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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 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Energetic and structural control of polyspecificity in a multidrug transporter

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues extending beyond the binding site, with mutations that reshape binding, coupling, conformational flexibility, and membrane interactions. Further, we apply a pH-based selection scheme to measure the effect of mutation on pH-dependent transport efficiency. By integrating these data, we reveal a fundamental relationship between efficiency and promiscuity: Highly efficient variants exhibit broad substrate profiles, while inefficient variants are narrower. In conclusion, these findings establish a direct link between energy coupling and polyspecificity, uncovering the biochemical logic underlying multidrug transport.

Biological Sciences↗
DOE OSTI2015

THE C({sup 3}P) + NH{sub 3} REACTION IN INTERSTELLAR CHEMISTRY. II. LOW TEMPERATURE RATE CONSTANTS AND MODELING OF NH, NH{sub 2}, AND NH{sub 3} ABUNDANCES IN DENSE INTERSTELLAR CLOUDS

A continuous supersonic flow reactor has been used to measure rate constants for the C({sup 3}P) + NH{sub 3} reaction over the temperature range 50–296 K. C({sup 3}P) atoms were created by the pulsed laser photolysis of CBr{sub 4}. The kinetics of the title reaction were followed directly by vacuum ultra-violet laser induced fluorescence of C({sup 3}P) loss and through H({sup 2}S) formation. The experiments show unambiguously that the reaction is rapid at 296 K, becoming faster at lower temperatures, reaching a value of (1.8 ± 0.2) × 10{sup −10} cm{sup 3} molecule{sup −1} s{sup −1} at 50 K. As this reaction is not currently included in astrochemical networks, its influence on interstellar nitrogen hydride abundances is tested through a dense cloud model including gas–grain interactions. In particular, the effect of the ortho-to-para ratio of H{sub 2}, which plays a crucial role in interstellar NH{sub 3} synthesis, is examined.

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

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits

Abstract The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein–protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Genetics & Heredity↗
DOE OSTI2016

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Comparative genomics approaches are broadly used for analysis of transcriptional regulation in bacterial genomes. In this work, we identified binding sites and reconstructed regulons for 33 orthologous groups of transcription factors (TFs) in 196 reference genomes from 21 taxonomic groups of Proteobacteria. Overall, we predict over 10 600 TF binding sites and identified more than 15 600 target genes for 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs from Esc herichia coli and/or Shewanella that are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages of Proteobacteria. By comparing gene contents of the reconstructed regulons, we identified the core, taxonomy-specific and genome-specific TF regulon members and classified them by their metabolic functions. Detailed analysis of ArgR, TyrR, TrpR, HutC, HypR and other amino-acid-specific regulons demonstrated remarkable differences in regulatory strategies used by various lineages of Proteobacteria. The obtained genomic collection of in silico reconstructed TF regulons contains a large number of new regulatory interactions that await future experimental validation. The collection provides a framework for future evolutionary studies of transcriptional regulatory networks in Bacteria. It can be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed regulons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Unlocking Flexibility: Energy Systems Integration [Guest Editorial]

The articles in this special section focus on energy systems integration (ESI). Electric power systems around the world are experiencing great changes, including the retirement of coal and nuclear plants along with a rapid increase in the use of natural gas turbines and variable renewable technologies such as wind and solar. There is also much more use of information and communications technologies to enhance the visibility and controllability of the grid. Flexibility of operation, the ability of a power system to respond to change in demand and supply, is critical to enable higher levels of variable generation. One way to unlock this potential flexibility is to tap into other energy domains. This concept of interconnecting energy domains is called ESI. ESI is the process of coordinating the operation and planning of energy systems across multiple pathways and/or geographical scales to deliver reliable, cost-effective energy services with minimal impact on the environment. Integrating energy domains adds flexibility to the electrical power system. ESI includes interactions among energy vectors and with other large-scale infrastructures including water, transport, and data and communications networks, which are an enabling technology for ESI.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Strain release through hydrogen bond–mediated layer twisting

Strain engineering, enabling the precise control over structure and functional properties, is a key strategy for the design of advanced materials. However, the mechanisms governing strain evolution and release at the nanoscale remain largely unexplored. In this study, we leverage in situ heating transmission electron microscopy and synchrotron x-ray spectroscopy to investigate the strain relaxation pathways of boehmite (γ-AlOOH) at 575 kelvin by revealing real-time structural dynamics. Through tracking the moiré pattern evolution, we identify distinct strain release mechanisms, including layer twisting, defect formation, and domain restructuring. Our neural network potential calculations reveal that energy fluctuations at small twist angles are dominated by an interference-like interaction modulation of hydrogen bonds between boehmite interlayers, with metastable twisted structures corresponding to local minima of the potential energy landscape. This work establishes a previously unidentified paradigm of two-dimensional layer twisting mediated by hydrogen bonding, offering insights into strain-driven transformation mechanisms, and thus may have broad implications for strain in material and earth sciences.

36 MATERIALS SCIENCE↗
DOE OSTI2025

GenomeFace v1.0

GenomeFace is meta-genome binning software. Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution of each based on characteristics of the input data. Trained on over 43,000 prokaryotic genomes, our network for composition-based binning is inspired by metric learning techniques used for facial recognition. Using a task-specific, multi-GPU accelerated algorithm to cluster the embeddings produced by our network, our binner leverages marker genes observed to be universally present in nearly all taxa to grade and select optimal clusters of sequences from a hierarchy of candidates. We evaluate our approach on four simulated datasets with known ground truth. Our linear time integration of marker genes recovers more near complete genomes than state of the art but computationally infeasible solutions using them, while being over an order of magnitude faster. Finally, we demonstrate the scalability and acuity of our approach by testing it on three of the largest metagenome assemblies ever performed. Compared to other binners, we produced 47%-183% more near complete genomes. From these datasets, we find over the genomes of over 3000 new candidate species which have never been previously cataloged, representing a potential 4% expansion of the known bacterial tree of life.

Lettich, Richard [Lawrence Berkeley National Labor↗
DOE OSTI2017

Integrated Nondestructive Assay Systems to Estimate Plutonium in Spent Fuel Assemblies

An integrated nondestructive assay (NDA) system combining active (neutron generator) and passive neutron detection and passive gamma (PG) detection is being analyzed in order to estimate the amount of plutonium, verify initial enrichment, burnup, and cooling time, and detect partial defects in a spent fuel assembly (SFA). Active signals are measured using the differential die-away (DDA), delayed neutron (DN), and delayed gamma (DG) techniques. Passive signals are measured using total neutron (TN) counts and both gross and spectral resolved gamma counts. To quantify how a system of several NDA techniques is expected to perform, all of the relevant NDA techniques listed above were simulated as a function of various reactor conditions such as initial enrichment, burnup, cooling time, assembly shuffling pattern, reactor operating conditions (including temperature, pressure, and the presence of burnable poisons) by simulating the NDA response for five sets of light water reactor assemblies. In this study, we compare the performance of several exploratory model-fitting options (including neural networks, adaptive regression with splines, iterative bias reduction smoothing, projection pursuit regression, and regression with quadratic terms and interaction terms) to relate data simulated with measurement and model error effects from various subsets of the NDA techniques to the total Pu mass. Isotope masses for SFAs and expected detector responses (DRs) for several NDA techniques are simulated using MCNP, and the DRs become inputs to the fitting process. Such responses include eight signals from DDA, one from DN, one from TN, and up to seven from PG; the DG signal will be examined separately. Results are summarized using the root-mean-squared estimation error for plutonium mass in held-out subsets of the data for a range of model and measurement error variances. Different simulation assumptions lead to different spent fuel libraries relating DRs to Pu mass. Some results for training with one library and testing with another library are also given.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2025

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗
DOE OSTI2022

ACES: Infrastructure As Code. Model Optimization and Performance Capability

Infrastructure as Code (IaC) refers to managing infrastructure (networks, physical/virtual machines, storage, and connection topology) in a descriptive model/language, rather than configuring it manually or using interactive configuration tools. Just like source code can be compiled to generate the same binary code, IaC enables generating the same environment every time it is applied. IaC is a key DevOps practice and is generally used in conjunction with continuous integration (CI) and continuous delivery (CD). In CI, all code changes are merged into a mainline branch and validated multiple times a day as developers check in their changes to the source code. In CD on the other hand, code changes are automatically packaged for a new release-to-production on a regular basis. This typically enables teams to deliver software changes much more quickly and often. Developing and managing the ACES platform using (IaC) is vital for the robust deployment and continued sustainment of this foundational computing capability. IaC and DevOps practices will help us solve many of the common challenges often encountered in developing and maintaining compute infrastructure. First, it will make the provisioning, deployment, and maintenance of the compute infrastructure across multiple environments much more efficient. Second, these processes help make the overall system much more stable by continuously testing new changes as they are introduced to the system. Third, it allows us to be much more confident of the security controls in place since they can be tested as part of the CI process and all new changes can be audited and tracked. Finally, IaC enables the ACES Platform to be adaptable to the emerging technologies due to its ability to spin up different test beds to evaluate and incorporate these technologies. This document addresses common infrastructure-management challenges, describes what happens if they are not addressed, and highlights the value of utilizing IaC to tackle them. Finally, we will provide a high-level overview of the IaC and DevOps practices being utilized by the ACES Platform team.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Coastal-Urban-Rural Atmospheric Gradient Experiment (CoURAGE) Science Plan

Understanding the mechanisms governing the urban atmospheric environment is critical for informing urban populations regarding the impacts of climate change and associated mitigation and adaptation measures. Earth system (climate and weather) models have not yet been adapted to provide accurate predictions of climate and weather variability within cities, nor do they provide well-tested representations of the impacts of urban systems on the atmospheric environment. These limitations are largely due to limited field data available for testing and development of these models. We will deploy the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility’s first Mobile Facility (AMF1) to the mid-Atlantic region surrounding the city of Baltimore for the Coast-Urban-Rural Atmospheric Gradient Experiment (CoURAGE). This deployment will create a four-node regional atmospheric observatory network including Baltimore and its three primary surrounding environments – rural, urban, and bay. CoURAGE investigators will study the interactions among the Earth’s surface, the atmospheric boundary layer, aerosols and atmospheric composition, clouds, radiation, and precipitation at each site, and examine how the spatial gradients across the region interact to create the climate conditions in Baltimore. This study will determine the degree to which Baltimore’s atmospheric environment depends on interactive feedbacks in the atmospheric system and the degree to which conditions in Baltimore depend on the surrounding environment. Some topics of interest include how urban land management exacerbates heat waves, the impact of regional mesoscale winds (nocturnal jet, bay breeze) on urban air pollution and cloud cover, and the impact of the urban heat island and aerosol production on heavy precipitation events. Understanding this integrated coast-urban-rural system quantitatively and with good accuracy and precision is critical to informing climate adaptation and mitigation efforts in the city of Baltimore. The understanding gained should be applicable to many similar coastal, mid-latitude urban centers. Another important objective of CoURAGE is to improve the representation of the climate of coastal cities in Earth systems models (ESMs). CoURAGE investigators will use the observations to test current ESMs, identify weaknesses and work towards improved simulations of this complex environment. The ARM core facility will be deployed in the city of Baltimore, complementing the Baltimore Social-Environmental Collaborative (BSEC), a DOE urban integrated field laboratory (UIFL). Ancillary sites will be deployed to rural Maryland northwest of Baltimore, and to the southern end of Kent Island within Chesapeake Bay. The fourth node will be a long-term atmospheric observatory operated in Beltsville, Maryland by Howard University and the Maryland Department of the Environment. Measurements will be conducted for one year, starting in December of 2024. There will be two intensive operational periods (IOPs), one in summer and one in winter, when the ancillary sites will be enhanced with additional balloon launches, tethered balloon system (TBS) operation, and added atmospheric composition measurements.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

T&D LIBRA: Simulation Framework for Transmission and Distribution Load and IBR Assessment

This paper introduces T&D LIBRA, a HELICS-based dynamic co-simulation framework designed for transmission and distribution (T&D) load and inverter-based resource assessment. This framework is designed to model interactions between single-phase induction motors (i.e., Motor-D), distributed energy resources (DERs) and the transmission network, emphasizing system stability during fault conditions. The primary objective of this research is to study the fault-induced delayed voltage recovery (FIDVR) behavior of the T&D networks using the co-simulation framework and to compare the results with conventional PSS/E only simulations. Simulations are validated using T&D co-simulations with a single distribution node and the IEEE 123-bus distribution test case. The co-simulation results demonstrate the value of using T&D co-simulations to capture motor stalling, DER tripping and other sources of voltage diversity on distribution networks.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS1985

Tail phenomena

An overview of tail phenomena is presented based on worldwide submissions to the Large-Scale Phenomena Discipline Specialist Team of the International Halley Watch. Examples of tail phenomena and science are presented along with estimates of total expected yield from the Network. The archive of this material will clearly be very valuable for studying the solar-wind/comet interaction during the 1985-1986 apparition of Halley's Comet.

Brandt, J. C.↗
NASA NTRS1990

Convective dynamics - Panel report

Aspects of highly organized forms of deep convection at midlatitudes are reviewed. Past emphasis in field work and cloud modeling has been directed toward severe weather as evidenced by research on tornadoes, hail, and strong surface winds. A number of specific issues concerning future thrusts, tactics, and techniques in convective dynamics are presented. These subjects include; convective modes and parameterization, global structure and scale interaction, convective energetics, transport studies, anvils and scale interaction, and scale selection. Also discussed are analysis workshops, four-dimensional data assimilation, matching models with observations, network Doppler analyses, mesoscale variability, and high-resolution/high-performance Doppler. It is also noted, that, classical surface measurements and soundings, flight-level research aircraft data, passive satellite data, and traditional photogrammetric studies are examples of datasets that require assimilation and integration.

Carbone, Richard↗
NASA NTRS1991

Light domain walls, massive neutrinos and the large scale structure of the Universe

Domain walls generated through a cosmological phase transition are considered, which interact nongravitationally with light neutrinos. At a redshift z greater than or equal to 10(exp 4), the network grows rapidly and is virtually decoupled from the matter. As the friction with the matter becomes dominant, a comoving network scale close to that of the comoving horizon scale at z of approximately 10(exp 4) gets frozen. During the later phases, the walls produce matter wakes of a thickness d of approximately 10h(exp -1)Mpc, that may become seeds for the formation of the large scale structure observed in the Universe.

Massarotti, Alessandro↗
NASA NTRS1993

The SSABLE system - Automated archive, catalog, browse and distribution of satellite data in near-real time

Historically, locating and browsing satellite data has been a cumbersome and expensive process. This has impeded the efficient and effective use of satellite data in the geosciences. SSABLE is a new interactive tool for the archive, browse, order, and distribution of satellite date based upon X Window, high bandwidth networks, and digital image rendering techniques. SSABLE provides for automatically constructing relational database queries to archived image datasets based on time, data, geographical location, and other selection criteria. SSABLE also provides a visual representation of the selected archived data for viewing on the user's X terminal. SSABLE is a near real-time system; for example, data are added to SSABLE's database within 10 min after capture. SSABLE is network and machine independent; it will run identically on any machine which satisfies the following three requirements: 1) has a bitmapped display (monochrome or greater); 2) is running the X Window system; and 3) is on a network directly reachable by the SSABLE system. SSABLE has been evaluated at over 100 international sites. Network response time in the United States and Canada varies between 4 and 7 s for browse image updates; reported transmission times to Europe and Australia typically are 20-25 s.

Simpson, James J.↗
NASA NTRS2003

Preserving the Finger Lakes for the Future: A Prototype Decision Support System for Water Resource Management, Open Space, and Agricultural Protection

As described herein, this project has progressed well, with the initiation or completion of a number of program facets at programmatic, technical, and inter-agency levels. The concept of the Virtual Management Operations Center has taken shape, grown, and has been well received by parties from a wide variety of agencies and organizations in the Finger Lakes region and beyond. As it has evolved in design and functionality, and to better illustrate its current focus for this project, it has been given the expanded name of Watershed Virtual Management Operations Center (W-VMOC). It offers the advanced, compelling functionality of interactive 3D visualization interfaced with 2D mapping, all accessed via Internet or virtually any kind of distributed computer network. This strong foundation will allow the development of a Decision Support System (DSS) with anticipated enhanced functionality to be applied to the myriad issues involved in the wise management of the Finger Lakes region.

Brower, Robert↗