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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗
DOE OSTI2020

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantum Chemistry-Driven Machine Learning Approach for the Prediction of the Surface Tension and Speed of Sound in Ionic Liquids

Ionic liquids (ILs) have unique solvent properties and have thus garnered significant interest. However, exhaustive experimental determination of the physicochemical properties of ILs is unrealistic due to the large structural diversity of anions and cations, their high cost, the requirements of elevated temperature and pressure, and the time required. To circumvent these experimental costs, computational approaches to accurately calculate these properties have emerged. Here in the present study, we present a demonstration of two machine learning (ML) models for the prediction of two critical IL physical properties, the surface tension and the speed of sound, across a wide range of temperatures and pressures. The models make use of molecular descriptors derived from the COSMO-RS, a quantum chemical-based model. The ML models show excellent agreement with experimental observations, with an R2 value of 0.96–0.99 and RMSE of 1.71 mN/m and 16.12 m/s for the surface tension and speed of sound, respectively. This work paves the way for the development of COSMO-RS-informed ML models for the prediction of IL properties which can help to further optimize and accelerate technology development for ILs.

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

Converting tabular data into images for deep learning with convolutional neural networks

Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabular data do not assume a spatial relationship between features, and thus are unsuitable for modeling using CNNs. To meet this challenge, we develop a novel algorithm, image generator for tabular data (IGTD), to transform tabular data into images by assigning features to pixel positions so that similar features are close to each other in the image. The algorithm searches for an optimized assignment by minimizing the difference between the ranking of distances between features and the ranking of distances between their assigned pixels in the image. We apply IGTD to transform gene expression profiles of cancer cell lines (CCLs) and molecular descriptors of drugs into their respective image representations. Compared with existing transformation methods, IGTD generates compact image representations with better preservation of feature neighborhood structure. Evaluated on benchmark drug screening datasets, CNNs trained on IGTD image representations of CCLs and drugs exhibit a better performance of predicting anti-cancer drug response than both CNNs trained on alternative image representations and prediction models trained on the original tabular data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The Use of Machine Learning Models for Predicting the Dielectric Strength of Gases

Technological advancements in high voltage systems have pushed sulfur hexafluoride (SF6) to its operational limits. Furthermore, this gas has other drawbacks including a high liquefaction temperature and a high global warming potential. Therefore, there has been an urgent need to find alternative gases with high dielectric strength (DS). In this work, density functional theory (DFT) is used to calculate molecular descriptors that are fed into an artificial neural network (ANN) and a random forest (RF). These machine learning (ML) models are then used to predict the DS for hundreds of molecules. A finite element model (FEM) is also used to calculate the electric field profile of multiple simple electrode geometries as the applied voltage to the system is increased. Results indicate that the random forest model has better generalization to unseen data than the neural network. The highest DS value predicted by the RF was 2.16 relative to the experimental DS of SF6. The results also demonstrate how choosing a gas with a higher DS and a geometry with minimal edges and corners can significantly increase the operating voltage of an electrical system. Due to its superior generalization, the RF represents the most promising path toward an accurate DS predictor once sufficient experimental data are available.

Mileski, Matthew [AFIT]↗
DOE OSTI2023

Artificial Neural Network Models for Octane Number and Octane Sensitivity: A Quantitative Structure Property Relationship Approach to Fuel Design

Octane sensitivity (OS), defined as the research octane number (RON) minus the motor octane number (MON) of a fuel, has gained interest among researchers due to its effect on knocking conditions in internal combustion engines. Compounds with a high OS enable higher efficiencies, especially within advanced compression ignition engines. RON/MON must be experimentally tested to determine OS, requiring time, funding, and specialized equipment. Thus, predictive models trained with existing experimental data and molecular descriptors (via quantitative structure-property relationships (QSPRs)) would allow for the preemptive screening of compounds prior to performing these experiments. Here, the present work proposes two methods for predicting the OS of a given compound: using artificial neural networks (ANNs) trained with QSPR descriptors to predict RON and MON individually to compute OS (derived octane sensitivity (dOS)), and using ANNs trained with QSPR descriptors to directly predict OS. Twenty-five ANNs were trained for both RON and MON and their test sets achieved an overall 6.4% and 5.2% error, respectively. Twenty-five additional ANNs were trained for both dOS and OS; dOS calculations were found to have 15.3% error while predicting OS directly resulted in 9.9% error. A chemical analysis of the top QSPR descriptors for RON/MON and OS is conducted, highlighting desirable structural features for high-performing molecules and offering insight into the inner mathematical workings of ANNs; such chemical interpretations study the interconnections between structural features, descriptors, and fuel performance showing that connectivity, structural diversity, and atomic hybridization consistently drive fuel performance.

09 BIOMASS FUELS↗
DOE OSTI2023

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗
DOE OSTI2025

Advanced Modeling and Process-Materials Co-Optimization Strategies for Swing Adsorption Based Gas Separations

This project devised a computational framework for simultaneously co-optimizing pressure swing adsorption process designs along with the sorbent materials (specifically, metal-organic frameworks) to be employed in the associated packed bed columns. The materials optimization aspect involved search over a design space that can describe the material’s molecular structure, while the process optimization aspect considered various process degrees of freedom for steps arising in various cycle configurations. This framework was demonstrated on the separation of nitrogen and carbon dioxide, which arises ubiquitously in a multitude of post-combustion carbon capture and “blue” hydrogen production applications. Our results led to metal-organic framework molecular descriptor choices that are predicted to outperform standard structures used in practice, providing guidance for future metal-organic framework synthesis efforts.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

From Structured Solvents to Hybrid Materials (SS2HM) for Chemically Selective Capture and Electromagnetic Release of CO 2 : Mechanisms, Stability and Interfaces (Final Report)

The goal of this research program was to develop high capacity sorbents amenable for alternative regeneration approaches for direct air capture (DAC) of CO 2 . In particular, the research aimed to develop an understanding of CO 2 binding mechanism, thermal and oxidative stability, and regeneration energetics of functionalized ionic liquids (ILs), deep eutectic solvents (DESs), and porous materials. ILs and DESs are high-dielectric solvents with structural tunability that permits the rational-design for energy-efficient regeneration approaches based on electromagnetic (EM) field and moisture-swing. By further incorporating these solvents into polymeric capsules and other structural supports, multi-scale interfaces for targeted CO 2 and energy transfers were achieved. Aspects related to CO 2 capacity, selectivity, stability, dielectric properties, and binding energies were examined through experimental and computational design to identify molecular descriptors to inform future design of structured solvents and hybrid materials for DAC. Enclosed final report details the key findings, science advancements, and workforce development efforts from this project.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Finch: Toxicity Dose Response Curve Prediction of Chemical Compounds and Mixtures

A paradigm shift in chemical risk assessment is emphasizing mixture testing over single compound analysis, eliminating animal testing, and adopting advanced modeling approaches to understand mixture activity profiles. However, existing computational models largely focus on single chemicals, with few effective solutions for modeling complex mixtures that account for synergistic or antagonistic effects and multiple Modes of Action (MoA). Conventional methods like concentration addition (CA) and independent action (IA) are insufficient for this task as they are designed for simplistic interactions and struggle to account for the dynamic and multifaceted nature of chemical mixtures, such as overlapping MoA and non-linear interactions. Finch offers a novel approach utilizing deep learning (DL) embeddings and multi-task quantitative structure-activity relationship (QSAR) models to improve chemical exposure prediction. By leveraging molecular descriptors, physiochemical properties, and large language model (LLM) embeddings from SMILES inputs, Finch preserves critical information in a latent space thereby enhancing predictive accuracy. The multi-task learning aspect of Finch is highly advantageous, as it simultaneously optimizes multiple loss functions, leveraging all available data across tasks to develop generalized representations that effectively capture complex ingredient interactions within mixtures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques

Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overdose contributing to the opioid crisis in the United States. Therefore, understanding the structure-activity relationship between MOR and its ligands is essential for predicting MOR binding of chemicals, which could assist in the development of non-addictive or less-addictive opioid analgesics. This study aimed to develop machine learning and deep learning models for predicting MOR binding activity of chemicals. Chemicals with MOR binding activity data were first curated from public databases and the literature. Molecular descriptors of the curated chemicals were calculated using software Mold2. The chemicals were then split into training and external validation datasets. Random forest, k-nearest neighbors, support vector machine, multi-layer perceptron, and long short-term memory models were developed and evaluated using 5-fold cross-validations and external validations, resulting in Matthews correlation coefficients of 0.528–0.654 and 0.408, respectively. Furthermore, prediction confidence and applicability domain analyses highlighted their importance to the models’ applicability. Our results suggest that the developed models could be useful for identifying MOR binders, potentially aiding in the development of non-addictive or less-addictive drugs targeting MOR.

Research & Experimental Medicine↗
DOE OSTI2022

In Silico Prediction of the Toxicity of Nitroaromatic Compounds: Application of Ensemble Learning QSAR Approach

In this work, a dataset of more than 200 nitroaromatic compounds is used to develop Quantitative Structure–Activity Relationship (QSAR) models for the estimation of in vivo toxicity based on 50% lethal dose to rats (LD 50 ). An initial set of 4885 molecular descriptors was generated and applied to build Support Vector Regression (SVR) models. The best two SVR models, SVR_A and SVR_B, were selected to build an Ensemble Model by means of Multiple Linear Regression (MLR). The obtained Ensemble Model showed improved performance over the base SVR models in the training set (R 2 = 0.88), validation set (R 2 = 0.95), and true external test set (R 2 = 0.92). The models were also internally validated by 5-fold cross-validation and Y-scrambling experiments, showing that the models have high levels of goodness-of-fit, robustness and predictivity. The contribution of descriptors to the toxicity in the models was assessed using the Accumulated Local Effect (ALE) technique. The proposed approach provides an important tool to assess toxicity of nitroaromatic compounds, based on the ensemble QSAR model and the structural relationship to toxicity by analyzed contribution of the involved descriptors.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2023

Progress in Predicting Ionic Cocrystal Formation: The Case of Ammonium Nitrate

In contrast to the mature predictive frameworks applied to neutral cocrystals, ionic cocrystals, those including an ion pair, are difficult to design. Furthermore, they are generally excluded categorically from studies which correlate specific molecular properties to cocrystal formation, leaving the prospective ionic cocrystal engineer with few clear avenues to success. Herein ammonium nitrate, an energetic oxidizing salt, is targeted for cocrystallization in a potential coformer group selected based on likely interactions with the nitrate ion as revealed in the Cambridge Structural Database; six novel ionic cocrystals were discovered. Molecular descriptors previously identified as being related to neutral cocrystal formation were examined across the screening group but showed no relationship with ionic cocrystal formation. High packing coefficient is shown to be a constant among the successful coformers in the set and is utilized to directly target two more successful coformers, bypassing the need for a large screening group.

Andrew J. Bennett↗
DOE OSTI2024

E min : A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability

Predicting the synthesizability of a new molecule remains an unsolved challenge that chemists have long tackled with heuristic approaches. Here, in this study, we report a new method for predicting synthesizability using a simple yet accurate thermochemical descriptor. We introduce E min , the energy difference between a molecule and its lowest energy constitutional isomer, as a synthesizability predictor that is accurate, physically meaningful, and first-principles based. We apply E min to 134,000 molecules in the QM9 data set and find that E min is accurate when used alone and reduces incorrect predictions of "synthesizable" by up to 52% when used to augment commonly used prediction methods. Our work illustrates how first-principles thermochemistry and heuristic approximations for molecular stability are complementary, opening a new direction for synthesizability prediction methods.

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

Machine Learning for Prediction of Thermodynamic Descriptors

Our objective is to apply machine learning (ML) algorithms for the prediction of molecular catalysis descriptors from geometric properties derived from experimental crystallographic databases. Catalysis is often considered a “low-data” discipline that is poorly suited for ML methods. An exception is the extensive structural information that is available for molecular catalysts through the Cambridge Structural Database (CSD), which contains atomically precise molecular structures from X-ray diffraction analysis for >600K metal complexes. As a proof-of-principle, we targeted the prediction of hydricity, a thermodynamic property that provides understanding and control of catalytic hydride transfer. We built a training set composed of ~100 molecular complexes with a known hydricity and structural information from the CSD. This data set was converted into a machine-readable format using the smooth overlap of atomic positions (SOAP) representation and further labeled with simple electronic descriptors for the metal centers. Multiple different neural networks were trained on this data set, and the accuracy of the hydricity predictions ranged from < 2 kcal/mol to 20 kcal/mol. The accuracy of each model was highly sensitive to which compounds were in the train versus test set, underscoring the challenges associated with small and chemically diverse data sets. Finally, to further augment the data set, we attempted to experimentally measure several new hydricity values, however these experiments were unsuccessful due to undesired chemical reactivity of the selected complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗