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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Real-time reconstruction of ground motion during small magnitude earthquakes: A pilot study

This study presents a pilot investigation into a novel method for reconstructing real-time ground motion during small magnitude earthquakes (M < 4.5), removing the need for computationally expensive source characterization and simulation processes to assess ground shaking. Small magnitude earthquakes, which occur frequently and can be modeled as point sources, provide ideal conditions for evaluating real-time reconstruction methods. Utilizing sparse observation data, the method applies the Gappy Auto-Encoder (Gappy AE) algorithm for efficient field data reconstruction. This is the first study to apply the Gappy AE algorithm to earthquake ground motion reconstruction. Numerical experiments conducted with SW4 simulations demonstrate the method’s accuracy and speed across varying seismic scenarios. The reconstruction performance is further validated using real seismic data from the Berkeley area in California, USA, demonstrating the potential for practical application of real-time earthquake data reconstruction using Gappy AE. As a pilot investigation, it lays the groundwork for future applications to larger and more complex seismic events.

58 GEOSCIENCES↗
DOE OSTI2020

ASCR@40: Highlights and Impacts of ASCR’s Programs

A report compiled by the ASCAC Subcommittee on the 40-year history of ASCR for the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The Office of Advanced Scientific Computing Research (ASCR) sits within the Office of Science in the Department of Energy (DOE). Per their web pages, “the mission of the ASCR program is to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” This succinct statement encompasses a wide range of responsibilities for computing and networking facilities; for procuring, deploying, and operating high performance computing, networking, and storage resources; for basic research in mathematics and computer science; for developing and sustaining a large body of software; and for partnering with organizations across the Office of Science and beyond. While its mission statement may seem very contemporary, the roots of ASCR are quite deep—long predating the creation of DOE. Applied mathematics and advanced computing were both elements of the Theoretical Division of the Manhattan Project. In the early 1950s, the Manhattan Project scientist and mathematician John von Neumann, then a commissioner for the AEC (Atomic Energy Commission), advocated for the creation of a Mathematics program to support the continued development and applications of digital computing. Los Alamos National Laboratory (LANL) scientist John Pasta created such a program to fund researchers at universities and AEC laboratories. Under several organizational name changes, this program has persisted ever since, and would eventually grow to become ASCR.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Leveraging In-Network Computing and Programmable Switches for Streaming Analysis of Scientific Data

With the emergence of programmable network devices that match the performance of fixed function devices, several recent projects have explored in-network computing, where the processing that is traditionally done outside the network is offloaded to the network devices. In-network computing has typically been applied to network functions (e.g., load balancing, NAT, and DNS), caching, data reduction/aggregation, and coordination/consensus functions. In some cases it has been used to accelerate stream-processing tasks that involve small payloads and simple operations. In this work we focus on leveraging in-network computing for stream processing of scientific datasets with large payloads that require complex operations such as floating-point computations and logarithmic functions. We demonstrate in-network computing for a real-world scientific application performing streaming normalization of a 2-D image from a light source experiment. We discuss the challenges we encountered and potential approaches to address them.

Sankaran, Ganesh↗
DOE OSTI2020

Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Three-point functions in $\mathrm{ABJM}$ and Bethe Ansatz

We develop an integrability-based framework to compute structure constants of two sub-determinant operators and a single-trace non-BPS operator in ABJM theory in the planar limit. In this first paper, we study them at weak coupling using a relation to an integrable spin chain. We first develop a nested Bethe ansatz for an alternating SU(4) spin chain that describes single-trace operators made out of scalar fields. We then apply it to the computation of the structure constants and show that they are given by overlaps between a Bethe eigenstate and a matrix product state. We conjecture that the determinant operator corresponds to an integrable matrix product state and present a closed-form expression for the overlap, which resembles the so-called Gaudin determinant. We also provide evidence for the integrability of general sub-determinant operators. The techniques developed in this paper can be applied to other quantities in ABJM theory including three-point functions of single-trace operators.

1/N Expansion↗
DOE OSTI2021

A Ranked-Orbital Approach to Select Active Spaces for High-Throughput Multireference Computation

The past decade has seen a great increase in the application of high-throughput computation to a variety of important problems in chemistry. However, one area which has been resistant to the high-throughput approach is multireference wave function methods, in large part due to the technicalities of setting up these calculations and in particular the not always intuitive challenge of active space selection. As we look toward a future of applying high-throughput computation to all areas of chemistry, it is important to prepare these methods for large-scale automation. Here, we propose a ranked-orbital approach to select active spaces with the goal of standardizing multireference methods for high-throughput computation. This method allows for the meaningful comparison of different active space selection schemes and orbital localizations, and we demonstrate the utility of this approach across 1120 multireference calculations for the excitation energies of small molecules. Our results reveal that it is helpful to distinguish the method used to generate orbitals from the method of ranking orbitals in terms of importance for the active space. Additionally, we propose our own orbital ranking scheme that estimates the importance of an orbital for the active space through a pair-interaction framework from orbital energies and features of the Hartree–Fock exchange matrix. Here, we call this new scheme the “approximate pair coefficient” (APC) method and we show that it performs quite well for the test systems presented.

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

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

Abstract Summary Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment. Availability and implementation This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Interface Coating Design for Dynamic Voltage Stability of Solid‐State Batteries

Abstract Intrinsic or interface thermodynamic voltage windows of solid electrolytes are often narrower than the operational voltage range needed by a full battery, thus various interface decomposition reactions can happen in a practical solid‐state battery. Experimentally, it is found that a proper battery design utilizing the reactions can lead to a dynamic evolution from interface instability to stability, giving the so‐called dynamic voltage stability for advanced battery performance. Here, first the state‐of‐the‐art understanding is articulated about how the dynamic voltage stability should be interpreted in physical picture and treated in computation, emphasizing the potential importance of nonequilibrium reaction pathways. The constrained ensemble computational approach is further applied across most types of solid‐state electrolytes to systematically evaluate and compare their dynamic stability voltage windows in response to the mechanical constriction effect. High‐throughput calculations are used to search for coating materials for different interfaces between sulfide, halide, and oxide electrolytes and typical cathode materials with enhanced dynamic voltage stability. A comparison with experiment is given to highlight the value of these computational predictions.

Wang, Yichao↗
DOE OSTI2022

Mapping Thermoelectric Transport in a Multicomponent Alloy Space

Abstract Interest in high entropy alloy thermoelectric materials is predicated on achieving ultralow lattice thermal conductivity κ L through large compositional disorder. However, here it is shown that for a given mechanism, such as mass contrast phonon scattering, κ L will be minimized along the binary alloy with highest mass contrast, such that adding an intermediate mass atom to increase atomic disorder can increase thermal conductivity. Only when each component adds an independent scattering mechanism (such as adding strain fluctuation to an existing mass fluctuation) is there a benefit. In addition, both charge carriers and heat‐carrying phonons are known to experience scattering due to alloying effects, leading to a trade‐off in thermoelectric performance. Analytic transport models are applied, based on perturbation and effective medium theories, to predict how alloy scattering will affect the thermal and electronic transport across the full compositional range of several pseudo‐ternary and pseudo‐quaternary alloy systems. To do so, a multicomponent extension is demonstrated to both thermal and electronic binary alloy scattering models based on the virtual crystal approximation. Finally, it is shown that common functional forms used in computational thermodynamics can be applied to this problem to further generalize the scattering behavior that is modeled.

36 MATERIALS SCIENCE↗
DOE OSTI2022

An overview of visualization and visual analytics applications in water resources management

Recent advances in information, communication, and environmental monitoring technologies have increased the availability, spatiotemporal resolution, and quality of water-related data, thereby leading to the emergence of many innovative big data applications. Among these applications, visualization and visual analytics, also known as the visual computing techniques, empower the synergy of computational methods (e.g., machine learning and statistical models) with human reasoning to improve the understanding and solution toward complex science and engineering problems. These approaches are frequently integrated with geographic information systems and cyberinfrastructure to provide new opportunities and methods for enhancing water resources management. Here, we present a comprehensive review of recent hydroinformatics applications that employ visual computing techniques to (1) support complex data-driven research problems, and (2) support the communication and decision-makings in the water resources management sector. Then, we conduct a technical review of the state-of-the-art web-based visualization technologies and libraries to share our experiences on developing shareable, adaptive, and interactive visualizations and visual interfaces for water resources management applications. We close with a vision that applies the emerging visual computing technologies and paradigms to develop the next generation of hydroinformatics applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Electronic excited states from a variance-based contracted quantum eigensolver

Electronic excited states of molecules are central to many physical and chemical processes, and yet they are typically more difficult to compute than ground states. Here, in this paper we leverage the advantages of quantum computers to develop an algorithm for the highly accurate calculation of excited states. We solve a contracted Schrödinger equation (CSE)—a contraction (projection) of the Schrödinger equation onto the space of two electrons—whose solutions correspond identically to the ground and excited states of the Schrödinger equation. While recent quantum algorithms for solving the CSE, known as contracted quantum eigensolvers (CQE), have focused on ground states, we develop a CQE based on the variance that is designed to optimize rapidly to a ground or excited state. We apply the algorithm to compute the ground and excited states of H 2 , H 4 , and BH.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

MIDAS2: Metagenomic Intra-species Diversity Analysis System

The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates

Single-cell RNA-sequencing technologies have greatly enhanced our understanding of heterogeneous cell populations and underlying regulatory processes. However, structural (spatial or temporal) relations between cells are lost during cell dissociation. These relations are crucial for identifying associated biological processes. Many existing tissue-reconstruction algorithms use prior information about subsets of genes that are informative with respect to the structure or process to be reconstructed. When such information is not available, and in the general case when the input genes code for multiple processes, including being susceptible to noise, biological reconstruction is often computationally challenging. We propose an algorithm that iteratively identifies manifold-informative genes using existing reconstruction algorithms for single-cell RNA-seq data as subroutine. We show that our algorithm improves the quality of tissue reconstruction for diverse synthetic and real scRNA-seq data, including data from the mammalian intestinal epithelium and liver lobules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Modular System for Increasing Predictiveness for Extreme Climate Predictions

We know that climate change is poised to reshape our world, but we lack clear enough predictions about precisely how. The preponderance of these changes is associated with human activity, specifically the emission of CO 2 and other greenhouse gases. Problematically, projections of climate change continue to be marred by unacceptably large uncertainties which hamper informed decision-making and cost society a chance to adapt proactively and effectively. These uncertainties stem from deficiencies in predictions of future greenhouse gas emissions, but also from inaccuracies in the representation of the physical models used to predict the climate response to such emissions. The uncertainties in projections associated with the inaccurate representation of climate physics, chemistry and biology are similar to those that plagued the first global climate models developed fifty years ago, despite more than a factor 10 8 increase in computer performance. Our transformational question is then, how can the accuracy of climate projections be dramatically improved by applying recent advances in the computational and data sciences to train the models with the wealth of data being constantly collected about the ongoing changes in the climate system?

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

AI-based design of a nuclear reactor core

The authors developed an artificial intelligence (AI)-based algorithm for the design and optimization of a nuclear reactor core based on a flexible geometry and demonstrated a 3× improvement in the selected performance metric: temperature peaking factor. The rapid development of advanced, and specifically, additive manufacturing (3-D printing) and its introduction into advanced nuclear core design through the Transformational Challenge Reactor program have presented the opportunity to explore the arbitrary geometry design of nuclear-heated structures. The primary challenge is that the arbitrary geometry design space is vast and requires the computational evaluation of many candidate designs, and the multiphysics simulation of nuclear systems is very time-intensive. Therefore, the authors developed a machine learning-based multiphysics emulator and evaluated thousands of candidate geometries on Summit, Oak Ridge National Laboratory’s leadership class supercomputer. The results presented in this work demonstrate temperature distribution smoothing in a nuclear reactor core through the manipulation of the geometry, which is traditionally achieved in light water reactors through variable assembly loading in the axial direction and fuel shuffling during refueling in the radial direction. The conclusions discuss the future implications for nuclear systems design with arbitrary geometry and the potential for AI-based autonomous design algorithms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗
DOE OSTI2021

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗