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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles

Photosystem II (PSII) catalyzes the oxidation of water at its active site that harbors a high-valent inorganic Mn 4 CaO x cluster called the oxygen-evolving complex (OEC). Extrinsic subunits generally serve to protect the OEC from reductants and stabilize the structure, but diversity in the extrinsic subunits exists between phototrophs. Recent cryo-electron microscopy experiments have provided new molecular structures of PSII with varied extrinsic subunits. We focus on the extrinsic subunit PsbQ, that binds to the mature PSII complex, and on Psb27, an extrinsic subunit involved in PSII biogenesis. PsbQ and Psb27 share a similar binding site and have a four-helix bundle tertiary structure, suggesting they are related. Here, we use sequence alignments, structural analyses, and binding simulations to compare PsbQ and Psb27 from different organisms. We find no evidence that PsbQ and Psb27 are related despite their similar structures and binding sites. Evolutionary divergence within PsbQ homologs from different lineages is high, probably due to their interactions with other extrinsic subunits that themselves exhibit vast diversity between lineages. This may result in functional variation as exemplified by large differences in their calculated binding energies. Psb27 homologs generally exhibit less divergence, which may be due to stronger evolutionary selection for certain residues that maintain its function during PSII biogenesis which is consistent with their more similar calculated binding energies between organisms. Previous experimental inconsistencies, low confidence binding simulations, and recent structural data suggest that Psb27 is likely to exhibit flexibility that may be an important characteristic of its activity. Furthermore, the analysis provides insight into the functions and evolution of PsbQ and Psb27, and an unusual example of proteins with similar tertiary structures and binding sites that probably serve different roles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Parameter extraction approaches for compact modeling of thermoelectric modules

Thermoelectric (TE) cooling has experienced rapid advancements with the foundational understanding of TE materials. TE modules, compact and lightweight devices, have become the prevalent approach for implementing TE technologies. Accurately quantifying TE physical parameters (Seebeck coefficient α, thermal conductivity κ, and thermal resistance ρ) is challenging due to the dynamic temperature changes in operation. Furthermore, extracting lumped property parameters is crucial for designing energy systems using TE modules. Existing research has several limitations, such as lack of comparative analysis between prevalent formulae, reliance on potentially inaccurate vendor-supplied data, disregard for fundamental assumptions, and absence of empirical measurements. Further, this study addresses these gaps by conducting TE material characterization, comparing three existing formulae using vendor datasheets, designing a laboratory test facility for model validation and refinement, and outlining a structured data extraction procedure. The study's novelty lies in multiple key contributions: (1) a detailed comparative analysis of existing formulae for extracting TE property parameter; (2) executing experimental work in a laboratory setting to validate the model and elucidate its limitations; (3) highlighting potential risks; (4) clarifying possible assumptions from both material and engineering perspectives; and (5) considering temperature differential impacts. This comprehensive approach addresses the current research gaps and provides valuable insights into the design and application of TE modules in various energy systems.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Regions of hepatitis C virus E2 required for membrane association

Hepatitis C virus (HCV) uses a hybrid entry mechanism. Current structural data suggest that upon exposure to low pH and Cluster of Differentiation 81 (CD81), the amino terminus of envelope glycoprotein E2 becomes ordered and releases an internal loop with two invariant aromatic residues into the host membrane. Here, we present the structure of an amino-terminally truncated E2 with the membrane binding loop in a bent conformation and the aromatic side chains sequestered. Comparison with three previously reported E2 structures with the same Fab indicates that this internal loop is flexible, and that local context influences the exposure of hydrophobic residues. Biochemical assays show that the amino-terminally truncated E2 lacks the baseline membrane-binding capacity of the E2 ectodomain. Thus, the amino terminal region is a critical determinant for both CD81 and membrane interaction. These results provide new insights into the HCV entry mechanism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Pressure-induced structural dimerization in the hyperhoneycomb iridate β - Li 2 IrO 3 at low temperatures

A pressure-induced collapse of magnetic ordering in β-Li 2 IrO 3 at P m similar to 1.5-2 GPa has previously been interpreted as evidence for potential emergence of spin liquid states in this hyperhoneycomb iridate, raising prospects for experimental realizations of the Kitaev model. Based on structural data obtained at room temperature, this magnetic transition is believed to originate in small lattice perturbations that preserve crystal symmetry, and related changes in bond-directional anisotropic exchange interactions. In this work, we report on the evolution of the crystal structure of β-Li 2 IrO 3 under pressure at low temperatures (T ≤ 50 K) and show that the suppression of magnetism coincides with a change in lattice symmetry involving Ir-Ir dimerization. The critical pressure for dimerization shifts from 4.4(2) GPa at room temperature to similar to 1.5-2 GPa below 50 K. While a direct Fddd → C-2/c transition is observed at room temperature, the low temperature transitions involve new as well as coexisting dimerized phases. Additional investigation of the Ir (L 3 /L 2 ) isotropic branching ratio in x-ray absorption spectra indicates that the previously reported departure of the electronic ground state from a J eff = 1/2 state is closely related to the onset of dimerized phases. In essence, our results suggest that the predominant mechanism driving the collapse of magnetism in β-Li 2 IrO 3 is the pressure-induced formation of Ir 2 dimers in the hyperhoneycomb network. The results further confirm the instability of the J eff = 1/2 moments and related noncollinear spiral magnetic ordering against formation of dimers in the low-temperature phase of compressed β-Li 2 IrO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1974

Compiler writing system detail design specification. Volume 2: Component specification

The logic modules and data structures composing the Meta-translator module are desribed. This module is responsible for the actual generation of the executable language compiler as a function of the input Meta-language. Machine definitions are also processed and are placed as encoded data on the compiler library data file. The transformation of intermediate language in target language object text is described.

Arthur, W. J.↗
NASA NTRS1979

FORTRAN subroutines for out-of-core solutions of large complex linear systems

The design and usage of two main subprograms using direct methods to solve large linear complex systems, of the form Ax = b, whose coeffficient matrices are too large to be stored in core are described. The first main subprogram is for systems whose coefficient matrices are of a particular sparse structure, namely, the matrix A can be written in the form B + D, where B is a block-banded system, and D has only a few columns of nonzeros. Key elements of the algorithms used in the subprograms include: the data structure, the strategy for preserving numerical stability, the adaptability of the algorithms for dense systems as well as for block-profile systems.

Yip, E. L.↗
NASA NTRS1992

Efficient use of high performance computers for integrated controls and structures design

Simply transporting design codes from sequential-scalar computers to parallel-vector computers does not fully utilize the computational benefits offered by high performance computers. By performing integrated controls and structures design on an experimental truss platform with both sequential-scalar and parallel-vector design codes, conclusive results are presented to substantiate this claim. The efficiency of a Cholesky factorization scheme in conjunction with a variable-band row data structure is presented. In addition, the Lanczos eigensolution algorithm has been incorporated in the design code for both parallel and vector computations. Comparisons of computational efficiency between the initial design code and the parallel-vector design code are presented. It is shown that the Lanczos algorithm with the Cholesky factorization scheme is far superior to the sub-space iteration method of eigensolution when substantial numbers of eigenvectors are required for control design and/or performance optimization. Integrated design results show the need for continued efficiency studies in the area of element computations and matrix assembly.

Belvin, W. K.↗
DOE OSTI2020

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Influence of Cation Size on the Electronic and Magnetic Structure of M CoO{sub 3} (M = Bi, La) from Ab Initio Calculations

Using the first-principle DFT method and LSDA+ U calculations, we have performed a detailed investigation on the structural and magnetic ground states of strongly correlated M CoO{sub 3} (M= Bi, La) perovskites. Magneticphase stabilities, structural behaviors and electronic properties of both materials have been investigated. LSDA+ U calculations show that the antiferromagnetic (AFM)-C phase in the tetragonal La/BiCoO{sub 3} is energetically more favorable than the other configurations, and both rhombohedral materials are nonmagnetic. All structural data of tetragonal BiCoO{sub 3} and rhombohedral LaCoO{sub 3} compounds are found in excellent agreement with the experiment for U{sub eff}= 6 eV. We have predicted also band gaps and magnetic moments with a good accuracy via the band structure calculations. From the total and partial densities of states, we have shown the important role of O p Co d and Bi/La s-O p hybridizations in both systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Structure of the EphB6 receptor ectodomain

Eph receptors are the largest group amongst the receptor tyrosine kinases and are divided into two subgroups, A and B, based on ligand binding specificities and sequence conservation. Through ligand-induced and ligand-independent activities, Ephs play central roles in diverse biological processes, including embryo development, regulation of neuronal signaling, immune responses, vasculogenesis, as well as tumor initiation, progression, and metastasis. The Eph extracellular regions (ECDs) are constituted of multiple domains, and previous structural studies of the A class receptors revealed how they interact with ephrin ligands and simultaneously mediate Eph-Eph clustering necessary for biological activity. Specifically, EphA structures highlighted a model, where clustering of ligand-bound receptors relies on two distinct receptor/receptor interfaces. Interestingly, most unliganded A class receptors also form an additional, third interface, between the ligand binding domain (LBD) and the fibronectin III domain (FN3) of neighboring molecules. Structures of B-class Eph ECDs, on the other hand, have never been reported. To further our understanding of Eph receptor function, we crystallized the EphB6-ECD and determined its three-dimensional structure using X-ray crystallography. EphB6 has important functions in both normal physiology and human malignancies and is especially interesting because this atypical receptor innately lacks kinase activity and our understanding of the mechanism of action is still incomplete. Our structural data reveals the overall EphB6-ECD architecture and shows EphB6-LBD/FN3 interactions similar to those observed for the unliganded A class receptors, suggesting that these unusual interactions are of general importance to the Eph group. We also observe unique structural features, which likely reflect the atypical signaling properties of EphB6, namely the need of co-receptor(s) for this kinase-inactive Eph. These findings provide new valuable information on the structural organization and mechanism of action of the B-class Ephs, and specifically EphB6, which in the future will assist in identifying clinically relevant targets for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

STAR - A computer language for hybrid AI applications

Constructing Artificial Intelligence application systems which rely on both symbolic and non-symbolic processing places heavy demands on the communication of data between dissimilar languages. This paper describes STAR (Simple Tool for Automated Reasoning), a computer language for the development of AI application systems which supports the transfer of data structures between a symbolic level and a non-symbolic level defined in languages such as FORTRAN, C and PASCAL. The organization of STAR is presented, followed by the description of an application involving STAR in the interpretation of airborne imaging spectrometer data.

Borchardt, G. C.↗
NASA NTRS2012

Systems and methods for an extensible business application framework

Method and systems for editing data from a query result include requesting a query result using a unique collection identifier for a collection of individual files and a unique identifier for a configuration file that specifies a data structure for the query result. A query result is generated that contains a plurality of fields as specified by the configuration file, by combining each of the individual files associated with a unique identifier for a collection of individual files. The query result data is displayed with a plurality of labels as specified in the configuration file. Edits can be performed by querying a collection of individual files using the configuration file, editing a portion of the query result, and transmitting only the edited information for storage back into a data repository.

Bell, David G.↗
DOE OSTI2017

A graph-based computational framework for simulation and optimisation of coupled infrastructure networks

Here, we present a computational framework that facilitates the construction, instantiation, and analysis of large-scale optimization and simulation applications of coupled energy networks. The framework integrates the optimization modeling package PLASMO and the simulation package DMNetwork (built around PETSc). These tools use a common graphbased abstraction that enables us to achieve compatibility between data structures and to build applications that use network models of different physical fidelity. We also describe how to embed these tools within complex computational workflows using SWIFT, which is a tool that facilitates parallel execution of multiple simulation runs and management of input and output data. We discuss how to use these capabilities to target coupled natural gas and electricity systems.

42 ENGINEERING↗
DOE OSTI2018

Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates

Inositol pyrophosphates (PP-InsPs) are “energetic” intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35-Å-resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae and a member of the protein tyrosine-phosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. Iin this work, we demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2-Å-deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively charged PP-InsPs. (a) The catalytic P-loop with the CX 5 R(S/T) PTP motif contains additional, positively charged residues. (b) A loop between the $α$5 and $α$6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that extend into the catalytic pocket due to displacement of the $α$5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues. (c) The general-acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Skluma: An extensible metadata extraction pipeline for disorganized data

To mitigate the effects of high-velocity data expansion and to automate the organization of filesystems and data repositories, we have developed Skluma-a system that automatically processes a target filesystem or repository, extracts content-and context-based metadata, and organizes extracted metadata for subsequent use. Skluma is able to extract diverse metadata, including aggregate values derived from embedded structured data; named entities and latent topics buried within free-text documents; and content encoded in images. Skluma implements an overarching probabilistic pipeline to extract increasingly specific metadata from files. It applies machine learning methods to determine file types, dynamically prioritizes and then executes a suite of metadata extractors, and explores contextual metadata based on relationships among files. The derived metadata, represented in JSON, describes probabilistic knowledge of each file that may be subsequently used for discovery or organization. Skluma's architecture enables it to be deployed both locally and used as an on-demand, cloud-hosted service to create and execute dynamic extraction workflows on massive numbers of files. It is modular and extensible-allowing users to contribute their own specialized metadata extractors. Thus far we have tested Skluma on local filesystems, remote FTP-accessible servers, and publicly-accessible Globus endpoints. We have demonstrated its efficacy by applying it to a scientific environmental data repository of more than 500,000 files. We show that we can extract metadata from those files with modest cloud costs in a few hours.

data swamp↗
DOE OSTI2026

Cyote-attack Chain Estimator

Attack Chain Estimator (ACE) Application Overview The Attack Chain Estimator (ACE) Application is a sophisticated tool designed for the ingestion, classification, sequencing, and enrichment of cybersecurity threat reports. This application leverages advanced machine learning models and extensive historical data to provide comprehensive insights into cyber threats, specifically targeting Industrial Control Systems (ICS). Purpose The primary functions of the ACE Application include: Ingestion of Cybersecurity Threat Reporting: Capable of ingesting text-based threat reports in markdown or text file format. Supports ingestion of structured data from other sources in STIX/JSON format. Classification of Report’s Text-Based Events: Utilizes a DeBERTa classifier, specifically trained on cybersecurity data, to map the events to MITRE ATT&CK for ICS Tactics and Techniques. Classification is performed using multiple Jupyter notebooks and machine learning workflows hosted as FastAPI microservices: regex_data deberta_base_35_train_hft_classifier_mlflow.ipynb hft_regex_classifier_mlflow.ipynb param_train_hft_classifier_mlflow.ipynb regex_tactic_tech.ipynb Ordering of Tactics, Techniques, and Observable Events: Sequences the identified tactics, techniques, and events to form a coherent attack chain. Enrichment with Historical Attack Chain Details: Enhances the attack chain with details from historical attacks using a Markov model developed from CyOTE Precursor Analysis Report data. The Markov model is available as a FastAPI endpoint for seamless integration. Enrichment with Adversary Emulation Capabilities Data: Integrates adversary emulation capabilities data using MITRE Caldera for OT adversary abilities UUIDs. Export of Output Files: Provides options to export the enriched attack chain in JSON or CSV formats. Routing of Output to Other Applications: Facilitates routing of output to various platforms and applications, including: Threat Intelligence Platforms COREII Scout for Threat Intelligence Analysis COREII Modeling and Simulation for Adversary Emulation Technical Description The ACE Application is an advanced cybersecurity tool designed to provide detailed threat analysis and sequence generation. It is built on a robust architecture that integrates natural language processing, machine learning, and historical data modeling. Key Components: Data Ingestion Module: Handles the input of threat reports and data from various formats, ensuring flexibility in data sources. Classification Engine: Employs DeBERTa-based classifiers hosted as FastAPI microservices to analyze and classify threat report events in accordance with the MITRE ATT&CK framework for ICS. Sequence Generator: Orders the classified events into a logical attack chain, providing clear insight into the sequence of tactics and techniques used in the threat. Enrichment Engine: Integrates historical data and adversary emulation capabilities to enhance the attack chain with valuable context and additional details. The historical data enrichment is powered by a Markov model, which is available as a FastAPI endpoint. Export and Routing Module: Facilitates the export of the enriched attack chain in multiple formats and routes the output to designated applications for further analysis or emulation.

Paul, Tony [Idaho National Laboratory (INL), Idaho↗
NASA NTRS2016

TAT-C: A Trade-Space Analysis Tool for Constellations

Under a changing technological and economic environment, there is growing interest in implementing future NASA Earth Science missions as Distributed Spacecraft Missions (DSM). The objective of our project is to provide a framework that facilitates DSM Pre-Phase A investigations and optimizes DSM designs with respect to a-priori Science goals. In this first version of our Trade-space Analysis Tool for Constellations (TAT-C), we are investigating questions such as: Which type of constellations should be chosen? How many spacecraft should be included in the constellation? Which design has the best costrisk value? This paper describes the overall architecture of TAT-C including: a User Interface (UI) interacting with multiple users - scientists, missions designers or program managers; an Executive Driver gathering requirements from UI and formulating Trade-space Search Requests for the Trade-space Search Iterator, which in collaboration with the Orbit Coverage, Reduction Metrics, and Cost Risk modules generates multiple potential architectures and their associated characteristics. UI will include Graphical, Command Line and Application Programmer Interfaces to respond to the demands of various levels of users expertise. Science inputs are grouped into various mission concepts, satellite specifications, and payload specifications, while science outputs are grouped into several types of metrics - spatial, temporal, angular and radiometric. Orbit Coverage leverages the use of the Goddard Mission Analysis Tool (GMAT) to compute coverage and ancillary data that are passed to Reduction Metrics. Then, for each architecture design, Cost Risk will provide estimates of the cost and life cycle cost as well as technical and cost risk of the proposed mission. Additionally, the Knowledge Base module is a centralized store of structured data readable by humans and machines. It will support both TAT-C analysis when composing new mission concepts from existing model inputs, and TAT-C exploration when discovering new mission concepts by querying previous results.

Science Data Processing↗