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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Knowledge graph-aided Bayesian active learning for top- K genetic interaction discovery

In silico methods for predicting the effects of multi-gene perturbations hold great promise for advancing functional genomics, computational drug discovery, and disease modeling. However, the development of these predictive algorithms for mammalian systems has been hampered by limited datasets and high experimental costs. In this study, we present a Bayesian active learning framework designed to discover pairwise host gene knockdowns that effectively inhibit viral proliferation in an in vitro HIV-1 infection model. Our method leverages a biological knowledge graph as side information and employs a computationally efficient batch diversification approach. We evaluated this framework using a dataset of viral load measurements obtained from multi-day dual-gene depletion experiments, encompassing all possible pairwise knockdowns of over 350 host genes associated with HIV infection. We demonstrate that our framework rapidly identifies the most effective gene knockdown pairs for reducing viral load. Furthermore, we show that incorporating side information enhances performance during the early stages of active learning (low data regime), while our batch diversification strategy significantly boosts performance in later stages (high data regime). This framework is general and can be adapted to explore gene interactions in other contexts, such as synthetic lethality prediction and mapping epistatic effects across quantitative trait loci.

Computational biology and bioinformatics↗
DOE OSTI2025

Semi-supervised permutation invariant particle-level anomaly detection

The development of analysis methods to distinguish potential beyond the Standard Model phenomena in a model-agnostic way can significantly enhance the discovery reach in collider experiments. However, the typical machine learning (ML) algorithms employed for this task require fixed length and ordered inputs that break the natural permutation invariance in collision events. To address this, a semi-supervised anomaly detection tool is presented that takes a variable number of particle-level inputs and leverages a signal model to encode this information into a permutation invariant, event-level representation via supervised training with a Particle Flow Network (PFN). Data events are then encoded into this representation and given as input to an autoencoder for unsupervised ANomaly deTEction on particLe flOw latent sPacE (ANTELOPE), classifying anomalous events based on a low-level and permutation invariant input modeling. Performance of the ANTELOPE architecture is evaluated on simulated samples of hadronic processes in a high energy collider experiment, showing good capability to distinguish disparate models of new physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Improving the accuracy of freight mode choice models: A case study using the 2017 CFS PUF data set and ensemble learning techniques

Here, the US Census Bureau has collected two rounds of experimental data from the Commodity Flow Survey, providing shipment-level characteristics of nationwide commodity movements, published in 2012 (i.e., Public Use Microdata) and in 2017 (i.e., Public Use File). With this information, data-driven methods have become increasingly valuable for understanding detailed patterns in freight logistics. In this study, we used the 2017 Commodity Flow Survey Public Use File data set to explore building a high-performance freight mode choice model, considering three main improvements: (1) constructing local models for each separate commodity/industry category; (2) extracting useful geographical features, particularly the derived distance of each freight mode between origin/destination zones; and (3) applying additional ensemble learning methods such as stacking or voting to combine results from local and unified models for improved performance. The proposed method achieved over 92% accuracy without incorporating external information, an over 19% increase compared to directly fitting Random Forests models over 10,000 samples. Furthermore, SHAP (Shapely Additive Explanations) values were computed to explain the outputs and major patterns obtained from the proposed model. The model framework could enhance the performance and interpretability of existing freight mode choice models.

42 ENGINEERING↗
DOE OSTI2022

Elucidating the temperature and density dependence of silver chloride hydration numbers in high-temperature water vapor: A first-principles molecular simulation study

Hydration numbers of metal complexes in low-density aqueous solutions are required for developing geochemical models for ore-forming metals and for designing supercritical desalination processes. In this study, we investigate the temperature and density dependence of the hydration numbers of silver chloride at 623 K, 673 K, and 713 K and densities of 10–100 kg/m 3 . Experimental estimates of the hydration number in the literature for AgCl at these conditions are inconclusive and possibly contradictory as to the temperature and density dependence. First-principles molecular simulation presents an attractive alternative to experimental measurements. Specifically, recent work shows that machine-learning-accelerated nested Monte Carlo simulations provide reliable estimates for the hydration numbers of CuCl at 623 K from 10 to 100 kg/m 3 . Using the same technique, we find a monotonic temperature dependence, with the hydration number decreasing slightly with increasing temperature. In addition, the simulation-predicted hydration numbers steadily increase with increasing density. These temperature and density trends are in agreement with certain experimental data sets. Therefore, this work demonstrates how first-principles Monte Carlo simulations assist in resolving discrepancies between experimental data sets. Our simulation results also correctly predict that the hydration number, and thus also the solubility, of AgCl is lower than that of CuCl under the same conditions. Furthermore, the bond length and angle formed between the water complex and AgCl differ from those for CuCl, consistent with the lower solubility of AgCl.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Panoramic Mapping of Phonon Transport from Ultrafast Electron Diffraction and Scientific Machine Learning

Abstract One central challenge in understanding phonon thermal transport is a lack of experimental tools to investigate frequency‐resolved phonon transport. Although recent advances in computation lead to frequency‐resolved information, it is hindered by unknown defects in bulk regions and at interfaces. Here, a framework that can uncover microscopic phonon transport information in heterostructures is presented, integrating state‐of‐the‐art ultrafast electron diffraction (UED) with advanced scientific machine learning (SciML). Taking advantage of the dual temporal and reciprocal‐space resolution in UED, and the ability of SciML to solve inverse problems involving coupled Boltzmann transport equations, the frequency‐dependent interfacial transmittance and frequency‐dependent relaxation times of the heterostructure from the diffraction patterns are reliably recovered. The framework is applied to experimental Au/Si UED data, and a transport pattern beyond the diffuse mismatch model is revealed, which further enables a direct reconstruction of real‐space, real‐time, frequency‐resolved phonon dynamics across the interface. The work provides a new pathway to probe interfacial phonon transport mechanisms with unprecedented details.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Toward a Climate OSSE Framework for Satellite Mission Design

The rich history of observing system simulation experiments (OSSEs) does not yet include a well-established framework for using climate models. The need for a climate OSSE is triggered by the need to quantify the value of a particular measurement for reducing the uncertainty in climate predictions, which differ from numerical weather predictions in that they depend on future atmospheric composition rather than the current state of the weather. However, both weather and climate modeling communities share a need for motivating major observing system investments. Here, we outline a new framework for climate OSSEs that leverages the use of machine learning to calibrate climate model physics against existing satellite data. We demonstrate its application using NASA’s GISS-E3 model to objectively quantify the value of potential future improvements in spaceborne measurements of Earth’s planetary boundary layer. A mature climate OSSE framework should be able to quantitatively compare the ability of proposed observing system architectures to answer a climate-related question, thus offering added value throughout the mission design process, which is subject to increasingly rapid advances in instrument and satellite technology. Technical considerations include selection of observational benchmarks and climate projection metrics, approaches to pinpoint the sources of model physics uncertainty that dominate uncertainty in projections, and the use of instrument simulators. Community and policy-making considerations include the potential to interface with an established culture of model intercomparison projects and a growing need to economically assess the value-driven efficiency of social spending on Earth observations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Reinforcement Learning-Guided Long-Timescale Simulation of Hydrogen Transport in Metals

Diffusion in alloys is an important class of atomic processes. However, atomistic simulations of diffusion in chemically complex solids are confronted with the timescale problem: the accessible simulation time is usually far shorter than that of experimental interest. In this work, long-timescale simulation methods are developed using reinforcement learning (RL) that extends simulation capability to match the duration of experimental interest. Two special limits, RL transition kinetics simulator (TKS) and RL low-energy states sampler (LSS), are implemented and explained in detail, while the meaning of general RL are also discussed. As a testbed, hydrogen diffusivity is computed using RL TKS in pure metals and a medium entropy alloy, CrCoNi, and compared with experiments. The algorithm can produce counter-intuitive hydrogen-vacancy cooperative motion. We also demonstrate that RL LSS can accelerate the sampling of low-energy configurations compared to the Metropolis–Hastings algorithm, using hydrogen migration to copper (111) surface as an example.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Direction-optimizing Label Propagation Framework for Structure Detection in Graphs: Design, Implementation, and Experimental Analysis

Label Propagation is not only a well-known machine learning algorithm for classification but also an effective method for discovering communities and connected components in networks. We propose a new Direction-optimizing Label Propagation Algorithm (DOLPA) framework that enhances the performance of the standard Label Propagation Algorithm (LPA), increases its scalability, and extends its versatility and application scope. As a central feature, the DOLPA framework relies on the use of frontiers and alternates between label push and label pull operations to attain high performance. It is formulated in such a way that the same basic algorithm can be used for finding communities or connected components in graphs by only changing the objective function used. Additionally, DOLPA has parameters for tuning the processing order of vertices in a graph to reduce the number of edges visited and improve the quality of solution obtained. We present the design and implementation of the enhanced algorithm as well as our shared-memory parallelization of it using OpenMP. We also present an extensive experimental evaluation of our implementations using the LFR benchmark and real-world networks drawn from various domains. Compared with an implementation of LPA for community detection available in a widely used network analysis software, we achieve at most five times the F-Score while maintaining similar runtime for graphs with overlapping communities. We also compare DOLPA against an implementation of the Louvain method for community detection using the same LFR-graphs and show that DOLPA achieves about three times the F-Score at just 10% of the runtime. For connected component decomposition, our algorithm achieves orders of magnitude speedups over the basic LP-based algorithm on large-diameter graphs, up to 13.2× speedup over the Shiloach-Vishkin algorithm, and up to 1.6× speedup over Afforest on an Intel Xeon processor using 40 threads.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Machine-Learning-aided Approach for Predicting the Thermal Expansion Behaviors in Advanced Test Reactor Capsules (NURETH-20 full paper)

Instrumented experiments at test reactors are essential to deploying new advanced reactor systems. Designing new experiments and generating data on specific conditions require both time and cost investment. A high-fidelity model of the experiment environment can be created using finite element analysis software to support the actual experiments, but computation time is still a concern in applying outcomes to real-time usage (e.g., a digital twin). This research proposes a machine-learning-aided approach to temperature and displacement predictions, based on the thickness of the outer gas gap on the experimental capsule used for the in-pile demonstration of a novel thermal conductivity probe in the Advanced Test Reactor. The capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. There were gas gaps between the fuel and rodlet and between the inner and outer capsule. The learning data consisted of an experimental capsule’s radial distributions of temperature and displacement, as obtained from Abaqus and the physical features. For the first step, temperature was predicted using three positional parameters. Then the displacement was predicted using six different positional parameters. Each physical feature was normalized to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement in all cases involving interpolation and extrapolation. Also, data similarity enhancement increased the similarity between training and target data increasing the predictive accuracy of machine-learning models. In some cases of extrapolation, the accuracy of the machine-learning model showed limited performance, but still data similarity enhancement improved the accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Artificial-intelligence-assisted analysis of 28 Si * → 7⁢𝛼 breakup data

Mid-weight 𝛼-conjugate nuclei are predicted to possess exotic toroid like resonances with high angular momenta. The search for these states in 28 Si* is the main point of two published experimental investigations of the peripheral 28 Si + 12 C reaction by Cao and collaborators and by Hannaman and collaborators. In this work, we develop a novel artificial intelligence (AI) based machine learning method utilizing the Gaussian Mixture Model (GMM) to analyze available experimental and theoretical data. Here, we additionally study the reaction with the Hybrid 𝛼-Cluster (H⁡𝛼⁢C) model. In all the examined data, our results suggest the presence of underlying structure which is close to that predicted for toroidal states.

Breakup reactions↗
DOE OSTI2020

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗
DOE OSTI2025

Converting sWeights to probabilities with density ratios

The use of machine learning approaches continues to have many benefits in experimental nuclear and particle physics. One common issue is generating training data which is sufficiently realistic to give reliable results. Here we advocate using real experimental data as the source of training data and demonstrate how one might subtract background contributions through the use of probabilistic weights which can be readily applied to training data. The sPlot formalism is a common tool used to isolate distributions from different sources. However, the negative sWeights produced by the sPlot technique can cause training problems and poor predictive power. This article demonstrates how density ratio estimation can be applied to convert sWeights to event probabilities, which we call drWeights. The drWeights can then be applied to produce the distributions of interest and are consistent with direct use of the sWeights. This article will also show how decision trees are particularly well suited to convert sWeights, with the benefit of fast prediction rates and adaptability to aspects of experimental data such as the data sample size and proportions of different event sources. We also show that a density ratio product approach in which the initial drWeights are reweighted by an additional converter gives substantially better results.

Glazier, Derek I. [Univ. of Glasgow, Scotland (Uni↗
DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗
DOE OSTI2025

DONUT: physics-aware machine learning for real-time X-ray nanodiffraction analysis

Coherent X-ray scattering techniques are critical for investigating the fundamental structural properties of materials at the nanoscale. While advancements have made these experiments more accessible, real-time analysis remains a significant bottleneck, often hindered by artifacts and computational demands. In scanning X-ray nanodiffraction microscopy, which is widely used to spatially resolve structural heterogeneities, this challenge is compounded by the convolution of the divergent beam with the sample’s local structure. To address this, we introduce DONUT (Diffraction with Optics for Nanobeam by Unsupervised Training), a physics-aware neural network designed for the rapid and automated analysis of nanobeam diffraction data. By incorporating a differentiable geometric diffraction model directly into its architecture, DONUT learns to predict crystal lattice strain and orientation in real-time. Crucially, this is achieved without reliance on labeled datasets or pre-training, overcoming a fundamental limitation for supervised machine learning in X-ray science. We demonstrate experimentally that DONUT accurately extracts all features within the data over 200 times more efficiently than conventional fitting methods.

Materials science↗
DOE OSTI2024

On ultrafast x-ray scattering methods for magnetism

With the introduction of x-ray free electron laser sources around the world, new scientific approaches for visualizing matter at fundamental length and time-scales have become possible. As it relates to magnetism and ‘magnetic-type’ systems, advanced methods are being developed for studying ultrafast magnetic responses on the time-scales at which they occur. We describe three capabilities which have the potential to seed new directions in this area and present original results from each: pump-probe x-ray scattering with low energy excitation, x-ray photon fluctuation spectroscopy, and ultrafast diffuse x-ray scattering. By combining these experimental techniques with advanced modeling together with machine learning, we describe how the combination of these domains allows for a new understanding in the field of magnetism. Finally, we give an outlook for future areas of investigation and the newly developed instruments which will take us there.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Operational experience with the Proto-DUNE NP02 and NP04 large volume liquid argon cryostats and their cryogenic systems at CERN

The far Detector of the Deep Underground Neutrino Experiment (DUNE) will be housed in several large volume (about 12.500 m$^{3}$) liquid argon cryostats. The design principle of these large cryostats, and of the cryogenic system belonging to them, are investigated through the design, construction and operation of a series of prototype installations.The Neutrino Platform 02 (NP02) and 04 (NP04) cryostats, placed at CERN, contain DUNE proto-type detectors, each of them housed in an about 600 m$^{3}$ liquid argon bath. These cryostats, based on the membrane cryostat principle, and their cryogenic systems have been designed according to the DUNE principle. Measurements performed in these test stands shall confirm the foreseen heat loads into the cryostat systems entering via its walls, via detector cabling and via the cold electronics, shall confirm the low temperature gradient over the active detector volume and shall certify the liquid argon purification principle.This paper introduces the requirements for the NP02 and NP04 cryostats and their cryogenic systems, describes the design principle applied to these two systems and gives an overview of the different modes in which the two systems have been operating. The experimental results are presented and discussed, and “lessons learned” for future installations are dawn.

43 PARTICLE ACCELERATORS↗