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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Predicting Large‐Scale Systematic Missing Pipe Attributes in Water Distribution Networks

Water distribution network (WDN) models are an essential tool used by water utilities for hydraulic analysis. Unfortunately, missing data and insufficient resources often make creating and maintaining these models unfeasible. Existing methods to address missing pipe properties, like sequential imputation for missing values and reconstruction using graph metrics, are designed to accommodate random patterns of missing information and require a significant percentage of the system's attributes to be known. However, these data completeness assumptions do not always align with real‐world scenarios where large sections of the WDN model have missing data. To address this challenge, this study proposes a data‐driven approach for estimating pipe diameter when considering different spatial patterns and degrees of data completeness (i.e., 0%–90%). Using data from 16 WDNs in Kentucky, this study compares the use of machine learning (ML) using topological and geospatial features against an existing deterministic approach. Results demonstrate that WDN models with pipe diameters predicted by the proposed ML method had comparable hydraulic performance to the ground truth models. Moreover, results showed that ML method performance varies between WDNs of differing topological classification. Insights from this study help advance the ability to leverage partial data to create and maintain WDN models amid uncertainty and inadequate resources.

Poff, Jason W. [Oregon State Univ., Corvallis, OR ↗
DOE OSTI2020

ExpoKids: An R-based tool for characterizing aggregate chemical exposure during childhood

Background: Aggregate exposure, the combined exposures to a single chemical from all pathways, is a critical children’s health issue. Objective: The primary objective is to develop a tool to illustrate potential differences in aggregate exposure at various childhood lifestages and the adult lifestage. Methods: We developed ExpoKids (an R-based tool) using oral exposure estimates across lifestages generated by US EPA’s Exposure Factors Interactive Resource for Scenarios Tool (ExpoFIRST). Results: ExpoKids is applied to illustrate aggregate oral exposure, for ten media, as average daily doses (ADD) and lifetime average daily doses (LADD) in five graphs organized across seven postnatal childhood lifestages and the adult lifestage. This data visualization tool conveys ExpoFIRST findings, from available exposure data, to highlight the relative contributions of media and lifestages to chemical exposure. To evaluate the effectiveness of ExpoKids, three chemical case examples (di[2-ethylhexyl] phthalate [DEHP], manganese, and endosulfan) were explored. Data available from the published literature and databases for each case example were used to explore research questions regarding media and lifestage contributions to aggregate exposure. Significance: These illustrative case examples demonstrate ExpoKids’ versatile application to explore a diverse set of children’s health risk assessment and management questions by visually depicting specific media and lifestage contributions to aggregate exposure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost

Bond dissociation enthalpies (BDEs) of organic molecules play a fundamental role in determining chemical reactivity and selectivity. However, BDE computations at sufficiently high levels of quantum mechanical theory require substantial computing resources. In this paper, we develop a machine learning model capable of accurately predicting BDEs for organic molecules in a fraction of a second. We perform automated density functional theory (DFT) calculations at the M06-2X/def2-TZVP level of theory for 42,577 small organic molecules, resulting in 290,664 BDEs. A graph neural network trained on a subset of these results achieves a mean absolute error of 0.58 kcal mol-1 (vs DFT) for BDEs of unseen molecules. We further demonstrate the model on two applications: first, we rapidly and accurately predict major sites of hydrogen abstraction in the metabolism of drug-like molecules, and second, we determine the dominant molecular fragmentation pathways during soot formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Density of states prediction for materials discovery via contrastive learning from probabilistic embeddings

Abstract Machine learning for materials discovery has largely focused on predicting an individual scalar rather than multiple related properties, where spectral properties are an important example. Fundamental spectral properties include the phonon density of states (phDOS) and the electronic density of states (eDOS), which individually or collectively are the origins of a breadth of materials observables and functions. Building upon the success of graph attention networks for encoding crystalline materials, we introduce a probabilistic embedding generator specifically tailored to the prediction of spectral properties. Coupled with supervised contrastive learning, our materials-to-spectrum (Mat2Spec) model outperforms state-of-the-art methods for predicting ab initio phDOS and eDOS for crystalline materials. We demonstrate Mat2Spec’s ability to identify eDOS gaps below the Fermi energy, validating predictions with ab initio calculations and thereby discovering candidate thermoelectrics and transparent conductors. Mat2Spec is an exemplar framework for predicting spectral properties of materials via strategically incorporated machine learning techniques.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility

Mechanistic understanding of large molecule conversion and the discovery of suitable heterogeneous catalysts have been lagging due to the combinatorial inventory of intermediates and the inability of humans to enumerate all structures. Here, we introduce an automated framework to predict stable configurations on transition metal surfaces and demonstrate its validity for adsorbates with up to 6 carbon and oxygen atoms on 11 metals, enabling the exploration of ~10 8 potential configurations. It combines a graph enumeration platform, force field, multi-fidelity DFT calculations, and first-principles trained machine learning. Clusters in the data reveal groups of catalysts stabilizing different structures and expose selective catalysts for showcase transformations, such as the ethylene epoxidation on Ag and Cu and the lack of C-C scission chemistry on Au. Deviations from the commonly assumed atom valency rule of small adsorbates are also manifested. This library can be leveraged to identify catalysts for converting large molecules computationally.

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

Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous systems: the amorphous structure of polymers requires multiple, repeated sampling to reduce noise and the slow relaxation requires long simulation time for convergence. Here, we accelerate the screening with a multi-task graph neural network that learns from a large amount of noisy, unconverged, short MD data and a small number of converged, long MD data. We achieve accurate predictions of 4 different converged properties and screen a space of 6247 polymers that is orders of magnitude larger than previous computational studies. Further, we extract several design principles for polymer electrolytes and provide an open dataset for the community. Our approach could be applicable to a broad class of material discovery problems that involve the simulation of complex, amorphous materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Deep reaction network exploration at a heterogeneous catalytic interface

Characterizing the reaction energies and barriers of reaction networks is central to catalyst development. However, heterogeneous catalytic surfaces pose several unique challenges to automatic reaction network characterization, including large sizes and open-ended reactant sets, that make ad hoc network construction the current state-of-the-art. Here, we show how automated network exploration algorithms can be adapted to the constraints of heterogeneous systems using ethylene oligomerization on silica-supported single-site Ga 3+ as a model system. Using only graph-based rules for exploring the network and elementary constraints based on activation energy and size for identifying network terminations, a comprehensive reaction network is generated and validated against standard methods. The algorithm (re)discovers the Ga-alkyl-centered Cossee-Arlman mechanism that is hypothesized to drive major product formation while also predicting several new pathways for producing alkanes and coke precursors. These results demonstrate that automated reaction exploration algorithms are rapidly maturing towards general purpose capability for exploratory catalytic applications.

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

Adsorbate chemical environment-based machine learning framework for heterogeneous catalysis

Abstract Heterogeneous catalytic reactions are influenced by a subtle interplay of atomic-scale factors, ranging from the catalysts’ local morphology to the presence of high adsorbate coverages. Describing such phenomena via computational models requires generation and analysis of a large space of atomic configurations. To address this challenge, we present Adsorbate Chemical Environment-based Graph Convolution Neural Network (ACE-GCN), a screening workflow that accounts for atomistic configurations comprising diverse adsorbates, binding locations, coordination environments, and substrate morphologies. Using this workflow, we develop catalyst surface models for two illustrative systems: (i) NO adsorbed on a Pt 3 Sn(111) alloy surface, of interest for nitrate electroreduction processes, where high adsorbate coverages combined with low symmetry of the alloy substrate produce a large configurational space, and (ii) OH* adsorbed on a stepped Pt(221) facet, of relevance to the Oxygen Reduction Reaction, where configurational complexity results from the presence of irregular crystal surfaces, high adsorbate coverages, and directionally-dependent adsorbate-adsorbate interactions. In both cases, the ACE-GCN model, trained on a fraction (~10%) of the total DFT-relaxed configurations, successfully describes trends in the relative stabilities of unrelaxed atomic configurations sampled from a large configurational space. This approach is expected to accelerate development of rigorous descriptions of catalyst surfaces under in-situ conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The learnability of Pauli noise

Recently, several quantum benchmarking algorithms have been developed to characterize noisy quantum gates on today’s quantum devices. A fundamental issue in benchmarking is that not everything about quantum noise is learnable due to the existence of gauge freedom, leaving open the question what information is learnable and what is not, which is unclear even for a single CNOT gate. Here we give a precise characterization of the learnability of Pauli noise channels attached to Clifford gates using graph theoretical tools. Our results reveal the optimality of cycle benchmarking in the sense that it can extract all learnable information about Pauli noise. We experimentally demonstrate noise characterization of IBM’s CNOT gate up to 2 unlearnable degrees of freedom, for which we obtain bounds using physical constraints. In addition, we show that an attempt to extract unlearnable information by ignoring state preparation noise yields unphysical estimates, which is used to lower bound the state preparation noise.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC’s assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD’s DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC’s dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA’s crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

ON-OFF neuromorphic ISING machines using Fowler-Nordheim annealers

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using a Fowler-Nordheim quantum mechanical tunneling based threshold-annealing process. The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing dynamics onto a network of integrate-and-fire neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer and the resulting spiking dynamics replicates the optimal escape mechanism and convergence of SA, particularly at low-temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved benchmark combinatorial optimization problems such as MAX-CUT and Max Independent Set. Across multiple runs, NeuroSA consistently generates distribution of solutions that are concentrated around the state-of-the-art results (within 99%) or surpass the current state-of-the-art solutions for Max Independent Set benchmarks. Furthermore, NeuroSA is able to achieve these superior distributions without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform.

42 ENGINEERING↗
DOE OSTI2025

Labels as a feature: Network homophily for systematically annotating human GPCR drug-target interactions

Machine learning has revolutionized drug discovery by enabling the exploration of vast, uncharted chemical spaces essential for discovering novel patentable drugs. Despite the critical role of human G protein-coupled receptors in FDA-approved drugs, exhaustive in-distribution drug-target interaction testing across all pairs of human G protein-coupled receptors and known drugs is rare due to significant economic and technical challenges. This often leaves off-target effects unexplored, which poses a considerable risk to drug safety. In contrast to the traditional focus on out-of-distribution exploration (drug discovery), we introduce a neighborhood-to-prediction model termed Chemical Space Neural Networks that leverages network homophily and training-free graph neural networks with labels as features. We show that Chemical Space Neural Networks’ ability to make accurate predictions strongly correlates with network homophily. Thus, labels as features strongly increase a machine learning model’s capacity to enhance in-distribution prediction accuracy, which we show by integrating labeled data during inference. We validate these advancements in a high-throughput yeast biosensing system (3773 drug-target interactions, 539 compounds, 7 human G protein-coupled receptors) to discover novel drug-target interactions for FDA-approved drugs and to expand the general understanding of how to build reliable predictors to guide experimental verification.

Hansson, Frederik G↗
DOE OSTI2022

Scale-invariant machine-learning model accelerates the discovery of quaternary chalcogenides with ultralow lattice thermal conductivity

We design an advanced machine-learning (ML) model based on crystal graph convolutional neural network that is insensitive to volumes (i.e., scale) of the input crystal structures to discover novel quaternary chalcogenides, AMM'Q 3 (A/M/M' = alkali, alkaline earth, post-transition metals, lanthanides, and Q = chalcogens). These compounds are shown to possess ultralow lattice thermal conductivity (κ l ), a desired requirement for thermal-barrier coatings and thermoelectrics. Upon screening the thermodynamic stability of ~1 million compounds using the ML model iteratively and performing density-functional theory (DFT) calculations for a small fraction of compounds, we discover 99 compounds that are validated to be stable in DFT. Taking several DFT-stable compounds, we calculate their κ l using Peierls–Boltzmann transport equation, which reveals ultralow κ l (<2 Wm -1 K -1 at room temperature) due to their soft elasticity and strong phonon anharmonicity. Our work demonstrates the high efficiency of scale-invariant ML model in predicting novel compounds and presents experimental-research opportunities with these new compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Robust training of machine learning interatomic potentials with dimensionality reduction and stratified sampling

Abstract Machine learning interatomic potentials (MLIPs) enable accurate simulations of materials at scales beyond that accessible by ab initio methods and play an increasingly important role in the study and design of materials. However, MLIPs are only as accurate and robust as the data on which they are trained. Here, we present DImensionality-Reduced Encoded Clusters with sTratified (DIRECT) sampling as an approach to select a robust training set of structures from a large and complex configuration space. By applying DIRECT sampling on the Materials Project relaxation trajectories dataset with over one million structures and 89 elements, we develop an improved materials 3-body graph network (M3GNet) universal potential that extrapolates more reliably to unseen structures. We further show that molecular dynamics (MD) simulations with the M3GNet universal potential can be used instead of expensive ab initio MD to rapidly create a large configuration space for target systems. We combined this scheme with DIRECT sampling to develop a reliable moment tensor potential for titanium hydrides without the need for iterative augmentation of training structures. This work paves the way for robust high-throughput development of MLIPs across any compositional complexity.

Qi, Ji (ORCID:0000000158089931)↗
DOE OSTI2024

Active learning of ternary alloy structures and energies

Abstract Machine learning models with uncertainty quantification have recently emerged as attractive tools to accelerate the navigation of catalyst design spaces in a data-efficient manner. Here, we combine active learning with a dropout graph convolutional network (dGCN) as a surrogate model to explore the complex materials space of high-entropy alloys (HEAs). We train the dGCN on the formation energies of disordered binary alloy structures in the Pd-Pt-Sn ternary alloy system and improve predictions on ternary structures by performing reduced optimization of the formation free energy, the target property that determines HEA stability, over ensembles of ternary structures constructed based on two coordinate systems: (a) a physics-informed ternary composition space, and (b) data-driven coordinates discovered by the Diffusion Maps manifold learning scheme. Both reduced optimization techniques improve predictions of the formation free energy in the ternary alloy space with a significantly reduced number of DFT calculations compared to a high-fidelity model. The physics-based scheme converges to the target property in a manner akin to a depth-first strategy, whereas the data-driven scheme appears more akin to a breadth-first approach. Both sampling schemes, coupled with our acquisition function, successfully exploit a database of DFT-calculated binary alloy structures and energies, augmented with a relatively small number of ternary alloy calculations, to identify stable ternary HEA compositions and structures. This generalized framework can be extended to incorporate more complex bulk and surface structural motifs, and the results demonstrate that significant dimensionality reduction is possible in thermodynamic sampling problems when suitable active learning schemes are employed.

Chemistry↗
DOE OSTI2025

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗