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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 OSTI2021

EpiCast: Simulating Epidemics with Extreme Detail

In early 2020, COVID-19 swept the globe. Governments attempted to “flatten the curve” through business shutdowns and stay-at-home orders, but the United States was hit hard. By the end of March, mere months after the virus first emerged in humans 7,000 miles away, the U.S. had recorded 192,300 cases and 5,300 deaths. While this unprecedented disaster sent shockwaves through every level of society and clouded an uncertain future, state and local governments turned to computational and mathematical epidemiology researchers to help formulate intervention strategies to limit the spread of the disease. Traditional forecasting models provided a reasonable understanding of how the near future was likely to look, but local policy makers and public health communities still struggled to understand how potential mitigations ought to be implemented. Decision makers needed a way to measure the impact of their policy choices—they needed better technology. EpiCast answered the call, bringing urgently needed answers to policymakers grappling with how to adjust school and business schedules. EpiCast is modeling software that generates a synthetic, representative population to simulate infectious disease transmission in the United States with extreme detail and granularity. The software models human behavior combined with community-specific information to provide a fine-grained preview of the effect of potential mitigation strategies for decision makers.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

MatCal Users Guide: Release 1.3.0

Any continuum mechanics model will require three components: (1) a discretized geometry of the boundary value problem being studied, (2) the partial differential equations to be solved, and (3) the initial conditions and boundary conditions for the problem. To describe material behavior in these computational models, material models contribute to (2) the underlying equations and, occasionally, to (3) the initial conditions for the simulation. These material models can exhibit a mathematical form that is empirically based, based on first principles, or developed from both empirical observations and known physics. In general, these models are meant to represent a class of materials with well understood behavior. As a result, material models have parameters that must be tuned or calibrated so that the model response matches characterization data available for the specific material it is intended to represent when used to simulate a specific system. For simple models, such as isotropic, linear elastic materials in solid mechanics, this calibration process can be a simple analytical calculation directly extracting the parameters from experimental measurements. For complex models that have many inputs and require many characterization datasets to adequately identify the material behavior, the model calibration process can require an inverse problem approach where an optimization is performed to tune the model parameters to the available data.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Baryon–antibaryon photoproduction cross sections off the proton

The GlueX experiment at Jefferson Lab has observed 𝑝⁢$\overline{p}$ and, for the first time, Λ$\overlineΛ$ and 𝑝$\overlineΛ$ photoproduction from a proton target at photon energies up to 11.6 GeV. The angular distributions are forward peaked for all produced pairs, consistent with Regge-like 𝑡-channel exchange. Asymmetric wide-angle antibaryon distributions show the presence of additional processes. In a phenomenological model, we find consistency with a double-𝑡-channel exchange process where antibaryons are created only at the middle vertex. The model matches all observed distributions with a small number of free parameters. In the hyperon channels, we observe a clear distinction between photoproduction of the Λ$\overlineΛ$ and 𝑝$\overlineΛ$ systems but general similarity to the 𝑝$\overline{p}$ system. We report both total cross sections and cross sections differential with respect to momentum transfer and the invariant masses of the created particle pairs. No narrow resonant structures were found in these reaction channels. The suppression of 𝑠$\overline{s}$ quark pairs relative to 𝑑$\overline{d}$ quark pairs is similar to what has been seen in other reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

The Aerosol Model Benchmarking Repository: A toolkit for model intercomparison

The Aerosol Model Benchmarking Repository and Standards (AMBRS) project was initiated to provide tools and to establish community standards for benchmarking aerosol models. This report describes a set of open-source tools for building, running, and analyzing aerosol box model simulations in a standardized framework. The framework consists of three core components: AMBuilder, a CMake-based build system that compiles supported models consistently; AMBRS, a Python module that defines unified numerical experiments and executes them with aligned inputs; and PyParticle, an aerosol analysis package that standardizes output, computes diagnostics, and visualizes simulation results. Together, these tools enable reproducible intercomparison of aerosol schemes and support process-level evaluation of how model simplifications affect predictions of size distributions, cloud condensation nuclei activity, and other relevant properties relevant for the Earth-Energy system. Beyond its role in benchmarking, AMBRS provides a platform for studying aerosol processes across scales and can be used to generate training data for AI/ML applications in support of a broader hierarchical aerosol modeling strategy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quench process modeling & simulation in the heat-treatment of critical aerospace components

To manufacture light-weight, advanced metal alloy components for gas turbine engines, quench heat-treatment processes are typically used. By quenching the component from elevated tempera-tures, the alloy sometimes undergoes a solid-state phase transformation which produces special microstructures with the required, enhanced mechanical properties. However, the quenching can also lead to cracks forming in the component. Addressing the quench cracking problems adds a significant burden to the cost, schedule, and energy demand of manufacture. Currently, optimizing the quench process to mitigate or avoid the cracking is performed largely by trial-and-error, relying heavily on costly experimental (thermocouple) trials to understand the local thermal gradients which cause the cracks to form. In this first part (Phase 1) of the work, high-performance computing is employed to establish the ability of modern CFD (computational fluid dynamics) to alleviate or wholly replace the experimental quenching trials by virtual testing. A baseline CFD model is defined and its accuracy established to be comparable to (and which usually exceeds) the accuracy of existing HTC (heat-transfer correlation) based simulation methods of quenching. As a first-principles based approach, “calibration” of the Baseline CFD model is independent of the quench process itself, but instead relies on the accuracy of the underlying (modeled), generic two-phase fluid processes which cannot be currently resolved by CFD for large, industrial-scale cases. A novel, high-fidelity DNS capability has been developed and verified to examine and further improve upon the mean-field closure submodels on which the Baseline CFD approach is based.

36 MATERIALS SCIENCE↗
DOE OSTI2021

CERES: CRISPR Engineering for the Rapid Enhancement of Strains

Previous strain development efforts for cyanobacteria have failed to achieve the necessary productivities needed to support economic biofuel production. We proposed to develop CRISPR Engineering for Rapid Enhancement of Strains (CERES). We developed genetic and computational tools to enable future high-throughput screening of CRISPR interference (CRISPRi) libraries in the cyanobacterium Synechococcus sp. PCC 7002, including: (1) Operon- SEQer: an ensemble of algorithms for predicting operon pairs using RNA-seq data, (2) experimental characterization and machine learning prediction of gRNA design rules for CRISPRi, and (3) a shuttle vector for gene expression. These tools lay the foundation for CRISPR library screening to develop cyanobacterial strains that are optimized for growth or metabolite production under a wide range of environmental conditions. The optimization of cyanobacterial strains will directly advance U.S. energy and climate security by enabling domestic biofuel production while simultaneously mitigating atmospheric greenhouse gases through photoautotrophic fixation of carbon dioxide.

09 BIOMASS FUELS↗
DOE OSTI2022

Demonstrate Improved Ag Diffusion and Describe the Basis for Pd Penetration Modeling in SiC

In past work, an effective diffusivity coefficient was determined for Ag transport through the silicon carbide layer of a tristructural isotropic fuel particle. The effective diffusivity coefficient accounts for the microstructure of the silicon carbide and includes both bulk diffusion and grain boundary diffusion of Ag. In this report, the model has been improved by accounting for the enhanced concentration of vacancies in the bulk due to irradiation, which substantially influence bulk diffusivity at low temperatures. To improve the BISON model and make it fission rate dependent, effective diffusivity calculations have been performed that incorporate the radiation modified bulk diffusivity. The microstructure and irradiation-dependent effective diffusivity has also been implemented into BISON, and its predictions for Ag release from tristructural isotropic fuel have been successfully compared to AGR-1 post irradiation measurements. Moreover, a new feature has been developed in the Multiphysics Object-Oriented Simulation Environment (MOOSE) to account for different grain boundary types. The Ag diffusivity in 5 (210)/[001] grain boundaries has been computed and was found to be greater than in random high-angle grain boundaries. The presence of the fission product Pd can also have an important effect on the properties of the silicon carbide layer in tristructural isotropic particles. The penetration of Pd into the silicon carbide layer causes a corrosion reaction that can lead to the failure of the silicon carbide layer; however, this corrosion reaction is not well understood. To enable an improved understanding of the mechanism, ab-initio molecular dynamics simulations of Pd interaction with bulk silicon carbide have been performed. The improved understanding of the reaction will form a basis for future improvements to the BISON’s Pd penetration failure model

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Sandia's Research in Support of COVID-19 Pandemic Response: Computing and Information Sciences

This report summarizes the goals and findings of eight research projects conducted under the Computing and Information Sciences (CIS) Research Foundation and related to the COVID- 19 pandemic. The projects were all formulated in response to Sandia's call for proposals for rapid-response research with the potential to have a positive impact on the global health emergency. Six of the projects in the CIS portfolio focused on modeling various facets of disease spread, resource requirements, testing programs, and economic impact. The two remaining projects examined the use of web-crawlers and text analytics to allow rapid identification of articles relevant to specific technical questions, and categorization of the reliability of content. The portfolio has collectively produced methods and findings that are being applied by a range of state, regional, and national entities to support enhanced understanding and prediction of the pandemic's spread and its impacts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement

Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Improving Gas Reactor Design with Complex Non-Standard Reaction Mechanisms in a Reactive Flow Model

Fluorinated gases are critical to a number of high-technology industries including semiconductor manufacturing and related processes such as flat panel display, LED, and photovoltaic manufacturing. These fluorinated gases have very high global warming potentials (GWPs) and, unfortunately are chemically very stable, in some cases lasting for thousands of years in the atmosphere. For environmental reasons, it is imperative that the release of these gases be minimized, but existing methods to destroy them requires a significant amount of energy. The goal of this project was to develop a more energy efficient method of destroying these high GWP gases using computational fluid dynamics, but the computational requirements are significant. In this project, we bring together resources available at the national labs, including high-performance computing hardware and modern computational methods, in order to explore an industrially important problem with key environmental and economic impact. In this project, we examined the state-of-the-art models for the physical processes involved, and made subtle changes to arrive at alternative formulations considerably better suited for computation and study. We examined several representative scenarios and developed a set of analyses techniques and tools that could be used to explore the systems in much greater detail. This exploratory project has demonstrated to ALZETA that HPC can indeed provide a unique view into their complex engineering problem - one that is simply inaccessible by any other means. The tools allow us to explore the details of the chemical process, and allow one to construct "what-if" scenarios to address shortcomings of the physical device in its current operating modes. However, as with many sources of completely new information, many new questions are illuminated with this capability. It will take considerable time, effort and experience before we learn to probe the solutions, pose operating scenarios and confirm modifications to the device that lead to real engineering advances.

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

Mesoscale informed parameter estimation through machine learning: A case-study in fracture modeling

Scale bridging is a critical need in computational sciences, where the modeling community has developed accurate physics models from first principles, of processes at lower length and time scales that influence the behavior at the higher scales of interest. However, it is not computationally feasible to incorporate all of the lower length scale physics directly into upscaled models. This is an area where machine learning has shown promise in building emulators of the lower length scale models, which incur a mere fraction of the computational cost of the original higher fidelity models. We demonstrate the use of machine learning using an example in materials science estimating continuum scale parameters by emulating, with uncertainties, complicated mesoscale physics. Additionally, we describe a new framework to emulate the fine scale physics, especially in the presence of microstructures, using machine learning, and showcase its usefulness by providing an example from modeling fracture propagation. Our approach can be thought of as a data-driven dimension reduction technique that yields probabilistic emulators. Our results show well-calibrated predictions for the quantities of interests in a low-strain simulation of fracture propagation at the mesoscale level. Furthermore, on average, we achieve ~10% relative errors on time-varying quantities like total damage and maximum stresses. Successfully replicating mesoscale scale physics within the continuum models is a crucial step towards predictive capability in multi-scale problems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Roadmap on methods and software for electronic structure based simulations in chemistry and materials

This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green's function based many-body perturbation theory, wave-function based and stochastic electronic structure approaches, relativistic effects and semiempirical electronic structure theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the electronic structure, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for electronic structure based modeling from the vantage point of industry environments. Overall, the field of electronic structure software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.

36 MATERIALS SCIENCE↗
DOE OSTI2024

UNNT: A novel Utility for comparing Neural Net and Tree-based models

The use of deep learning (DL) is steadily gaining traction in scientific challenges such as cancer research. Advances in enhanced data generation, machine learning algorithms, and compute infrastructure have led to an acceleration in the use of deep learning in various domains of cancer research such as drug response problems. In our study, we explored tree-based models to improve the accuracy of a single drug response model and demonstrate that tree-based models such as XGBoost (eXtreme Gradient Boosting) have advantages over deep learning models, such as a convolutional neural network (CNN), for single drug response problems. However, comparing models is not a trivial task. To make training and comparing CNNs and XGBoost more accessible to users, we developed an open-source library called UNNT (A novel Utility for comparing Neural Net and Tree-based models). The case studies, in this manuscript, focus on cancer drug response datasets however the application can be used on datasets from other domains, such as chemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling the Impacts of Material Properties on Oscillatory Neuron Behavior

In this study, neuromorphic computing, which mimics the functions of biological brains, offers improvements in both latency and energy efficiency over typical von Neumann computing architectures. Spiking neural networks can be especially power-efficient because they encode information temporally and can use more sparse electrical inputs. Here, we study the design of volatile memristors (variable resistors with memory) for neuronal devices, with particular consideration toward the feasibility of all-on-chip oscillation using built-in capacitance. We use circuit simulations to model the behavior of oscillator neurons with a range of realistic material properties. We find that energy inputs increase with insulating-phase resistivity, thermal conductivity, and device aspect ratio. However, we also find that the minimum capacitance needed for oscillation decreases with increasing insulating-phase resistivity, which opposes the constraints for power efficiency. Based on published data on NbO 2 , VO 2 , and EuNiO 3 , we find that existing materials can be engineered for all-on-chip spiking using their parasitic capacitance.

36 MATERIALS SCIENCE↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗