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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The MURAVES muon telescope: a low power consumption muon tracker for muon radiography applications

Muon Radiography or muography is based on the measurement of the absorption or scattering of cosmic muons, as they pass through the interior of large scale bodies, In particular, absorption muography has been applied to investigate the presence of hidden cavities inside the pyramids or underground, as well as the interior of volcanoes’ edifices. The MURAVES project has the challenging aim of investigating the density distribution inside the summit of Mt. Vesuvius. The information, together with that coming from gravimetric measurements, is useful as input to models, to predict how an eruption may develop. The MURAVES apparatus is a robust and low power consumption muon telescope consisting of an array of three identical and independent muon trackers, which provide in a modular way a total sensitive area of three square meters. Each tracker consists of four doublets of planes of plastic scintillator bars with orthogonal orientation, optically coupled to Silicon photomultipliers for the readout of the signal. The muon telescope has been installed on the slope of the volcano and has collected a first set of data, which are being analyzed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Heat metrics and thresholds reshape population exposure and inequality signals

Extreme heat is intensifying worldwide, yet estimates of heat hazard and exposure inequality depend on both the heat metric and how extreme days are defined. Using summer 2022 across the Mediterranean, we quantify population heat exposure with four metrics—land surface temperature (LST), air temperature (Ta), heat index (HI), and wet-bulb globe temperature (WBGT)—under absolute (fixed-value) and relative (anomaly-based) thresholds. Under absolute thresholds, total heat exposure differs by more than two orders of magnitude across metrics (31.3 billion person-days for Ta vs 0.3 billion for HI). Geographic hotspots also diverge: WBGT concentrates in humid coastal North Africa (e.g. the Nile Delta), whereas Ta and LST are more widespread. Under relative thresholds, exposure totals converge and cross-metric hotspot agreement increases (e.g. Ta–WBGT top-tercile overlap increases from 10.7% to 29.0%), shifting hotspots toward densely populated southern Europe. Crucially, the exposure–deprivation relationship also reverses across threshold frameworks: absolute thresholds concentrate exposure in more deprived North Africa and the Middle East, whereas relative thresholds shift the burden toward less-deprived European cities. This sensitivity is decision-relevant: city rankings based on WBGT exposure duration are almost completely reordered when switching threshold frameworks. Threshold choice therefore systematically reshapes hotspot patterns and inequality signals. Reporting both absolute and relative exposures can reveal hidden hotspots and support more targeted heat-risk monitoring and intervention planning.

Mediterranean↗
DOE OSTI2022

The SAGEX review on scattering amplitudes Chapter 2: An invitation to color-kinematics duality and the double copy

Abstract Advances in scattering amplitudes have exposed previously-hidden color-kinematics and double-copy structures in theories ranging from gauge and gravity theories to effective field theories such as chiral perturbation theory and the Born–Infeld model. These novel structures both simplify higher-order calculations and pose tantalizing questions related to a unified framework underlying relativistic quantum theories. This introductory mini-review article invites further exploration of these topics. After a brief introduction to color-kinematics duality and the double copy as they emerge at tree and loop-level in gauge and gravity theories, we present two distinct examples: (1) an introduction to the web of double-copy-constructible theories, and (2) a discussion of the application of the double copy to calculation relevant to gravitational-wave physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Determination of latent dimensionality in international trade flow

Currently, high-dimensional data is ubiquitous in data science, which necessitates the development of techniques to decompose and interpret such multidimensional (aka tensor) datasets. Finding a low dimensional representation of the data, that is, its inherent structure, is one of the approaches that can serve to understand the dynamics of low dimensional latent features hidden in the data. Moreover, decomposition methods with non-negative constraints are shown to extract more insightful factors. Nonnegative RESCAL is one such technique, particularly well suited to analyze self-relational data, such as dynamic networks found in international trade flows. Particularly, non-negative RESCAL computes a low dimensional tensor representation by finding the latent space containing multiple modalities. Furthermore, estimating the dimensionality of this latent space is crucial for extracting meaningful latent features. Here, to determine the dimensionality of the latent space with non-negative RESCAL, we propose a latent dimension determination method which is based on clustering of the solutions of multiple realizations of non-negative RESCAL decompositions. We demonstrate the performance of our model selection method on synthetic data. We then apply our method to decompose a network of international trade flows data from International Monetary Fund and shows that with a correct latent dimension determination, the resulting features are able to capture relevant empirical facts from economic literature.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A detailed study of interpretability of deep neural network based top taggers

Abstract Recent developments in the methods of explainable artificial intelligence (XAI) allow researchers to explore the inner workings of deep neural networks (DNNs), revealing crucial information about input–output relationships and realizing how data connects with machine learning models. In this paper we explore interpretability of DNN models designed to identify jets coming from top quark decay in high energy proton–proton collisions at the Large Hadron Collider. We review a subset of existing top tagger models and explore different quantitative methods to identify which features play the most important roles in identifying the top jets. We also investigate how and why feature importance varies across different XAI metrics, how correlations among features impact their explainability, and how latent space representations encode information as well as correlate with physically meaningful quantities. Our studies uncover some major pitfalls of existing XAI methods and illustrate how they can be overcome to obtain consistent and meaningful interpretation of these models. We additionally illustrate the activity of hidden layers as neural activation pattern diagrams and demonstrate how they can be used to understand how DNNs relay information across the layers and how this understanding can help to make such models significantly simpler by allowing effective model reoptimization and hyperparameter tuning. These studies not only facilitate a methodological approach to interpreting models but also unveil new insights about what these models learn. Incorporating these observations into augmented model design, we propose the particle flow interaction network model and demonstrate how interpretability-inspired model augmentation can improve top tagging performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Improving materials property predictions for graph neural networks with minimal feature engineering *

Graph neural networks (GNNs) have been employed in materials research to predict physical and functional properties, and have achieved superior performance in several application domains over prior machine learning approaches. Recent studies incorporate features of increasing complexity such as Gaussian radial functions, plane wave functions, and angular terms to augment the neural network models, with the expectation that these features are critical for achieving a high performance. Here, we propose a GNN that adopts edge convolution where hidden edge features evolve during training and extensive attention mechanisms, and operates on simple graphs with atoms as nodes and distances between them as edges. As a result, the same model can be used for very different tasks as no other domain-specific features are used. With a model that uses no feature engineering, we achieve performance comparable with state-of-the-art models with elaborate features for formation energy and band gap prediction with standard benchmarks; we achieve even better performance when the dataset size increases. Although some domain-specific datasets still require hand-crafted features to achieve state-of-the-art results, our selected architecture choices greatly reduce the need for elaborate feature engineering and still maintain predictive power in comparison.

42 ENGINEERING↗
DOE OSTI2024

Mapping causal pathways with structural modes fingerprint for perovskite oxides

Abstract Causality is innate to the determination of the fundamental mechanism controlling any physical phenomena. However, combining causality within the standard practices of computational modelling to understand structure-functionality connections is extremely rare. This work proposes a fingerprint based on key structural modes for ABO 3 -type perovskite oxides and its derivatives, combined with causal models, for predicting Kohn–Sham energies. Our study of causal models captures the inherent coupling between structural modes such as rotation, tilt and antiferroelectric displacements, responsible for phase transition, polarization, magnetization and metal–insulator transition, exhibited by these materials. Although developed for modelling specific functionality, this method is universally applicable to derive other functionalities and even different material classes while tracking hidden causal mechanisms via structural distortions.

42 ENGINEERING↗
DOE OSTI2025

Exploring the energy landscape of RBMs: reciprocal space insights into bosons, hierarchical learning and symmetry breaking

Deep generative models have become ubiquitous due to their ability to learn and sample from complex distributions. Despite the proliferation of various frameworks, the relationships among these models remain largely unexplored, a gap that hinders the development of a unified theory of AI learning. In this work, we address two central challenges: clarifying the connections between different deep generative models and deepening our understanding of their learning mechanisms. We focus on Restricted Boltzmann Machines (RBMs), a class of generative models known for their universal approximation capabilities for discrete distributions. By introducing a reciprocal space formulation for RBMs, we reveal a connection between these models, diffusion processes, and systems of coupled bosons. Our analysis shows that at initialization, the RBM operates at a saddle point, where the local curvature is determined by the singular values of the weight matrix, whose distribution follows the Marc̆enko-Pastur law and exhibits rotational symmetry. During training, this rotational symmetry is broken due to hierarchical learning, where different degrees of freedom progressively capture features at multiple levels of abstraction. This leads to a symmetry breaking in the energy landscape, reminiscent of Landau’s theory. This symmetry breaking in the energy landscape is characterized by the singular values and the weight matrix eigenvector matrix. We derive the corresponding free energy in a mean-field approximation. We show that in the limit of infinite size RBM, the reciprocal variables are Gaussian distributed. Our findings indicate that in this regime, there will be some modes for which the diffusion process will not converge to the Boltzmann distribution. To illustrate our results, we trained replicas of RBMs with different hidden layer sizes using the MNIST dataset. Our findings not only bridge the gap between disparate generative frameworks but also shed light on the fundamental processes underpinning learning in deep generative models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Latent Twins

Over the past decade, scientific machine learning has transformed the development of mathematical and computational frameworks for analyzing, modeling, and predicting complex systems. From inverse problems to numerical partial differential equations (PDEs), dynamical systems, and model reduction, these advances have pushed the boundaries of what can be simulated. Yet they have often progressed in parallel, with representation learning and algorithmic solution methods evolving largely as separate pipelines. With Latent Twins, we propose a unifying mathematical framework that creates a hidden surrogate in latent space for the underlying equations. Whereas digital twins mirror physical systems in the digital world, Latent Twins mirror mathematical systems in a learned latent space governed by operators. Through this lens, classical modeling, inversion, model reduction, and operator approximation all emerge as special cases of a single principle. We establish the fundamental approximation properties of Latent Twins for both ordinary differential equations (ODEs) and PDEs and demonstrate the framework across three representative settings: (i) canonical ODEs, capturing diverse dynamical regimes; (ii) a PDE benchmark using the shallow-water equations, contrasting Latent Twin simulations with deep operator network and forecasts with a four-dimensional variational method baseline; and (iii) a challenging real-data geopotential reanalysis dataset, reconstructing and forecasting from sparse, noisy observations. Latent Twins provide a compact, interpretable surrogate for solution operators that evaluate across arbitrary time gaps in a single-shot, while remaining compatible with scientific pipelines such as assimilation, control, and uncertainty quantification. Looking forward, this framework offers scalable, theory-grounded surrogates that bridge data-driven representation learning and classical scientific modeling across disciplines.

Latent Twins↗
DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2025

NEAR: Neural Embeddings for Amino acid Relationships

Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be prone to a high rate of false labeling. Here, we present NEAR, a method based on neural representation learning that is designed to improve both speed and accuracy of search for likely homologs in a large protein sequence database. NEAR’s ResNet embedding model is trained using contrastive learning guided by trusted sequence alignments. It computes per-residue embeddings for target and query protein sequences, and identifies alignment candidates with a pipeline consisting of residue-level k-NN search and a simple neighbor aggregation scheme. Tests on a benchmark consisting of trusted remote homologs and randomly shuffled decoy sequences reveal that NEAR substantially improves accuracy relative to state-of-the-art PLMs, with lower memory requirements and faster embedding and search speed. While these results suggest that the NEAR model may be useful for standalone homology detection with increased sensitivity over standard alignment-based methods, in this manuscript we focus on a more straightforward analysis of the model’s value as a high-speed pre-filter for sensitive annotation. In that context, NEAR is at least 5x faster than the pre-filter currently used in the widely-used profile hidden Markov model (pHMM) search tool HMMER3, and also outperforms the pre-filter used in our fast pHMM tool, nail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi

Abstract This review highlights new advances in the emerging field of ‘Fungi-on-a-Chip’ microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Induced microseismicity and tremor signatures illuminate different slip behaviours in a natural shale fault reactivated by a fluid pressure stimulation (Mont Terri)

SUMMARY Fault slip induced by fluid perturbation in shale formations may only lead to a sparse seismicity. However, fault slip may strongly impact the integrity of shale formations that serve as caprocks for geological reservoirs holding buoyant fluids such as CO2, natural gas or hydrogen. A better understanding of the fluid reactivation processes of fault and the seismic triggering process is therefore critical for reservoir monitoring and fault stability. Here we analyse the seismic responses of a shale fault exposed to fluid pressurization during an in situ field-scale injection experiment at ∼340 m depth in the Mont Terri underground research laboratory (Switzerland). Two main types of seismic signals are observed as the fault was activated and started to slowly slip. After an aseismic phase, we observed tremor signatures and an increase in noise amplitude, which were directly associated with the slowly propagating fault slip in response to fluid injection. These signatures were later followed by micro-earthquakes that seem to occur further away from the fluid-pressurized area. We interpret these micro-earthquakes to be triggered by stress perturbations from the main slip growth. These two classes of seismic responses therefore highlight two different processes. Tremors seem to be a more direct observation for the fluid-induced slip propagation than micro-earthquakes. Even hidden in the noise, they precede earthquake failures, thus providing a useful tool for monitoring fluid leakage activated by slow deformation on low permeable shale faults, with applications for sealing integrity of caprocks.

De Barros, Louis (ORCID:0000000255419162)↗
DOE OSTI2023

A unified and constructive framework for the universality of neural networks

Abstract One of the reasons why many neural networks are capable of replicating complicated tasks or functions is their universal approximation property. Though the past few decades have seen tremendous advances in theories of neural networks, a single constructive and elementary framework for neural network universality remains unavailable. This paper is an effort to provide a unified and constructive framework for the universality of a large class of activation functions including most of the existing ones. At the heart of the framework is the concept of neural network approximate identity (nAI). The main result is as follows: any nAI activation function is universal in the space of continuous functions on compacta. It turns out that most of the existing activation functions are nAI, and thus universal. The framework induces several advantages over the contemporary counterparts. First, it is constructive with elementary means from functional analysis, probability theory, and numerical analysis. Second, it is one of the first unified and constructive attempts that is valid for most of the existing activation functions. Third, it provides new proofs for most activation functions. Fourth, for a given activation and error tolerance, the framework provides precisely the architecture of the corresponding one-hidden neural network with a predetermined number of neurons and the values of weights/biases. Fifth, the framework allows us to abstractly present the first universal approximation with a favorable non-asymptotic rate. Sixth, our framework also provides insights into the developments, and hence providing constructive derivations, of some of the existing approaches.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Evidence for a high-energy tail in the gamma-ray spectra of globular clusters

Millisecond pulsars are very likely the main source of gamma-ray emission from globular clusters. However, the relative contributions of two separate emission processes – curvature radiation from millisecond pulsar magnetospheres versus inverse Compton emission from relativistic pairs launched into the globular cluster environment by millisecond pulsars – have long been unclear. To address this, we search for evidence of inverse Compton emission in 8-yr Fermi–LAT data from the directions of 157 Milky Way globular clusters. We find a mildly statistically significant (3.8σ) correlation between the measured globular cluster gamma-ray luminosities and their photon field energy densities. However, this may also be explained by a hidden correlation between the photon field densities and the stellar encounter rates of globular clusters. Analysed in toto, we demonstrate that the gamma-ray emission of globular clusters can be resolved spectrally into two components: (i) an exponentially cut-off power law and (ii) a pure power law. The latter component – which we uncover at a significance of 8.2σ – has a power index of 2.79 ± 0.25. It is most naturally interpreted as inverse Compton emission by cosmic-ray electrons and positrons injected by millisecond pulsars. Here, we find the luminosity of this power-law component is comparable to, or slightly smaller than, the luminosity of the curved component, suggesting the fraction of millisecond pulsar spin-down luminosity into relativistic leptons is similar to the fraction of the spin-down luminosity into prompt magnetospheric radiation.

79 ASTRONOMY AND ASTROPHYSICS↗