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K-RET: knowledgeable biomedical relation extraction system

Abstract Motivation Relation extraction (RE) is a crucial process to deal with the amount of text published daily, e.g. to find missing associations in a database. RE is a text mining task for which the state-of-the-art approaches use bidirectional encoders, namely, BERT. However, state-of-the-art performance may be limited by the lack of efficient external knowledge injection approaches, with a larger impact in the biomedical area given the widespread usage and high quality of biomedical ontologies. This knowledge can propel these systems forward by aiding them in predicting more explainable biomedical associations. With this in mind, we developed K-RET, a novel, knowledgeable biomedical RE system that, for the first time, injects knowledge by handling different types of associations, multiple sources and where to apply it, and multi-token entities. Results We tested K-RET on three independent and open-access corpora (DDI, BC5CDR, and PGR) using four biomedical ontologies handling different entities. K-RET improved state-of-the-art results by 2.68% on average, with the DDI Corpus yielding the most significant boost in performance, from 79.30% to 87.19% in F-measure, representing a P-value of 2.91×10−12. Availability and implementation https://github.com/lasigeBioTM/K-RET.

Sousa, Diana F. (ORCID:0000000305979273)↗

The Role of Nuclear Data Sensitivities in Prompt α-Eigenvalue Predictions of Delayed Critical Benchmarks

Alpha (α) eigenvalues, which describe the logarithmic time derivative of the neutron population in a multiplying system, are integral to time-dependent behavior and diagnostic applications. However, uncertainties in the evaluated nuclear data can significantly impact the accuracy of transport simulations for such quantities. This work explores the use of machine learning models to predict two key outputs, α-eigenvalues and keff bias, using input features derived from α-eigenvalue sensitivities to nuclear data. The criticality safety benchmark models used in this study come from the International Handbook of Evaluated Criticality Safety Benchmark Experiments. Three models, random forest, XGBoost, and NGBoost, are trained on both energy-resolved and energy-summed α sensitivities. For the α-eigenvalue bias prediction, NGBoost achieved the highest R 2 (0.9476) using energy-resolved features, while XGBoost performed best using summed sensitivities. In contrast, when predicting the keff bias, all the models showed moderate predictive capability (best R 2 ≈ 0.72), as the mapping from the static α-sensitivities to the static keff bias was less direct. SHAP (SHapley Additive exPlanations) analysis was used to interpret the model predictions. Across both prediction tasks, the features associated with neutron capture [H-1 (n, γ)], uranium scattering reactions (such as 235 U elastic/inelastic), and actinide capture/fission reactions (such as 239 Pu and 234 U) were consistently identified as the most impactful. This highlights the key role of specific nuclear reactions and energy ranges in shaping both time-dependent and steady-state criticality behavior. These results demonstrated that α-sensitivities, despite being computed for time-dependent metrics, can provide valuable insights for predicting both α-eigenvalues and the keff bias. Moreover, machine learning models offer a promising pathway for uncovering important nuclear data dependencies and guiding future data evaluation efforts.

Nuclear data↗

Prioritizing Uncertainties in Hydrogen Contribution to Risk in Post-Crash Outcomes for Rail

This report presents analysis from Sandia National Laboratories predicting contributions to risk associated with the use of hydrogen technology for rail. Event sequence diagrams are used to describe possible accident scenarios and progressions. Initiating event frequencies and branch event probabilities for each scenario are quantified with uncertainty using distributions fit to Federal Railroad Administration and U.S. Department of Transportation Pipeline and Hazardous Materials Safety Administration data on applicable accidents from 2000 to 2020. Uncertainty is propagated through the event sequence diagram to estimate the frequency and conditional probability of accident end states. The analysis identifies four scenarios with significant contributions to risk from hydrogen that are predicted to occur relatively frequently, which may inform priorities for reducing uncertainty. These scenarios are 1) overpressure events resulting from collisions with hydrogen release due to mechanical damage and delayed ignition, 2) jet fire events resulting from collisions with hydrogen release due to mechanical damage and immediate ignition, 3) jet fires resulting from fire or explosion initiating events involving the hydrogen tank and correct operation of the thermally-activated pressure relief device (TPRD) subsequent to the thermal insult, and 4) pressure burst resulting from fire or explosion initiating events involving the hydrogen tank and failure of the TPRD. Delayed and immediate hydrogen ignition probabilities are identified as being highly uncertain and potential candidates for reducing conservatism in the predicted frequencies for these two scenarios.

08 HYDROGEN↗

Weather and Random Forest-based Load Profiling Approximation Models and its Transferability across Climate Zones

This study is to provide predictive understanding of the associations of various weather attributes with residential and commercial load profiles, for a variety of climate zones and seasons. In this work, machine learning (ML) approaches were used to identify and quantify the impacts of various weather attributes on residential and commercial electricity demand and its components across the western United States. Performance and transferability of the developed ML models were then evaluated across different temperate zones (e.g., southern, middle, and northern US) and across coastal, mid-continent, and wet zones, with inputs of weather condition data from the National Oceanic and Atmospheric Administration (NOAA) at representative weather stations. The predictive models were developed based on the ranked/screened factors using the regression tree (RT) and random forest (RF) approaches, for five different scenarios (seasons).

load composite, Random Forest, regression tree, lo↗

Search for long-lived particles produced in association with a Z boson in proton-proton collisions at $\sqrt{s}$ = 13 TeV

A search for long-lived particles (LLPs) produced in association with a Z boson is presented. The study is performed using data from proton-proton collisions with a center-of-mass energy of 13 TeV recorded by the CMS experiment during 2016–2018, corresponding to an integrated luminosity of 117 fb -1 . The LLPs are assumed to decay to a pair of standard model quarks that are identified as displaced jets within the CMS tracker system. Triggers and selections based on Z boson decays to electron or muon pairs improve the sensitivity to light LLPs (down to 15 GeV). This search provides sensitivity to beyond the standard model scenarios which predict LLPs produced in association with a Z boson. In particular, the results are interpreted in the context of exotic decays of the Higgs boson to a pair of scalar LLPs (H → SS). The Higgs boson decay branching fraction is constrained to values less than 6% for proper decay lengths of 10–100 mm and for LLP masses between 40 and 55 GeV. In the case of low-mass (≈ 15 GeV) scalar particles that subsequently decay to a pair of b quarks, the search is sensitive to branching fractions B(H → SS) < 20% for proper decay lengths of 10–50 mm. The use of associated production with a Z boson increases the sensitivity to low-mass LLPs of this analysis with respect to gluon fusion searches. In the case of 15 GeV scalar LLPs, the improvement corresponds to a factor of 2 at a proper decay length of 30 mm.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulation of Peach Bottom turbine trip transient with RETRAN-3D using BXFGEN

The Peach Bottom 2 Turbine Trip transient is used to evaluate the capabilities and accuracy of coupled 3-D neutronics/thermal hydraulics best estimate calculations for support of safety analysis. Selected results, obtained with RETRAN-3D, are compared to available measurements and benchmark results. The comparisons are analyzed and the application of RETRAN-3D for a best estimate analysis approach within the safety analysis methodology is discussed. Overall, both the thermal-hydraulic and neutronic results show a good comparison to the experimental data, and the model is considered to accurately predict test data. In particular, the initial acoustic response of the main steam line and the subsequent main pressurization stages are well-predicted. During the main pressurization stage, the timing and magnitude of the in-core local pressurization and associated void compression are properly predicted based upon the agreement between local power range monitors (LPRM) predictions upwards, but the shift is slightly underpredicted. This indicates the methodology is well-posed for simulating this class of transient response.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Environmentally Assisted Fatigue in Light Water Reactor Environment

This report summarizes the Environmentally Assisted Fatigue (EAF) research conducted at ANL under the US DOE Light Water Reactor Sustainability (LWRS) program. Starting from a rich background in theoretical and experimental EAF, ANL previously developed an approach to evaluate fatigue performance of reactor materials in light water reactor environments with the correction factor F en . The approach was based on a large body of experimental work performed at ANL and elsewhere, and was consistent with American Society of Mechanical Engineers (ASME)’s methodology governing the design and construction of reactor components. In recent years, the program was focused on component fatigue prediction and made several major and fundamental contributions in this area. These accomplishments help meet the needs identified by the industry concerning component level fatigue predictions in complex, transient conditions. The main contribution of the ANL program involved the development of a system-level model for estimating residual strain and life of nuclear reactor coolant system components under connected-system-thermal-mechanical boundary conditions. The goal was to predict the stress hotspots, strain residuals, strain amplitudes and the resulting fatigue lives. Thermal-mechanical stress analysis was performed considering thermal stratification and a design-basis reactor loading cycle. Based on the finite element (FE) model results, the strain residuals, strain amplitudes and resulting fatigue lives of reactor coolant system (RCS) components were predicted. The results show that some of the RCS components can have significantly different strain amplitudes, residual strain, and fatigue lives, despite having similar geometry and material. In addition, the simulated component-level strain profile can guide the selection of appropriate test inputs for conducting laboratory-scale EAF tests. Building upon the system-level model, ANL developed a digital twin (DT) framework to predict the structural states and associated fatigue life of components in real-time. This framework is a comprehensive system designed to predict the structural states and fatigue lives of reactor components. It includes multiple models and integrates artificial intelligence (AI), machine learning (ML), and FE based modeling tools to evaluate the structural states and fatigue lives.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

FY26 Progress on Demonstration of a Multiphysics Steady State Capability for Modeling Core Radial Expansion in SFRs

Under the U.S. Department of Energy Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism in liquid metal-cooled fast reactors and involves multiphysics effects including radiation transport, fluid flow, heat transfer, and mechanical response to temperature and flux gradients. This report summarizes recent progress on developing a multiphysics, MOOSE-based workflow to predict core bowing and associated reactivity feedback. Significant new capabilities in the reactor physics code Griffin - sodium backfill and pin power reconstruction for deformed geometries - were applied in this effort. This year’s work included verification, code comparisons, sensitivity studies, and coupled demonstrations that advance the state of MOOSE-based core bowing workflow. Griffin’s sodium backfill capability was verified by demonstrating that its automated treatment of geometry expansion and material-density updates reproduces manual calculations exactly, confirming solid mass conservation and proper coolant backfilling in expanded geometries. Reconstructed pin powers were compared for Griffin’s ductheterogeneous and ring-heterogeneous treatments in single-, seven-, and nineteen-assembly cases, with best agreement observed in lower-leakage configurations and the duct-heterogeneous approach offering substantially lower computational cost. Thermal-hydraulic sensitivity sensitivities showed that MOOSE SCM, SAM, and CFD are expected to produce similar deformation predictions despite variances in their temperature predictions, and that explicit treatment of inter-assembly flow becomes increasingly important as gap flow rate increases. Finally, coupled demonstrations on small multi-assembly configurations using Griffin, MOOSE Solid Mechanics, MOOSE SCM, and Heat Conduction produced physically consistent reactivity feedback from thermal expansion and bowing. The coupled demonstrations simulated grid plate expansion as well as resultant core bowing at full power conditions. Simplifications were made in current workflow, namely the assumption of instantaneous full power conditions following hot zero power, and pre-expanding the Griffin geometry axially due to lack of an axial fuel pin expansion model and temperature feedback to Griffin.

Wozniak, Nicholas↗

Monte Carlo Global QCD Analyses of the Pion Parton Distribution Functions

As the lightest hadron, the pion presents itself as a dichotomy. While being the pseudo Goldstone boson associated with chiral symmetry breaking, it is simultaneously regarded as the lightest pseudoscalar meson typically composed of constituent quark and antiquark. As the chiral symmetry shares the same global symmetry as QCD, studying the pion and its internal structure is key in understanding one of the four fundamental forces of nature, namely the quantum chromodynamic strong interaction. We study the pion's parton distribution functions (PDFs), which are universal quantities that describe the structure of the pion in terms of its constituent quarks, antiquarks, and gluons. Our goal is to discover what the available data reveal for these universal quantities, namely the PDFs. Through the use of factorization theorems and perturbative QCD, we use Monte Carlo (MC) methods to extract the PDFs from the available Drell-Yan (DY) and leading neutron (LN) data. While the DY process involves two hadrons colliding, the LN electroproduction involves an electron beam incident on a target nucleon. We can constrain well the pion PDFs at large momentum fraction using DY data, and at low momentum fraction using LN data. We also use threshold resummation in the DY process to gather predictable higher order terms associated with the soft gluon radiation because their contributions to the cross section are nontrivial. In this dissertation, we parametrize the pion PDFs and fit those parameters to the available data. We make use of Bayesian inference and use MC techniques to sample the parameter space. Three sets of results are presented. We first extract the pion PDFs by fitting the DY and LN data. Then, we include transverse momentum dependent DY data in conjunction with the DY and LN data to extract the pion PDFs. Finally, we apply various methods of threshold resummation to the DY cross section and extract pion PDFs. The pion PDFs presented here are the first global QCD analyses performed as well as the first MC extracted pion PDFs, which are at the forefront of the pion PDF community.

Barry, Patrick↗

Using spin alignment of inelastically excited nuclei in fast beams to assign spins: The spectroscopy of 13 O as a test case

Excited states in O 13 were investigated using inelastic scattering of an E / A = 69.5 MeV O 13 beam off of a Be 9 target. The excited states were identified in the invariant-mass spectra of the decay products. Both single-proton and sequential two-proton decays of the excited states were examined. Furthermore, for a number of the excited states, the protons were emitted with strong anisotropy where emissions transverse to the beam axis are favored. The measured proton-decay angular distributions were compared to predictions from distorted-wave Born-approximation calculations of the spin alignment which was shown to be largely independent of the excitation mechanism. The deduced O 13 level scheme is compared to ab initio no-core shell model with continuum predictions. The lowest-energy excited states decay isotropically consistent with predictions of strong proton 1 s 1 / 2 structure. Above these states in the level scheme, we observed a number of higher-spin states not predicted within the model. Possibly these are associated with rotational bands built on deformed cluster configurations predicted by antisymmetrized molecular dynamics calculations. The spin alignment mechanism is shown to be useful for making spin assignments and may have widespread use.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

RARE EARTH AND CRITICAL ELEMENT RELATIONSHIPS TO COAL DEPOSIT LITHOLOGIES IN SOUTHWEST WYOMING AND NORTHWEST COLORADO

Rare earth elements (REE) and critical minerals (CM) are vital components in a wide variety of applications, not only in the renewable energy sector but also in military, telecommunication, and other civilian uses. The association of REE and CM with coal deposits is widely known but not thoroughly understood. While individual coal samples or beds themselves might not host significant concentrations of REE, recent studies indicate temporal relationships among some REE with coal beds and their immediately adjacent non-coal bounding strata, including interbeds. These strata most commonly include clays, carbonaceous shales, and ash beds, but other related strata are possible in different coal-bearing settings. Variations in REE and CM concentrations and their direct or indirect association with coal beds are not always predictable. This study presents recent findings from studying different associations between coal beds and adjacent rocks to identify possible relationships between REE-CM concentrations and the coals and adjacent rocks. For this study we collected and analyzed several dozen samples from the U.S. Geological Survey’s Core Research Center (CRC). Additionally, a small number of coal mine outcrops and their adjacent non-coal rocks were included. Most samples are of Cretaceous age. Previous work has shown a potential link between coals in the Upper Cretaceous Williams Fork Formation and REE occurrences in the Yampa ash bed in northwest Colorado. While data are uncommon and sparse, this possible link may suggest REE or CM enrichment from leaching or reworking of the ash bed. Trace element geochemistry, whole rock data, and microscopic examinations are used here to explore these relationships and guide future studies.

REE, CM, ash, volcanic ash, coal↗

Stability of expanding accretion shocks for an arbitrary equation of state

We present a theoretical stability analysis for an expanding accretion shock that does not involve a rarefaction wave behind it. The dispersion equation that determines the eigenvalues of the problem and the explicit formulae for the corresponding eigenfunction profiles are presented for an arbitrary equation of state and finite-strength shocks. For spherically and cylindrically expanding steady shock waves, we demonstrate the possibility of instability in a literal sense, a power-law growth of shock-front perturbations with time, in the range of $h_c< h<1+2 {\mathcal {M}}_2$ , where $h$ is the D'yakov-Kontorovich parameter, $h_c$ is its critical value corresponding to the onset of the instability and ${\mathcal {M}}_2$ is the downstream Mach number. Shock divergence is a stabilizing factor and, therefore, instability is found for high angular mode numbers. As the parameter $h$ increases from $h_c$ to $1+2 {\mathcal {M}}_2$ , the instability power index grows from zero to infinity. This result contrasts with the classic theory applicable to planar isolated shocks, which predicts spontaneous acoustic emission associated with constant-amplitude oscillations of the perturbed shock in the range $h_c< h<1+2 {\mathcal {M}}_2$ . Examples are given for three different equations of state: ideal gas, van der Waals gas and three-terms constitutive equation for simple metals.

Huete, César (ORCID:0000000232278520)↗

Reducing the Cost of Energy Differences in Variational Monte Carlo with Spotlight Sampling

Here, we investigate an approximate sampling scheme that can significantly reduce the cost scaling of variational Monte Carlo when it is employed to predict the energy differences associated with local chemical changes. Inspired by side-chaining and embedding methods, this spotlight sampling approach adopts an approximate fragmented Hamiltonian and correlated sampling to reduce cost scaling to the point that it is essentially linear with system size, with the potential to go sublinear if certain conditions are met. In tests on bond stretching energies in alcohols, hydrogen dimer chains, and molecules with various degrees of π-system delocalization, we observe the anticipated linear scaling and an explicit cost crossover with standard variational Monte Carlo.

Bumann, Sonja [University of California, Berkeley,↗

Ocean fronts and eddies force atmospheric rivers and heavy precipitation in western North America

Atmospheric rivers (ARs) are responsible for over 90% of poleward water vapor transport in the mid-latitudes and can produce extreme precipitation when making landfall. However, weather and climate models still have difficulty simulating and predicting landfalling ARs and associated extreme precipitation, highlighting the need to better understand AR dynamics. Here, using high-resolution climate models and observations, we demonstrate that mesoscale sea-surface temperature (SST) anomalies along the Kuroshio Extension can exert a remote influence on landfalling ARs and related heavy precipitation along the west coast of North America. Inclusion of mesoscale SST forcing in the simulations results in approximately a 40% increase in landfalling ARs and up to a 30% increase in heavy precipitation in mountainous regions and this remote impact occurs on two-week time scales. The asymmetrical response of the atmosphere to warm vs. cold mesoscale SSTs over the eddy-rich Kuroshio Extension region is proposed as a forcing mechanism that results in a net increase of moisture flux above the planetary boundary layer, prompting AR genesis via enhancing moisture transport into extratropical cyclones in the presence of mesoscale SST forcing.

54 ENVIRONMENTAL SCIENCES↗

Dissociation-induced depletion of high-energy reactant molecules as a mechanism for pressure-dependent rate constants for bimolecular reactions

In 1922, Lindemann proposed the now-well-known mechanism for pressure-dependent rate constants for unimolecular reactions: reactant molecules with sufficiently high energies dissociate more quickly than collisions can reestablish the Boltzmann distribution of the internal energies of the molecule during its dissociation at low pressures – yielding pressure-dependent rate constants for unimolecular reactions due to the preferential depletion of the high energy states capable of dissociation. In the last century, incredible progress has been made in achieving a far greater understanding of and quantitative predictions for unimolecular and association reactions. In the modern era, pressure-dependent phenomenological rate constants are now nearly universally used to describe the rates of unimolecular and associative reactions in phenomenological kinetic modeling. However, there is a second, more indirect, implication of Lindemann’s mechanism that relates to how these dissociation-induced non-equilibrium distributions impact bimolecular reactions, including non-associative bimolecular reactions – which are generally not considered to have pressure-dependent rate constants. Yet, as we show herein, the same high energy states depleted due to dissociation would otherwise react most rapidly in high-activation-energy bimolecular reactions – yielding a mechanism for pressure-dependent rate constants for bimolecular reactions (including non-associative reactions). Here, we present results from a case study for CH 2 O dissociation, isomerization, and bimolecular reaction with O2 to explore this question. Results from our master equation calculations indicate that the effect of dissociation-induced non-equilibrium distributions on bimolecular reactions can be substantial – even when chemical timescales are well separated from internal energy relaxational timescales (i.e. when the traditional rate constant description would be thought to apply). This effect is found to be more pronounced – and more complex – for bimolecular reactions involving molecular entities whose chemical timescales are merged with the internal energy relaxational timescales. Lastly, we present some ideas for discussion regarding what should be considered as “chemical species” in phenomenological kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Fidelity CFD Assessments of Flow Resistance in a 61-Pin Wire-Wrapped Assembly with Partially Blocked Channels

The examination of thermal-hydraulic behaviors in wire-wrapped rod bundles continues to be an active area of research. The sodium fast reactor, a prominent candidate in next-generation nuclear designs, utilizes a hexagonal configuration of wire-wrapped fuel pins. Here, the potential for channel blockage within this compact arrangement poses a significant safety challenge, spurring a number of recent experimental and computational investigations to evaluate its impact on flow and heat transfer. The present work aims to benchmark the high-fidelity NekRS computational fluid dynamics (CFD) solver in predicting the pressure drops associated with substantial blockages, using available experimental data as a reference. A 61-pin wire-wrapped fuel assembly with two flow blockage configurations has been simulated and investigated at a range of low to moderate Reynolds numbers (487 ≤ Re ≤ 14 600). The NekRS solver demonstrates an exponential reduction of spatial discretization error with increasing polynomial order. The high level of agreement between the numerical results and measured data confirms the accuracy and consistency of the present numerical approach. This benchmark study establishes the capability of NekRS to perform reliable hydrodynamic simulations for sodium fast reactor applications and supports its use in design, licensing, and safety analyses.

CFD Benchmarking↗

Quantum entanglement correlations in double quark PDFs

Methods from Quantum Information Theory are used to scrutinize quantum correlations encoded in the two-quark density matrix over light-cone momentum fractions x 1 and x 2 . A nonperturbative three quark model light-cone wavefunction predicts significant nonclassical correlations associated with the “entanglement negativity” measure for asymmetric and small quark momentum fractions. We perform one step of QCD scale evolution of the entire density matrix, not just its diagonal (dPDF), by computing collinearly divergent corrections due to the emission of a gluon. Finally, we present first qualitative numerical results for single-step scale evolution of quantum entanglement correlations in double quark PDFs. At a higher Q 2 scale, the nonclassical correlations manifest in the dPDF for nearly symmetric momentum fractions.

Entanglement in field theory↗

Phase Switching as the Origin of Large Piezoelectric Response in Organic-Inorganic Perovskites: A First-Principles Study

Piezoelectrics are critical functional components of many practical applications such as sensors, ultrasonic transducers, actuators, medical imaging, telecommunications. So far, the best performing piezoelectrics are ferroelectric ceramics, many of which are toxic, heavy, hard, and cost-ineffective. Recently, a groundbreaking discovery of extraordinarily large piezoelectric coefficients in the family of organic-inorganic perovskites gave a hope for a cheaper, environmentally friendly, inexpensive, light-weight and flexible alternative. However, the origin of such response in organic-inorganic ferroelectrics whose spontaneous polarization is an order of magnitude smaller than for inorganic counterparts remains unclear. In this study we employ first-principles simulations to predict that the mechanism associated with large piezoelectric constants is of extrinsic origin and associated with switching between the stable phase and previously overlooked energetically competitive metastable phase that can be stabilized by the external stress. Here, the phase switching changes the polarization direction and, therefore, gives origin to large piezoelectric response, similar to PbZr$_{1-x}$Ti$_x$O$_3$ near morphotropic phase boundary. Existence of such metastable phases is likely to manifest as the dynamical molecular disorder above the Curie temperature and, therefore, could be intrinsic to the entire family of organic-inorganic ferroelectrics with such disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗