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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family

The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from Streptomyces coelicolor , to structurally characterize using a combination of a wild-type and a Arg306Gln variant in apo , cofactor product AMP-bound, and cofactor reactant ATP-bound complexes. The kinetics in the family has been limited by solubility and reporter assays, so we have developed a label-free kinetics assay utilizing a single-injection isothermal-titration-calorimetry-based method. We report second-order rate constants that are 50 times higher than the previous estimations for DesD. Our Arg306Gln DesD variant was also tested under identical buffer and substrate conditions, and its undetectable activity was confirmed. These are the first reported structures for DesD, and they describe the critical cofactor coordination. This is also the first label-free assay to unambiguously determine the kinetics for an NIS synthetase.

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

Automated Symbolic Upscaling: 2. Model Generation for Extended Applicability Regimes

Abstract In this second part of the two paper series, we detail an algorithmic procedure for systematically implementing the generalized closure form strategy presented in Part 1. This strategy extends the applicability of homogenized models with respect to classical homogenization theory, as demonstrated in Part 1 where upscaled models are rigorously derived in moderately reactive physical regimes. After encoding the algorithm into Symbolica, an automated upscaling framework, we upscale two reactive mass transport problems and numerically validate the resulting nonlinear homogenized models by showing the absolute error estimates predicted by homogenization theory are satisfied. In both problems, nontrivial closure forms and closure problems are automatically formulated using the encoded strategy with no human interaction, nor prior knowledge regarding the closure required for the systems. We hope these demonstrations spark further interest in automated analytical frameworks for multiscale modeling, as such capabilities are invaluable for generating rigorous multiscale models of complex phenomena in porous media.

Pietrzyk, Kyle↗
DOE OSTI2021

hydro-hifem v.1.0

SAND2021-3180 O The hydro-hifem 1.0 software is used to simulate transient physical processes in large geologic environments consisting of complex fractures and man-made infrastructures with affordable computational cost and mesh refinement. The Earth models with such complex model features can be designed by considering the reduction of insignificant dimensions of fractures/infrastructures and embracing their corresponding hierarchical material properties, and their computational meshes are generated by using Cubit. The finite element solutions are automatically distributed across nodes of parallel cluster for efficient computation of transient fluid flow or heat conduction in geologic media. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Beskardes, GungorDidem↗
DOE OSTI2024

Effective many-body interactions in reduced-dimensionality spaces through neural network models

Accurately describing properties of challenging problems in physical sciences often requires complex mathematical models that are unmanageable to tackle head on. Therefore, developing reduced-dimensionality representations that encapsulate complex correlation effects in many-body systems is crucial to advance the understanding of these complicated problems. However, a numerical evaluation of these predictive models can still be associated with a significant computational overhead. To address this challenge, in this paper we discuss a combined framework that integrates recent advances in the development of active-space representations of coupled cluster (CC) downfolded Hamiltonians with neural network approaches. The primary objective of this effort is to train neural networks to eliminate the computationally expensive steps required for evaluating hundreds or thousands of Hugenholtz diagrams, which correspond to multidimensional tensor contractions necessary for evaluating a many-body form of downfolded effective Hamiltonians. Using small molecular systems (the H 2 O and HF molecules) as examples, we demonstrate that training neural networks employing effective Hamiltonians for a few nuclear geometries of molecules can accurately interpolate or extrapolate their forms to other geometrical configurations characterized by different intensities of correlation effects. We also discuss differences between effective interactions that define CC downfolded Hamiltonians with those of bare Hamiltonians defined by Coulomb interactions in the active spaces. Published by the American Physical Society 2024

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Leveraging public AI tools to explore systems biology resources in mathematical modeling

Predictive mathematical modeling is an essential part of systems biology and is interconnected with information management. Systems biology information is often stored in specialized formats to facilitate data storage and analysis. These formats are not designed for easy human readability and thus require specialized software to visualize and interpret results. Therefore, comprehending modeling and underlying networks and pathways is contingent on mastering systems biology tools, which is particularly challenging for users with no or little background in data science or system biology. To address this challenge, we investigated the usage of public Artificial Intelligence (AI) tools in exploring systems biology resources in mathematical modeling. We tested public AI’s understanding of mathematics in models, related systems biology data, and the complexity of model structures. Our approach can enhance the accessibility of systems biology for non-system biologists and help them understand systems biology without a deep learning curve.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Models and Methods for Sparse (Hyper)Network Science in Business, Industry, and Government

The authors are hosting an AMS sponsored Mathematics Research Community (MRC) focusing on two themes that have garnered intense attention in network models of complex relational data: (1) how to faithfully model multi-way relations in hypergraphs, rather than only pairwise interactions in graphs; and (2) challenges posed by modelling networks with extreme sparsity. Here we introduce and explore these two themes and their challenges. In this work, we hope to generate interest from researchers in pure and applied mathematics and computer science.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Physics-Guided, Physics-Informed, and Physics-Encoded Neural Networks and Operators in Scientific Computing: Fluid and Solid Mechanics

Abstract Advancements in computing power have recently made it possible to utilize machine learning and deep learning to push scientific computing forward in a range of disciplines, such as fluid mechanics, solid mechanics, materials science, etc. The incorporation of neural networks is particularly crucial in this hybridization process. Due to their intrinsic architecture, conventional neural networks cannot be successfully trained and scoped when data are sparse, which is the case in many scientific and engineering domains. Nonetheless, neural networks provide a solid foundation to respect physics-driven or knowledge-based constraints during training. Generally speaking, there are three distinct neural network frameworks to enforce the underlying physics: (i) physics-guided neural networks (PgNNs), (ii) physics-informed neural networks (PiNNs), and (iii) physics-encoded neural networks (PeNNs). These methods provide distinct advantages for accelerating the numerical modeling of complex multiscale multiphysics phenomena. In addition, the recent developments in neural operators (NOs) add another dimension to these new simulation paradigms, especially when the real-time prediction of complex multiphysics systems is required. All these models also come with their own unique drawbacks and limitations that call for further fundamental research. This study aims to present a review of the four neural network frameworks (i.e., PgNNs, PiNNs, PeNNs, and NOs) used in scientific computing research. The state-of-the-art architectures and their applications are reviewed, limitations are discussed, and future research opportunities are presented in terms of improving algorithms, considering causalities, expanding applications, and coupling scientific and deep learning solvers.

Computer Science↗
DOE OSTI2023

Explaining machine-learning models for gamma-ray detection and identification

As more complex predictive models are used for gamma-ray spectral analysis, methods are needed to probe and understand their predictions and behavior. Recent work has begun to bring the latest techniques from the field of Explainable Artificial Intelligence (XAI) into the applications of gamma-ray spectroscopy, including the introduction of gradient-based methods like saliency mapping and Gradient-weighted Class Activation Mapping (Grad-CAM), and black box methods like Local Interpretable Model-agnostic Explanations (LIME) and SHapley Additive exPlanations (SHAP). In addition, new sources of synthetic radiological data are becoming available, and these new data sets present opportunities to train models using more data than ever before. In this work, we use a neural network model trained on synthetic NaI(Tl) urban search data to compare some of these explanation methods and identify modifications that need to be applied to adapt the methods to gamma-ray spectral data. We find that the black box methods LIME and SHAP are especially accurate in their results, and recommend SHAP since it requires little hyperparameter tuning. We also propose and demonstrate a technique for generating counterfactual explanations using orthogonal projections of LIME and SHAP explanations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Wind ramp events validation in NWP forecast models during the second Wind Forecast Improvement Project (WFIP2) using the Ramp Tool and Metric (RT&M)

The second Wind Forecast Improvement Project (WFIP2) is a multi-agency field campaign held in the Columbia Gorge area (October 2015 - March 2017). The main goal of the project is to understand and improve the forecast skill of numerical weather prediction (NWP) models in complex terrain, particularly beneficial for the wind energy industry. This region is well-known for its excellent wind resource. One of the biggest challenges for wind power production is the accurate forecasting of wind ramp events (large changes of generated power over short periods of time). Poor forecasting of the ramps requires large and sudden adjustments in conventional power generation, ultimately increasing the costs of power. A Ramp Tool and Metric (RT&M) was developed during the first WFIP experiment, held in the U.S. Great Plains (September 2011 - August 2012). The RT&M was designed to explicitly measure the skill of NWP models at forecasting wind ramp events. Here we apply the RT&M to 80-m (turbine hub-height) wind speeds measured by 19 sodars and 3 lidars, and to forecasts from the High Resolution Rapid Refresh (HRRR), 3-km, and from the High Resolution Rapid Refresh Nest (HRRRNEST), 750-m horizontal grid spacing, models. The diurnal and seasonal distribution of ramp events are analyzed, finding a noticeable diurnal variability for spring and summer but less for fall and especially winter. Also, winter has fewer ramps compared to the other seasons. The model skill at forecasting ramp events, including the impact of the modification to the model physical parameterizations, was finally investigated.

Djalalova, Irina V.↗
DOE OSTI2021

Transforming a Simple Structure Model to Represent a Complex Dynamic System with Unknown Boundary Restraints

Imposing a boundary condition on a structure can significantly alter its dynamic properties. However, sometimes the specifics of the new boundary conditions are not known. When the effects of a boundary condition are uncertain or there is not enough information, engineers need to excite the complex structure to obtain these modified properties. In order to experimentally obtain the new properties, engineers need multiple experiments and many outputs for interpolation in order to sufficiently represent the entire structure. In this study, the researchers attached a stinger to a cantilever beam, acting as a new transverse restraint of unknown properties. This paper presents a conversion expression that predicts the dynamic behavior of any point in the system with the new boundary condition. This expression relies only on one impact hammer experiment with one output and the model of the stinger-free cantilever beam, referred to as the simple structure. Researchers estimated the Transfer Function (TRF) of the beam and compared it with an experimentally measured TRF to validate the method. The mean absolute error of the estimated TRF compared to the experimental TRF is 1.99 dB. This demonstrates the use of the proposed method for estimating unmeasured TRFs in a system with an uncertain boundary condition using a single input, single output (SISO) test and a model of the simple structure.

42 ENGINEERING↗
DOE OSTI2021

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Abstract Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

Environmental Sciences & Ecology↗
DOE OSTI2021

Efficient Learning of Accurate Surrogates for Simulations of Complex Systems

Machine learning methods are increasingly deployed to construct surrogate models for complex physical systems at a reduced computational cost. However, the predictive capability of these surrogates degrades in the presence of noisy, sparse, or dynamic data. We introduce an online learning method empowered by optimizer-driven sampling that has two advantages over current approaches: it ensures that all local extrema (including endpoints) of the model response surface are included in the training data and it employs a continuous validation and update process in which surrogates undergo retraining when their performance falls below a validity threshold. We find, using benchmark functions, that optimizer-directed sampling generally outperforms traditional sampling methods in terms of accuracy around local extrema even when the scoring metric is biased towards assessing overall accuracy. Finally, the application to dense nuclear matter demonstrates that highly accurate surrogates for a nuclear equation of state model can be reliably auto-generated from expensive calculations using few model evaluations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Efficient learning of accurate surrogates for simulations of complex systems

Machine learning methods are increasingly deployed to construct surrogate models for complex physical systems at a reduced computational cost. However, the predictive capability of these surrogates degrades in the presence of noisy, sparse or dynamic data. Here, we introduce an online learning method empowered by optimizer-driven sampling that has two advantages over current approaches: it ensures that all local extrema (including endpoints) of the model response surface are included in the training data, and it employs a continuous validation and update process in which surrogates undergo retraining when their performance falls below a validity threshold. We find, using benchmark functions, that optimizer-directed sampling generally outperforms traditional sampling methods in terms of accuracy around local extrema even when the scoring metric is biased towards assessing overall accuracy. Finally, the application to dense nuclear matter demonstrates that highly accurate surrogates for a nuclear equation-of-state model can be reliably autogenerated from expensive calculations using few model evaluations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Kinetic mixing, dark photons and extra dimensions. Part III. Brane localized dark matter

Extra dimensions have proven to be a very useful tool in constructing new physics models. In earlier work, we began investigating toy models for the 5-D analog of the kinetic mixing/vector portal scenario where the interactions of dark matter, taken to be, e.g., a complex scalar, with the brane-localized fields of the Standard Model (SM) are mediated by a massive U(1) D dark photon living in the bulk. These models were shown to have many novel features differentiating them from their 4-D analogs and which, in several cases, avoided some well-known 4-D model building constraints. However, these gains were obtained at the cost of the introduction of a fair amount of model complexity, e.g., dark matter Kaluza-Klein excitations. In the present paper, we consider an alternative setup wherein the dark matter and the dark Higgs, responsible for U(1) D breaking, are both localized to the ‘dark’ brane at the opposite end of the 5-D interval from where the SM fields are located with only the dark photon now being a 5-D field. The phenomenology of such a setup is explored for both flat and warped extra dimensions and compared to the previous more complex models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Prediction of alkaline earth metal ion adsorption on goethite for various background electrolytes with the CD-MUSIC model

As water scarcity drives the use of more saline water sources, contaminant fate and transport models must capture the impact of high concentrations of alkaline earth metal ions (AEMs) and background electrolytes in these more complex waters. By utilizing macroscopic adsorption data from various electrolyte systems, a Charge Distribution – Multisite Complexation (CD-MUSIC) model, capable of incorporating electrolyte adsorption, was able to accurately simulate the adsorption behavior of alkaline earth metal ions onto goethite. The modeling effort was guided by previous spectroscopic and surface complexation modeling of alkaline earth metal adsorption and built on previous CD-MUSIC modeling that accounted for changes in crystal face contributions to the surface site density as a function of specific surface area. Further, the model was constrained to consider only two dominant surface complex species for each metal ion adsorption reaction. These two species were selected from 44 possible species through objective curve fitting of single-solute macroscopic adsorption data. While most of the alkaline earth metal surface complexes formed outer-sphere complexes at the goethite surface, an inner-sphere species was utilized for Mg 2+ . With the surface complex species and equilibrium constants obtained from this study, the calibrated model successfully predicted alkaline earth metal ion adsorption over a wide range of solution and surface conditions; the model predictions encompassed a wide range of pH (5–11), solute/solid ratio (1.37 × 10 -5 – 8.33 × 10 -4 mol -solute /g -solid ), ionic strengths (0.01 M – 0.7 M), and background electrolytes (Na + , Cs + , Rb + , Cl - , and NO 3 - ) using the same crystal face contribution methodology for site density, capacitance values, and surface acidity constants adopted for proton and cadmium adsorption in previous work (Han and Katz, 2019). Model simulations for a range of background water chemistries demonstrated the potential for Mg 2+ to reduce Cd 2+ adsorption to goethite in model seawater and oil- and gas-produced waters.

42 ENGINEERING↗
DOE OSTI2023

Emissions and Energy Impacts of the Inflation Reduction Act

If goals set under the Paris Agreement are met, the world may hold warming well below 2 degrees C (1); however, parties are not on track to deliver these commitments (2), increasing focus on policy implementation to close the gap between ambition and action. Recently, the US government passed its most prominent piece of climate legislation to date - the Inflation Reduction Act of 2022 (IRA) - designed to invest in a wide range of programs that, among other provisions, incentivize clean energy and carbon management, encourage electrification and efficiency measures, reduce methane emissions, promote domestic supply chains, and address environmental justice concerns (3). IRA's scope and complexity make modeling important to understand impacts on emissions and energy systems. We leverage results from nine independent, state-of-the-art models to examine potential implications of key IRA provisions, showing economy-wide emissions reductions between 43 and 48% below 2005 levels by 2035.

electricity↗
DOE OSTI2020

Guidelines to Achieving High Selectivity for the Hydrogenation of α,β-Unsaturated Aldehydes with Bimetallic and Dilute Alloy Catalysts: A Review

Selective hydrogenation of unsaturated aldehydes to unsaturated alcohols is a challenging class of reactions, yielding valuable intermediates for the production of pharmaceuticals, perfumes, and flavorings. On monometallic heterogeneous catalysts, the formation of the unsaturated alcohols is thermodynamically disfavored over the saturated aldehydes. Hence, new catalysts are required to achieve the desired selectivity. In this work, the literature of three major research areas in catalysis is integrated as a step toward establishing the guidelines for enhancing the selectivity: reactor studies of complex catalyst materials at operating temperature and pressure, surface science studies of crystalline surfaces in ultrahigh vacuum, and first-principles modeling using density functional theory calculations. Aggregate analysis shows that bimetallic and dilute alloy catalysts significantly enhance the selectivity to the unsaturated alcohols compared to monometallic catalysts. This comprehensive review focuses primarily on the role of different metal surfaces as well as the factors that promote the adsorption of the unsaturated aldehyde via its C=O bond, most notably by electronic modification of the surface and formation of the electrophilic sites. Furthermore, challenges, gaps, and opportunities are identified to advance the rational design of efficient catalysts for this class of reactions, including the need for systematic studies of catalytic processes, theoretical modeling of complex materials, and model studies under ambient pressure and temperature.

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

Practical and Optimal Sequential Bayesian Experimental Design for Complex Systems Incorporating Human Experimenter Preferences (Final Scientific/Technical Report)

Experiments are indispensable for developing models of complex systems. Carefully designed experiments can provide substantial savings for these expensive data-acquisition opportunities. However, designs based on heuristics are often suboptimal for systems with multiphysics, nonlinear dynamics, and uncertain and noisy environments. Optimal experimental design, while leveraging predictive models, seeks to systematically quantify and maximize the value of experiments. In this project, we focused on the design of multiple experiments, where current approaches are largely suboptimal: batch-design does not adapt to new data acquired during the experiment campaign (no feedback), and greedy/myopic design ignores future dynamics and consequences (no lookahead). We developed the mathematical framework and computational methods for sequential optimal experimental design (sOED) for complex systems. We enabled tractable model-based sOED in a rigorous manner through novel algorithms based on reinforcement learning, and investigated the effects of human experimenters on the design process. Our methods are fully Bayesian, able to quantify and update uncertainty in a principled manner. The traits aimed by our approach—mathematical rigor and optimality, human effects and uncertainty quantification, computational practicality—are crucial for elevating the standards of artificial intelligence (AI) to support decision-making in scientific domains, and contribute toward trust and realistic adoption of AI in experimental design practice.

97 MATHEMATICS AND COMPUTING↗