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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
NASA NTRS2018

Climate Modeling of a Potential Exovenus

The planetary mass and radius sensitivity of exoplanet discovery capabilities has reached into the terrestrial regime. The focus of such investigations is to search within the Habitable Zone where a modern Earth-like atmosphere may be a viable comparison. However, the detection bias of the transit and radial velocity methods lies close to the host star where the received flux at the planet may push the atmosphere into a runaway greenhouse state. One such exoplanet discovery, Kepler-1649b, receives a similar flux from its star as modern Venus does from the Sun, and so was categorized as a possible exoVenus. Here we discuss the planetary parameters of Kepler-1649b in relation to Venus to establish its potential as a Venus analog. We utilize the general circulation model ROCKE-3D to simulate the evolution of the surface temperature of Kepler-1649b under various assumptions, including relative atmospheric abundances. We show that in all our simulations the atmospheric model rapidly diverges from temperate surface conditions toward a runaway greenhouse with rapidly escalating surface temperatures. We calculate transmission spectra for the evolved atmosphere and discuss these spectra within the context of the James Webb Space Telescope Near-Infrared Spectrograph capabilities. We thus demonstrate the detectability of the key atmospheric signatures of possible runaway greenhouse transition states and outline the future prospects of characterizing potential Venus analogs.

Astrobiology↗
NASA NTRS2018

Climate Modeling of a Potential ExoVenus

The planetary mass and radius sensitivity of exoplanet discovery capabilities has reached into the terrestrial regime. The focus of such investigations is to search within the Habitable Zone where a modern Earth-like atmosphere maybe a viable comparison. However, the detection bias of the transit and radial velocity methods lies close to the host star where the received flux at the planet may push the atmosphere into a runaway greenhouse state. One such exoplanet discovery, Kepler-1649b, receives a similar flux from its star as modern Venus does from the Sun, and so was categorized as a possible exoVenus. Here we discuss the planetary parameters of Kepler-1649b in relation to Venus to establish its potential as a Venus analog. We utilize the general circulation model ROCKE-3D (Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics) to simulate the evolution of the surface temperature of Kepler-1649b under various assumptions, including relative atmospheric abundances. We show that in all our simulations the atmospheric model rapidly diverges from temperate surface conditions toward a runaway greenhouse with rapidly escalating surface temperatures. We calculate transmission spectra for the evolved atmosphere and discuss these spectra within the context of the James Webb Space Telescope Near-Infrared Spectrograph capabilities. We thus demonstrate the detectability of the key atmospheric signatures of possible runaway greenhouse transition states and outline the future prospects of characterizing potential Venus analogs.

Astrobiology↗
NASA NTRS1975

Thermospheric composition

The global view of the atmosphere provided by satellite observations and radar backscatter measurements has shown a pattern of composition variability resulting largely from dynamic processes. Important progress has been made in defining composition variability at 120 km, which has greatly improved models which previously had fixed boundary conditions at that altitude. The discovery of the early morning maximum in helium abundance and the better definition of diurnal variation in relative composition have provided a basis for more sophisticated dynamical models. Similarly, models of meridional wind systems have been developed which can account for the better-defined winter enhancements in helium and atomic oxygen. Finally, composition variability has indicated the presence of a high-latitude heat source which during periods of magnetic activity profoundly modifies the state of the atmosphere.

Carignan, G. R.↗
NASA NTRS2011

Data Farming and Defense Applications

.Data farm,ing uses simulation modeling, high performance computing, experimental design and analysis to examine questions of interest with large possibility spaces. This methodology allows for the examination of whole landscapes of potential outcomes and provides the capability of executing enough experiments so that outliers might be captured and examined for insights. It can be used to conduct sensitivity studies, to support validation and verification of models, to iteratively optimize outputs using heuristic search and discovery, and as an aid to decision-makers in understanding complex relationships of factors. In this paper we describe efforts at the Naval Postgraduate School in developing these new and emerging tools. We also discuss data farming in the context of application to questions inherent in military decision-making. The particular application we illustrate here is social network modeling to support the countering of improvised explosive devices.

Horne, Gary↗
DOE OSTI2022

Hypothesis Learning in Automated Experiment: Application to Combinatorial Materials Libraries

Machine learning is rapidly becoming an integral part of experimental physical discovery via automated and high-throughput synthesis, and active experiments in scattering and electron/probe microscopy. This, in turn, necessitates the development of active learning methods capable of exploring relevant parameter spaces with the smallest number of steps. In this work, an active learning approach based on conavigation of the hypothesis and experimental spaces is introduced. This is realized by combining the structured Gaussian processes containing probabilistic models of the possible system's behaviors (hypotheses) with reinforcement learning policy refinement (discovery). This approach closely resembles classical human-driven physical discovery, when several alternative hypotheses realized via models with adjustable parameters are tested during an experiment. This approach is demonstrated for exploring concentration-induced phase transitions in combinatorial libraries of Sm-doped BiFeO 3 using piezoresponse force microscopy, but it is straightforward to extend it to higher-dimensional parameter spaces and more complex physical problems once the experimental workflow and hypothesis generation are available.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Accelerating Large Data Analysis By Exploiting Regularities

We present techniques for discovering and exploiting regularity in large curvilinear data sets. The data can be based on a single mesh or a mesh composed of multiple submeshes (also known as zones). Multi-zone data are typical to Computational Fluid Dynamics (CFD) simulations. Regularities include axis-aligned rectilinear and cylindrical meshes as well as cases where one zone is equivalent to a rigid-body transformation of another. Our algorithms can also discover rigid-body motion of meshes in time-series data. Next, we describe a data model where we can utilize the results from the discovery process in order to accelerate large data visualizations. Where possible, we replace general curvilinear zones with rectilinear or cylindrical zones. In rigid-body motion cases we replace a time-series of meshes with a transformed mesh object where a reference mesh is dynamically transformed based on a given time value in order to satisfy geometry requests, on demand. The data model enables us to make these substitutions and dynamic transformations transparently with respect to the visualization algorithms. We present results with large data sets where we combine our mesh replacement and transformation techniques with out-of-core paging in order to achieve significant speed-ups in analysis.

Moran, Patrick J.↗
DOE OSTI2020

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗
DOE OSTI2023

Adaptive language model training for molecular design

Abstract The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

CACTUS: Chemistry Agent Connecting Tool Usage to Science

Large language models (LLMs) have shown remarkable potential in various domains but often lack the ability to access and reason over domain-specific knowledge and tools. In this article, we introduce Chemistry Agent Connecting Tool-Usage to Science (CACTUS), an LLM-based agent that integrates existing cheminformatics tools to enable accurate and advanced reasoning and problem-solving in chemistry and molecular discovery. We evaluate the performance of CACTUS using a diverse set of open-source LLMs, including Gemma-7b, Falcon-7b, MPT-7b, Llama3-8b, and Mistral-7b, on a benchmark of thousands of chemistry questions. Our results demonstrate that CACTUS significantly outperforms baseline LLMs, with the Gemma-7b, Mistral-7b, and Llama3-8b models achieving the highest accuracy regardless of the prompting strategy used. Moreover, we explore the impact of domain-specific prompting and hardware configurations on model performance, highlighting the importance of prompt engineering and the potential for deploying smaller models on consumer-grade hardware without a significant loss in accuracy. By combining the cognitive capabilities of open-source LLMs with widely used domain-specific tools provided by RDKit, CACTUS can assist researchers in tasks such as molecular property prediction, similarity searching, and drug-likeness assessment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Designing the Protocols for Programmable Ammonia Catalysis

Programmable catalysis can provide a more energy-efficient and cost-effective route to enhancing commercial ammonia production, a key process in the advancement of renewable energy technologies and the manufacture of fertilizers and basic chemicals. This work explores the computational discovery of optimal forcing protocols to drive such dynamic catalysis models. By employing matrix-free time-stepper methods, coupled with an optimization approach, that integrates Bayesian optimization with a Bayesian continuation strategy to efficiently discover the periodic steady states of such periodically forced systems, we enable the discovery of complex optimal catalyst strain waveforms, while ensuring robust solver convergence. We demonstrate the flexibility of our approach to discover optimized forcing protocols under varying physical constraints on strain modulation or other catalyst operating parameters. We show that these can have a temporal structure more complex than simple step functions. In order to detect undesirable catalytic loops that may correlate with overall reduced performance, we perform a study using graph-theoretical analysis to investigate the dynamics of catalytic kinetic networks formed.

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

Homogenization of Dendritic Structures and the High-Temperature Strength of the Refractory High-Entropy Alloy MoNbTaVW

MoNbTaVW, a pioneering refractory high-entropy alloy (RHEA), is renowned for its exceptional strength at elevated temperatures. Like most RHEAs, it solidifies into a dendritic microstructure with steep concentration gradients, necessitating heat treatment for equilibration. Steep concentration gradients typically complicate mechanical property analysis and modeling, key challenges for high-throughput alloy discovery. This study examines the effects of high-temperature homogenization (1800 °C for 8 hours) on the microstructure and mechanical properties of MoNbTaVW across temperatures up to 1200 °C. Postmortem microstructural analysis, coupled with chemical, crystallographic, and mechanical assessments, revealed that yield strength was surprisingly insensitive to homogenization, with less than a 3 pct difference between as-cast and heat-treated materials. Nanoindentation confirmed minimal nanohardness changes across the dendritic structure at room temperature. However, homogenization significantly enhanced high-temperature work hardening, producing higher peak compressive strength. Both as-cast and homogenized MoNbTaVW exhibited room-temperature strengths of 1400 MPa, exceeding previously reported values. These findings demonstrate that high-temperature treatment enables microstructural homogenization without compromising strength, a unique behavior among RHEAs. In conclusion, while not universally applicable, this insight highlights the importance of understanding microstructural development in experimental alloys and offers a pathway to design alloys that achieve homogeneous-like properties without heat treatment.

Rietema, C. J. [Lawrence Livermore National Labora↗
DOE OSTI2022

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

All-Atom Biomolecular Simulation in the Exascale Era

Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML techniques, that model biomolecular motions over unprecedented length and time scales. This new capability holds the potential to revolutionize our understanding of fundamental biological processes. Herein we report on some of the major advances that were discussed at a recent CECAM workshop in Pisa, Italy, on the topic with a primary focus on atomic-level simulations. First, we highlight examples of current large-scale biomolecular simulations and the future possibilities enabled by crossing the exascale threshold. Next, we discuss challenges to be overcome in optimizing the usage of these powerful resources. Finally, we close by listing several grand challenge problems that could be investigated with this new computer architecture.

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

Crystal structure prediction with host-guided inpainting generation and foundation potentials

Unconditional crystal structure generation with diffusion models faces challenges in identifying symmetric crystals as the unit cell size increases. Here, we present the crystal host-guided generation (CHGGen) framework to address this challenge through conditional generation using an inpainting method, which optimizes a fraction of atomic positions within a predefined and symmetrized host structure to improve the success rate for symmetric structure generation. By integrating inpainting structure generation with a foundation potential for structure optimization, we demonstrate the method on the ZnS–P 2 S 5 and Li–Si chemical systems, where the inpainting method generates a higher fraction of symmetric structures than unconditional generation. The practical significance of CHGGen extends to enabling the structural modification of crystal structures, particularly for systems with partial occupancy or intercalation chemistry. The inpainting method also allows for seamless integration with other generative models, providing a versatile framework for accelerating materials discovery.

Zhong, Peichen [University of California, Berkeley↗
DOE OSTI2020

Featureless adaptive optimization accelerates functional electronic materials design

Electronic materials that exhibit phase transitions between metastable states (e.g., metal-insulator transition materials with abrupt electrical resistivity transformations) are challenging to decode. For these materials, conventional machine learning methods display limited predictive capability due to data scarcity and the absence of features that impede model training. In this article, we demonstrate a discovery strategy based on multi-objective Bayesian optimization to directly circumvent these bottlenecks by utilizing latent variable Gaussian processes combined with high-fidelity electronic structure calculations for validation in the chalcogenide lacunar spinel family. We directly and simultaneously learn phase stability and bandgap tunability from chemical composition alone to efficiently discover all superior compositions on the design Pareto front. Previously unidentified electronic transitions also emerge from our featureless adaptive optimization engine. Our methodology readily generalizes to optimization of multiple properties, enabling co-design of complex multifunctional materials, especially where prior data is sparse.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Digital twins and deep learning segmentation of defects in monolayer MX 2 phases

Developing methods to understand and control defect formation in nanomaterials offers a promising route for materials discovery. Monolayer MX 2 phases represent a particularly compelling case for defect engineering of nanomaterials due to the large variability in their physical properties as different defects are introduced into their structure. However, effective identification and quantification of defects remain a challenge even as high-throughput scanning transmission electron microscopy methods improve. This study highlights the benefits of employing first principles calculations to produce digital twins for training deep learning segmentation models for defect identification in monolayer MX 2 phases. Around 600 defect structures were obtained using density functional theory calculations, with each monolayer MX 2 structure being subjected to multislice simulations for the purpose of generating the digital twins. Several deep learning segmentation architectures were trained on this dataset, and their performances evaluated under a variety of conditions such as recognizing defects in the presence of unidentified impurities, beam damage, grain boundaries, and with reduced image quality from low electron doses. Further, this digital twin approach allows benchmarking different deep learning architectures on a theory dataset, which enables the study of defect classification under a broad array of finely controlled conditions. It thus opens the door to resolving the underpinning physical reasons for model shortcomings and potentially chart paths forward for automated discovery of materials defect phases in experiments.

36 MATERIALS SCIENCE↗