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At least 91 records · Page 5

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

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↗

High-performance and high-fidelity Monte Carlo solutions to the BEAVRS benchmark

The BEAVRS (Benchmark for Evaluation and Validation of Reactor Simulation) benchmark is solved by PRAGMA, the GPU-based continuous energy Monte Carlo code. The resulting solutions are comprised of the detailed simulation results of two cycles, each of which consists of the zero power physics test (ZPPT) and the core depletion calculations. The ZPPT consists of characteristic parameters, such as critical boron concentration (CBC), control rod bank worth, isothermal temperature coefficients, and assembly-wise detector signal, which are compared with measured data provided by the benchmark administration. The core depletion calculations were performed for both the hot full power and the load follow modes, and the comparison was made with the measured or deduced CBCs and assembly-wise detector signals. In the load follow calculations, the operating power history was approximately applied to simulate the real operation as closely as possible. PRAGMA performed the various calculations with a tremendous number of histories ranging up to hundreds of millions per cycle, exploiting GPUs' massively parallel performance. The load follow run time was shorter than 16 hours on a single rack of computing nodes mounded with 24 gaming GPUs with a remarkable agreement with the measurements for most comparisons. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Evaluation of Sandia NCS Benchmark Suite Updates

The Sandia Nuclear Criticality Safety (NCS) program’s benchmark suite was recently updated. This suite is used to ensure that NCS calculations using computer-based neutron transportation codes have an established baseline comparison of calculated versus known experimental results. The Evaluated Nuclear Data File (ENDF) version used for the MCNP models in the suite was changed from ENDF/B-VII.1 to ENDF/B-VIII.0. Additionally, relevant thermal scattering law data libraries (TSLs) were updated. The sensitivity of the calculational bias of each benchmark model to these changes is discussed. Implementation of the ENDF/B-VIII.0 library and updated TSLs results in improvements to bias distribution in the intermediate enriched uranium, plutonium, and mixed uranium–plutonium (IEU, PU, and MIX) fissionable material benchmark categories, but a small bias increase in low- and high-enriched uranium categories (LEU and HEU, respectively). The results also highlight the sensitivity of the benchmarks, with average lethargy of neutrons causing fission energies (EALF) in the intermediate energy range to ENDF/B library changes. The most numerous bias changes were observed in the thermal energy region when transitioning from ENDF/B-VII.1 to ENDF/B-VIII.0. In conclusion, most of the unique bias changes observed in MCNP 6.3.0 between the two nuclear data libraries were in the LEU-COMP-THERM evaluation subset.

ICSBEP↗

Initial Development of Fusion Magnet Simulation Capabilities for Performance and Safety Evaluation Using the MOOSE Framework

Fusion energy holds the promise of being a transformative technology as a carbon-neutral, sustainable source of energy. Whole device modeling and the development of fusion digital twins will be increasingly important for emerging fusion device concepts at both national laboratories and within the commercial fusion industry. However, meeting the challenge of whole device modeling of fusion energy devices requires robust, multiphysics, multiscale modeling and simulation technologies capable of running on large-scale supercomputers. Detailed analysis of individual systems at-scale is also required to ensure safe and efficient operation as well as provide the safety basis for future device designs and licensing activities. In a tokamak, toroidal and poloidal magnets confine and shape the fusion plasma to promote the fusion reaction. High plasma temperatures and high magnetic field requirements in modern design concepts (leading to high amounts of energy stored within each magnet) impose electrical, thermal, and mechanical loads on the magnet components, which in turn impacts the safety considerations of the magnet and their supporting systems. Idaho National Laboratory (INL) has a history of working in this space, including development and benchmarking of the Magnetic System Circuitry Analysis Program (MSCAP) and Magnet Arcing (MAGARC) codes to study magnet quench events; notably, MAGARC was used to study quenching during the ITER Engineering Design Activity. However, these legacy codes and capabilities are not parallel and scalable, and new tools are required for future advances in this area, which leads to the INL-developed Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. Developed originally for fission reactor systems under United States Department of Energy, Office of Nuclear Energy modeling and simulation programs, the MOOSE framework has been well-suited to multiscale, multiphysics modeling and simulation needs for nuclear systems. The framework is open-source, well-tested, under continuous development and deployment, and developed to a Nuclear Quality Assurance, Level 1 software quality standard. MOOSE has also been used in the fusion space previously in several projects: INL’s Tritium Migration Analysis Program, Version 8 (TMAP8) for tritium migration, UK Atomic Energy Authority’s A Unified Resource for OpenMC (fusion) Reactor Applications (AURORA) code for fusion thermo-mechanical and neutronics analysis, and Argonne National Laboratory’s Cardinal for high-fidelity computational fluid dynamics and neutronics. However, to model superconducting magnets, several MOOSE enhancements are required: additions to the current MOOSE electromagnetic capabilities, new material libraries for superconductors of interest (such as YBCO), as well as fusion-specific models for thermo-mechanics. This talk will discuss initial development activities to build these capabilities in MOOSE, focusing on initial validation and benchmarking activities. Proposed coupling workflows and future work to support the simulation of fusion magnets and magnet structural assemblies for performance and safety evaluation in MOOSE will also be discussed.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measuring binary fluidization of nonspherical and spherical particles using machine learning aided image processing

Abstract The binary fluidization of Geldart D type nonspherical wood particles and spherical low density polyethylene (LDPE) particles was investigated in a laboratory‐scale bed. The experiment was performed for varying static bed height, wood particles count, as well as superficial gas velocity. The LDPE velocity field were quantified using particle image velocimetry (PIV). The wood particles orientation and velocity are measured using particle tracking velocimetry (PTV). A machine learning pixel‐wise classification model was trained and applied to acquire wood and LDPE particle masks for PIV and PTV processing, respectively. The results show significant differences in the fluidization behavior between LDPE only case and binary fluidization case. The effects of wood particles on the slugging frequency, mean, and variation of bed height, and characteristics of the particle velocities/orientations were quantified and compared. This comprehensive experimental dataset serves as a benchmark for validating numerical models.

Li, Cheng↗

Well-Balanced Second-Order Convex Limiting Technique for Solving the Serre–Green–Naghdi Equations

In this article, we introduce a numerical method for approximating the dispersive Serre–Green–Naghdi equations with topography using continuous finite elements. The method is an extension of the hyperbolic relaxation technique introduced in Guermond et al. (J Comput Phys 450:110809, 2022). It is explicit, second-order accurate in space, third-order accurate in time, and is invariant-domain preserving. It is also well balanced and parameter free. Special attention is given to the convex limiting technique when physical source terms are added in the equations. The method is verified with academic benchmarks and validated by comparison with laboratory experimental data.

97 MATHEMATICS AND COMPUTING↗

A new 181 Ta neutron resolved resonance region evaluation

A new 181 Ta neutron resolved resonance region evaluation has been performed from the thermal energy range up to approximately 2.5 keV. The R-matrix SAMMY code was used with the Reich–Moore approximation to evaluate resonance parameters from several experimental data sets. A Monte Carlo approach was used for resonance spin assignments and generating 59 small fictitious resonance levels which were shown to improve the cumulative level, Porter-Thomas, and Wigner distributions as compared to theoretical predictions. Covariance information was also generated for the entire resolved resonance region. Finally, the positive impact of the new evaluation was validated through benchmark calculations which were sensitive to the 181 Ta cross section and showed improvement in the reactivity bias for several benchmark cases.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A finite difference informed random walker (FDiRW) solver for strongly inhomogeneous diffusion problems

In nature, many complex multi-physics coupling problems exhibit strong diffusivity inhomogeneity. For instance, in the context of radionuclide absorption by porous wasteform materials within a flowing waste stream, the difference of species’ diffusivity in solid and liquid phases spans by 3~8 orders of magnitude. To solve the diffusion equations with strongly inhomogeneous diffusivity, traditional discretization-based methods, such as the Finite Difference Method (FDM), require infinitesimally small time steps (<10 -10 ) as high spatial resolutions are employed in most microstructure evolution processes, leading to prohibitively high computational costs. Here, this work developed an integrated numerical approach (FDiRW: Finite Difference informed Random Walk) to tackle this challenge. The idea is that utilizing the Random Walk concept, the fast diffusion is modeled as a superposition of point source’s solution for a concentration distribution while FDM is used to obtain the point source’s solution at each node. A mesh-coarsening algorithm is developed to generate an exclusive coarse mesh for FDiRW approach to maximize its efficiency. The effectiveness of the coarse mesh-based FDiRW approach is validated by benchmarking Finite Difference solutions. Numerical results demonstrated that FDiRW achieves a remarkable 1000x computational efficiency improvement over FDM while preserving desired accuracy for a medium-sized model of 192 × 192 × 192 grids. Finally, as models scale up, a floating-point operations (PLOPs) analysis of the FDiRW algorithm reveals that its computational complexity grows quadratically in terms of the number of nodes employed in computation.

36 MATERIALS SCIENCE↗

TRANSLATE - a Monte Carlo simulation of electron transport in liquid argon

Here, the microphysics of electron and photon propagation in liquid argon is a key component of detector design and calibrations needed to construct and perform measurements within a wide range of particle physics experiments. As experiments grow in scale and complexity, and as the precision of their intended measurements increases, the development of tools to investigate important microphysics effects impacting such detectors becomes necessary. In this paper we present a new time-domain Monte Carlo simulation of electron transport in liquid argon. The simulation models the TRANSport in Liquid Argon of near-Thermal Electrons (TRANSLATE) with the aim of providing a multi-purpose software package for the study and optimization of detector environments, with a particular focus on ongoing and next generation liquid argon neutrino experiments utilizing the time projection chamber technology. TRANSLATE builds on previous work of Wojcik and Tachiya, amongst others, introducing additional processes, including ionization, thus modeling the full range of drift electron scattering interactions. The simulation is validated by benchmarking its performance with swarm parameters from data collected in experimental setups operating in gas and liquid.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A simple and fast algorithm for estimating the capacity credit of solar and storage

Energy storage is a leading option to enhance the resource adequacy contribution of solar energy. Detailed analysis of the capacity credit of solar energy and energy storage is limited in part due to the data intensive and computationally complex nature of probabilistic resource adequacy assessments. This paper presents a simple algorithm for calculating the capacity credit of energy-limited resources that, due to the low computational and data needs, is well suited to exploratory analysis. Validation against benchmarks based on probabilistic techniques shows that it can yield similar insights. The method is used to evaluate the impact of different solar and storage configurations, particularly with respect to the strategy for coupling storage and solar photovoltaic systems. Furthermore, application of the method to a case study of utilities in Florida, where solar is rapidly growing and demand peaks in the winter and summer, demonstrates that it can improve on rules of thumb used in practice by some utilities. If storage is required to charge only from solar, periods of high demand driven by cold weather events accompanied by lower solar production can result in a capacity credit of solar and storage that is less than the capacity credit of storage alone.

14 SOLAR ENERGY↗

Models implemented in the methodological approach to design the initial STEP first wall contour

The official Spherical Tokamak for Energy Production mission aims to demonstrate the ability to generate net electricity from fusion with the STEP Prototype Power plant. One of the key technological and engineering challenges in fusion power plants is managing the loads on the first wall within acceptable limits. Therefore, the conceptual design development of the STEP Prototype Power plant needs to be based on load estimates derived using legitimate plasma physics assumptions through dynamic and flexible tools. The current design foresees the STEP main chamber first wall to withstand steady-state heat loads of up to ~1 MW/m 2 , excluding critical regions expected to receive higher heat loads such as the baffle regions approaching the divertors. These critical areas will require ad hoc assessments and will be designed with the presence of limiters. This article focuses on the models and methodology adopted for designing the 2-D poloidal contour of the STEP first wall, based on the anticipated charged particle and radiation heat loads during normal operation. Firstly, the models adopted for calculating the charged particle and radiation heat loads are introduced. The first model is validated through benchmarking against the particle tracing code SMARDDA, while the second model is verified by comparing it with data from the MAST-U experiment. Secondly, the model used to design the 2-D first wall contour according to the heat loads is explained. We acknowledge that this preliminary design stage assumes certain simplifications, notably an axisymmetric geometry, for computational efficiency and clarity in presentation. It is understood that subsequent design phases will address the complexities of real-world engineering, including non-axisymmetric effects, transient plasma scenarios, and the impact of disruptions on the first wall design. Finally, an automatic procedure based on these models is presented for defining the 2-D poloidal contour of the STEP first wall to minimize heat loads, taking into account the need to radiate most of the alpha-particle and auxiliary heating power. Here, by providing an overview of the models, methodology, and an automatic procedure, this paper contributes to the design process of the STEP first wall, addressing the engineering challenges associated with fusion power plant development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Transport model comparison studies of intermediate-energy heavy-ion collisions

Transport models are the main method to obtain physics information on the nuclear equation of state and in-medium properties of particles from low to relativistic-energy heavy-ion collisions. The Transport Model Evaluation Project (TMEP) has been pursued to test the robustness of transport model predictions in reaching consistent conclusions from the same type of physical model. To this end, calculations under controlled conditions of physical input and set-up were performed with various participating codes. These included both calculations of nuclear matter in a box with periodic boundary conditions, which test separately selected ingredients of a transport code, and more realistic calculations of heavy-ion collisions. Over the years, six studies have been performed within this project. In this intermediate review, we summarize and discuss the present status of the project. We also provide condensed descriptions of the 26 participating codes, which contributed to some part of the project. These include the major codes in use today. After a compact description of the underlying transport approaches, we review the main results of the studies completed so far. They show, that in box calculations the differences between the codes can be well understood and a convergence of the results can be reached. These studies also highlight the systematic differences between the two families of transport codes, known under the names of Boltzmann–Uehling–Uhlenbeck (BUU) and Quantum Molecular Dynamics (QMD) type codes. However, when the codes were compared in full heavy-ion collisions using different physical models, as recently for pion production, they still yielded substantially different results. This calls for further comparisons of heavy-ion collisions with controlled models and of box comparisons of important ingredients, like momentum-dependent fields, which are currently underway. Furthermore, our evaluation studies often indicate improved strategies in performing transport simulations and thus can provide guidance to code developers. Results of transport simulations of heavy-ion collisions from a given code will have more significance if the code can be validated against benchmark calculations such as the ones summarized in this review.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Tree-ring evidence marks year 2022 as the driest spring season in nearly four centuries in the Western Himalayas

The Hindukush-Karakoram-Himalayan region is a crucial freshwater source for billions across South Asia, yet its climate remains poorly understood due to limited long-term records. Winter and spring precipitation govern snow accumulation and downstream water availability in dry months particularly across the Western Himalayas (WH), but recent decades show intensifying droughts with unclear long-term context. Here, we have reconstructed a nearly four-century-long spring i.e. February to May (FMAM) precipitation for the Lahaul region of the (WH), an area dominated by the Western Disturbances. This record was developed using moisture-sensitive Cedrus deodara (Deodar) tree-rings from three high-elevation sites. A regional composite tree-ring-width chronology, developed through a Nested Principal Component Analysis and modeled with a nonlinear Generalized Additive Model (GAM) that explains 71 % of the variance during the calibration period. We identified the last two decades as the most precipitation deficit phase and the year 2022 showing the driest FMAM on record. The observed rise in the FMAM dry episodes post 1999 CE in our reconstruction, corresponds to the meteorological records. This recent drying is linked to a northward shift of the subtropical westerly jet and reduced moisture transport, both associated with unusual sea surface temperature patterns in the tropical Indian Ocean and the Western Pacific Ocean. Our results provide compelling evidence of long-term hydroclimatic instability in the WH and emphasize the value of tree-ring records in extending precipitation histories beyond the instrumental observations. Such reconstructions can be benchmarks to validate high-resolution climate models and formulate adaptation policies to mitigate future risks.

Cedrus deodara↗

Global biogeography of fungal and bacterial biomass carbon in topsoil

Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients including mean annual temperature, mean annual precipitation, net primary productivity, root C density, soil temperature, soil moisture, and edaphic factors. At the biome level, tundra has the highest FBC and BBC densities at 3684 (95% confidence interval: 1678–8084) mg kg -1 and 428 (237–774) mg kg -1 , respectively; desert has the lowest FBC and BBC densities at 16.92 (14.4–19.89) mg kg -1 and 6.83 (6.1–7.65) mg kg -1 , respectively. The F:B ratio varies dramatically, ranging from 1.8 (1.6–2.1) in savanna to 8.6 (6.7–11.0) in tundra. An empirical model was developed for the F:B ratio and it is combined with a global dataset of soil microbial biomass C to produce global maps for FBC and BBC in 0–30 cm topsoil. Across the globe, the highest FBC is found in boreal forest and tundra while the highest BBC is in boreal forest and tropical/subtropical forest, the lowest FBC and BBC are in shrub and desert. Global stocks of living microbial biomass C were estimated to be 12.6 (6.6–16.4) Pg C for FBC and 4.3 (0.5–10.3) Pg C for BBC in topsoil. These findings advance our understanding of the global distribution of fungal and bacterial biomass, which facilitates the incorporation of fungi and bacteria into Earth system models. The global maps of bacterial and fungal biomass serve as a benchmark for validating microbial models in simulating the global C cycle under a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗

Forecasting of in situ electron energy loss spectroscopy

Abstract Forecasting models are a central part of many control systems, where high-consequence decisions must be made on long latency control variables. These models are particularly relevant for emerging artificial intelligence (AI)-guided instrumentation, in which prescriptive knowledge is needed to guide autonomous decision-making. Here we describe the implementation of a long short-term memory model (LSTM) for forecasting in situ electron energy loss spectroscopy (EELS) data, one of the richest analytical probes of materials and chemical systems. We describe key considerations for data collection, preprocessing, training, validation, and benchmarking, showing how this approach can yield powerful predictive insight into order-disorder phase transitions. Finally, we comment on how such a model may integrate with emerging AI-guided instrumentation for powerful high-speed experimentation.

36 MATERIALS SCIENCE↗

Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering

Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO) 2 ), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO) 2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗