposite thin films with combined multifunctionalities on flexible substrates is desired for flexible device design and applications. For example, combined plasmonic and magnetic properties could lead to unique optical switchable magnetic devices and sensors. In this work, a multiphase TiN-Au-Ni nanocomposite system with core–shell-like Au-Ni nanopillars embedded in a TiN matrix has been demonstrated on flexible mica substrates. The three-phase nanocomposite film has been compared with its single metal nanocomposite counterparts, i.e., TiN-Au and TiN-Ni. Magnetic measurement results suggest that both TiN-Au-Ni/mica and TiN-Ni/mica present room-temperature ferromagnetic property. Tunable plasmonic property has been achieved by varying the metallic component of the nanocomposite films. The cyclic bending test was performed to verify the property reliability of the flexible nanocomposite thin films upon bending. This work opens a new path for integrating complex nitride-based nanocomposite designs on mica towards multifunctional flexible nanodevice applications.

42 ENGINEERING↗

Friction and wear of nuclear graphite exposed to molten FLiNaK salt environment

This report formally documents the completion of the Advanced Reactor Technologies Level 3 Milestone (M3TG-25OR0501104), “Initiate graphite wear studies of graphite samples exposed to molten salt environment,” due August 1, 2025. The report summarizes the ongoing activities aimed at characterizing the friction and wear behavior of graphite in molten LiF–NaF–KF (FLiNaK) salt environment. The wear and friction behavior of self-mated ET-10 nuclear graphite were tested at varying temperatures (550°C and 650°C), contact loads (40 and 80 N) and sliding speeds (1 and 10 mm/s) in a controlled argon environment. The results were compared to the wear and friction behavior of the same graphite material in a dry argon environment. This report presents initial studies on the friction and wear behavior of graphite in sliding contact mode, with future work focused on investigating the graphite matrix materials, as well as rolling and impact contact modes. The outcomes of this report could provide insights into assessing the integrity of the graphitic components of pebble-bed fluoride salt–cooled high-temperature reactors (PB-FHRs) to enhance their safe operation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Studies on the Encapsulation of Brine Generated from a Process Using Selective Electrodialysis Reversal

This topical report summarizes the laboratory testing, geochemical modeling, and mineralogical testing conducted to examine the efficacy of wastewater encapsulation for the brine generated from the Saltworks Flex electrodialysis reversal technology. Within the laboratory testing, the short- and long-term physical properties of seven separate mix designs were examined along with the leaching of each mix design. Additionally, geochemical thermodynamic modeling was used along with mineralogical analyses to help gain a fundamental understanding of the chemistry involved in the encapsulation process. Encapsulation is a process that results in the immobilization of constituents of interest by creating an engineered material that contains the waste within its matrix, both physically and chemically, in such a manner that the receiving environment is protected from adverse effects. Within the context of this study, encapsulation mix designs involved mixing the Saltworks brine with fly ash and various additives, principally lime (calcium oxide) and cement, to form a paste that eventually sets and hardens into a monolith upon placement in a landfill. Moisture conditioning fly ash with wastewater sources for on-site landfill disposal is a process that is in use at some sites and has been presented as a viable option to dispose of liquid wastes. However, because chemical reactions that can lead to sequestration of constituents of interest are not optimized, leaching can occur. Therefore, in this study, mixes were created to mimic moisture conditioning, as well as engineered pastes of varying mix designs. The study found that engineered encapsulation mixes provide significant resistance to leaching compared to moisture conditioning alone. The best performing encapsulation mix used lime as the additive, which proved superior to the use of cement. After 90 days of curing, this encapsulated mix was 5.5 times stronger than the moisture conditioned mix. Additionally, this mix exhibited an approximate 2.5 order of magnitude drop in hydraulic conductivity compared to the moisture conditioned mix. When comparing leaching, nearly all the chloride was found to evolve from the moisture conditioned mix, whereas only 6.7% of the chlorine contained in the best performing encapsulated mix leached out. Mineralogical analysis via X-ray diffraction (XRD) showed a significant concentration of the chloride sequestering mineral, Friedel’s salt, in the best performing encapsulation mix, whereas none was observed in the moisture conditioned mix, pointing to it being the primary chemical mechanism for chloride retention, along with the physical impermeability of the material. With respect to the modeling study, the model was successful in predicting the presence of most mineral phases observed in the XRD analysis.

01 COAL, LIGNITE, AND PEAT↗

Towards a real-time computation of timelike hadronic vacuum polarization and light-by-light scattering: Schwinger Model tests

Hadronic vacuum polarization (HVP) and light-by-light scattering (HLBL) are crucial for evaluating the Standard Model predictions concerning the muon’s anomalous magnetic moment. However, direct first-principle lattice gauge theory-based calculations of these observables in the timelike region remain challenging. Discrepancies persist between lattice quantum chromodynamics (QCD) calculations in the spacelike region and dispersive approaches relying on experimental data parametrization from the timelike region. Here, we introduce a methodology employing 1+1-dimensional quantum electrodynamics (QED), i.e. the Schwinger Model, to investigate the HVP and HLBL. To that end, we use both tensor network techniques, specifically matrix product states, and classical emulators of digital quantum computers. Demonstrating feasibility in a simplified model, our approach sets the stage for future endeavors leveraging digital quantum computers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A High-Throughput Method to Define Additive Manufacturing Process Parameters: Application to Haynes 282

This paper demonstrates how an analytical and experimental method can be used to rapidly define the 45 additive manufacturing settings for a new alloy where the process parameters were previously unknown. A nickel-based superalloy, Haynes 282, was chosen for the analysis. An experimental matrix of focused processing parameters was predicted with a dimensionless number and 100 samples were printed using the Selective Laser Melting technique. High-throughput measurements validated the predicted process conditions needed to achieve desired density and hardness. The whole process was completed in 16 hours. The new technique was confirmed with analytical processing maps adopted by the metal additive manufacturing community. With the predicted set of process parameters, microstructural characterizations and tensile testing were used to confirm the predictions. The resultant as-fabricated microstructures have refined length scales of both microsegregation and secondary phase distributions. As a result, the mechanical properties were comparable within the predicted processing window and exhibited high strength and high ductility.

Laser Material Processing↗

Thermo-mechanical behavior of hypoeutectic Ni-Y-Zr alloys

Microstructure refinement and optimized alloying can improve metallic alloy performance: stable nanocrystalline (NC) alloys with immiscible second phases, e.g., Cu-Ta, are stronger than unstable NC alloys and their coarse-grained (CG) counterparts, but higher melting point matrices are needed. Hypoeutectic, CG Ni-Y-Zr alloys were produced via arc-melting to explore their potential as high-performance materials. Microstructures were studied to determine phases present, local composition and length scales, while heat treatments allowed investigating microstructural stability. Alloys had a stable, hierarchical microstructure with ~250 nm ultrafine eutectic, ~10 µm dendritic arm spacing and ~1 mm grain size. Hardness and uniaxial compression tests revealed that mechanical properties of Ni-0.5Y-1.8Zr (in wt%) were comparable to Inconel 617 despite the small alloying additions, due to its hierarchical microstructure. Here, uniaxial compression at 600 °C showed that ternary alloys outperformed Ni-Zr and Ni-Y binary alloys in flow stress and hardening rates, which indicates that the Ni 17 Y 2 phase was an effective reinforcement for the eutectic, which supplemented the matrix hardening due to increased solubility of Zr. Results suggest that ternary Ni-Y-Zr alloys hold significant promise for high temperature applications.

36 MATERIALS SCIENCE↗

MATAR: A performance portability and productivity implementation of data-oriented design with Kokkos

There is a need for simple, fast, and memory-efficient multidimensional data structures for dense and sparse storage that arise with numerical methods and in software applications. The data structures must perform equally well across multiple computer architectures, including CPUs and GPUs. For this purpose, we developed MATAR, a C++ software library that allows for simple creation and use of intricate data structures that is also portable across disparate architectures using Kokkos. Here, the performance aspect is achieved by forcing contiguous memory layout (or as close to contiguous as possible) for multidimensional and multi-size dense or sparse MATrix and ARray (hence, MATAR) types. Our results show that MATAR has the capability to improve memory utilization, performance, and programmer productivity in scientific computing. This is achieved by fitting more work into the available memory, minimizing memory loads required, and by loading memory in the most efficient order. This document describes the purpose of the work, the implementation of each of the data types, and the resulting performance both in some simple baseline test cases and in an application code.

97 MATHEMATICS AND COMPUTING↗

CO 2 -Soluble Nonionic Surfactants for Enhanced CO 2 Storage via In Situ Foam Generation

Geologic carbon storage (GCS) is a rapidly evolving technology with the potential to reduce the environmental impact of fos-sil fuels. Saline aquifers, which comprise a sandstone matrix with brine in the pores, make up much of the pore space availa-ble for CO 2 storage in the United States. When CO 2 is injected in saline aquifers, however, capillary fingering occurs and only a small percentage of the pore space is filled with CO 2 . This is due to the low viscosity of CO 2 , which is roughly ten times less viscous than brine. To address this problem, we tested the ability of inexpensive, commercially available nonionic surfactants to be dissolved in the injected CO 2 and increase the apparent viscosity of CO 2 by generating CO 2 -in-water foams in situ.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab initio estimation of E 2 strengths in Li 8 and its neighbors by normalization to the measured quadrupole moment

For electric quadrupole (E2) observables, which depend on the large-distance tails of the nuclear wave function, ab initio no-core configuration interaction (NCCI) calculations converge slowly, making meaningful predictions challenging to obtain. Nonetheless, the calculated values for different E2 matrix elements, particularly those involving levels with closely-related structure (e.g., within the same rotational band) are found to be robustly proportional. This observation suggests that a known value for one observable may be used to determine the overall scale of E2 strengths, and thereby provide predictions for others. In particular, we demonstrate that meaningful predictions for E2 transitions may be obtained by calibration to the ground-state quadrupole moment. Here, we test this approach for well-measured low-lying E2 transitions in 7 Li and 9 Be, then provide predictions for transitions in 8 Li and 9 Li. In particular, we address the 2 + → 1 + transition in 8 Li, for which the reported measured strength exceeds ab initio Green's function Monte Carlo (GFMC) predictions by over an order of magnitude.

6 ≤ A ≤ 19↗