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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

INtegrated Fluid & paRticles simulatioN cOde (INF&RNO) v1.0

INF&RNO (INtegrated Fluid & paRticle simulation cOde) is a 2D cylindrical (r-z) code to model the interaction of short laser pulse(s) with an underdense plasma. The code is based on an envelope model for the laser field, and the action of the laser on the plasma is modeled with the time-averaged ponderomotive force approximation. The code features an improved laser envelope solver which enables an accurate description of the laser pulse evolution deep into depletion even at a reasonably low resolution.

Benedetti, Carlo [Lawrence Berkeley National Labor↗
DOE OSTI2021

Waterlevel, geochemical, and borehole data from Rifle, Colorado from 2006-2016

The files included in this data package provide site wide water level data, geochemical data, and borehole information associated with the Rifle site in Colorado during the Lawrence Berkeley National Lab (LBNL) led Integrated Field Research Challenge (IFRC) and Scientific Focus Area (SFA) research projects. The data informs hydrogeochemical interactions occurring in the watershed. The readme file contains detailed metadata for the files, including naming conventions, column headers, and data validation.The borehole information is provided in the file called rifle_boreholes.csv. It provides names and location for boreholes/wells at the Rifle. The waterlevel data is provided in the folder rifle_waterlevels. The geochemical data is provided in two folders: the rifle_floodplain_geochemistry folder has data which was collected from wells across the floodplain and a variety of offsite locations that contribute solutes to the floodplain given their upgradient locations. The rifle_plotC_geochemistry folder has data which was collected primarily in plot C, which was a focused study area in which a large number of groundwater manipulation / biostimulation experiments were conducted. While not all geochemical constituents are included for each well location and sampling date, they include anions, cations, trace metals, dissolved organic and inorganic carbon, stable isotopes of water and sulfur (as sulfate), and water quality parameters including pH, groundwater electrical conductivity (EC) and dissolved oxygen (DO). All files are in csv or txt format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The Baryonic Content of Galaxies Mapped by MaNGA and the Gas Around Them

We analyze the cool gas in and around 14 nearby galaxies (at z < 0.1) mapped with the Sloan Digital Sky Survey IV MaNGA survey by measuring absorption lines produced by gas in spectra of background quasars/active galactic nuclei at impact parameters of 0–25 effective radii from the galactic centers. Using Hubble Space Telescope/Cosmic Origins Spectrograph, we detect absorption at the galactic redshift and measure or constrain column densities of neutral (H I, N I, O I, and Ar I), low-ionization (Si II, S II, C II, N II, and Fe II), and high-ionization (Si III, Fe III, N v, and O vI) species for 11 galaxies. We derive the ionization parameter and ionization-corrected metallicity using cloudy photoionization models. The H i column density ranges from ~1013 to ~1020 cm-2 and decreases with impact parameter for r ≳ Re. Galaxies with higher stellar mass have weaker H I absorption. Comparing absorption velocities with MaNGA radial velocity maps of ionized gas line emissions in galactic disks, we find that the neutral gas seen in absorption corotates with the disk out to ~10 R e . Sight lines with lower elevation angles show lower metallicities, consistent with the metallicity gradient in the disk derived from MaNGA maps. Higher-elevation angle sight lines show higher ionization, lower H I column density, supersolar metallicity, and velocities consistent with the direction of galactic outflow. Our data offer the first detailed comparisons of circumgalactic medium (CGM) properties (kinematics and metallicity) with extrapolations of detailed galaxy maps from integral field spectroscopy; similar studies for larger samples are needed to more fully understand how galaxies interact with their CGM.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Hands-On, Heads-Up: Blending Cyber T&E with Data Science-Driven Training in Jupyter Notebooks

In an era of increasingly sophisticated threats to critical infrastructure, cybersecurity professionals must be more than just aware; they must be immersed, agile, and equipped to operate in environments where failure is not an option. Nowhere is this truer than in the nuclear sector, where cyber-physical systems, regulatory scrutiny, and insider threat potential demand a new generation of hands-on, technically fluent defenders. This paper presents a unified training approach that integrates Cybersecurity Test and Evaluation (T&E) with data science techniques using Jupyter Notebooks as the interactive lab environment. The program centers on a modular, scenario-driven curriculum designed to build not just knowledge but practical capability in the assessment and defense of radiation detection systems, firmware interfaces, and operational security postures.

98 - NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL↗
DOE OSTI2021

Subsurface Characterization of Hydraulic Fracture Test Site-2 (HFTS-2), Delaware Basin

Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Wolfcamp Formation of the Permian (Delaware) Basin. This paper focuses on integration, advanced geological characterization, and 3D subsurface modeling of the comprehensive HFTS-2 dataset. The study showcases a multidisciplinary reservoir characterization approach that incorporates geology, petrophysics, geochemistry, geomechanics, microseismic, and subsurface engineering analysis. Subsurface characterization of organic-rich mudstone formations requires understanding complex hydraulic fracture network growth in relation to inherent lithology, geomechanical properties, and interaction with pre-existing natural fractures. This paper presents a characterization workflow incorporating pre- and post-stimulation subsurface data, unique to the HFTS-2 dataset. The study integrated: (1) rock properties from logs, cores, and thin sections; (2) natural and hydraulic fracture descriptions from cores and image logs; (3) local and regional stresses; (4) geomechanics; (5) microseismic; (6) fiber optic (FO) and bottomhole pressure gauge (BHPG) response; and (7) produced fluids analysis. During a stimulation treatment, creation of the stimulated rock volume (SRV) is influenced by several subsurface factors. Key contributing factors include structural context, stress conditions, lithology, facies architecture, pre-existing natural fractures, and geomechanical properties. The HFTS-2 subsurface data integration indicates that the SRV is comprised of a complex juxtaposition of hydraulic fracture swarms, as evidenced by image logs analysis, core description, and microseismic monitoring. The HFTS-2 microseismic event density was used to generate 3D heat maps that serve as a representative SRV footprint, corroborated by secondary datasets. These maps were further integrated with petrophysical and geomechanical characteristics, as well as responses from FO and BHPG, to estimate the lateral and vertical dimensions of the effective fractures. The geological characterization for the HFTS-2 dataset combined with 3D modeling for petrophysical and geomechanical properties provides a strong foundation for subsurface simulation and optimization studies. Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/1-21URTC/D011S005R001/2477501/urtec-2021-5243-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5243 The workflow improved our understanding of HFTS-2 hydraulic fracture propagation and characteristics in relation to offset pressure depletion and interaction with pre-existing natural fractures. Analysis showed that fracture geometry varies by stage and by well, and a complex fracture network is generated with varying fracture density. The multidisciplinary workflow presented herein for integration and characterization serves as a foundation to evaluate completion efficiency and estimate areal and vertical stimulation and depletion extent for the project. Furthermore, the workflow and learnings can also be transferred to other unconventional plays.

58 GEOSCIENCES↗
DOE OSTI2021

Integration of full divertor detachment with improved core confinement for tokamak fusion plasmas

Divertor detachment offers a promising solution to the challenge of plasma-wall interactions for steady-state operation of fusion reactors. Here, we demonstrate the excellent compatibility of actively controlled full divertor detachment with a high-performance (β N ~ 3, H 98 ~ 1.5) core plasma, using high-β p (poloidal beta, β p > 2) scenario characterized by a sustained core internal transport barrier (ITB) and a modest edge transport barrier (ETB) in DIII-D tokamak. The high-β p high-confinement scenario facilitates divertor detachment which, in turn, promotes the development of an even stronger ITB at large radius with a weaker ETB. This self-organized synergy between ITB and ETB, leads to a net gain in energy confinement, in contrast to the net confinement loss caused by divertor detachment in standard H-modes. These results show the potential of integrating excellent core plasma performance with an efficient divertor solution, an essential step towards steady-state operation of reactor-grade plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

FENIX: An Open-Source Multiphysics Integrated Framework Enabling Collaborative Development of Plasma Facing Component Modeling Capabilities

Advanced modeling and simulation tools have a crucial role to play in accelerating fusion energy deployment as a sustainable power source. Multiphysics, high-fidelity computational tools can help understand, model, and quantify the complex interactions between materials performance, plasma and neutron exposure, and engineering processes. As a result, they accelerate the design, safety analysis, and performance evaluation of fusion systems. This webinar introduces the Fusion ENergy Integrated multiphys-X (FENIX) framework, an open-source multiphysics tool for plasma facing component modeling. FENIX leverages the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, which has been developed by the United States Department of Energy Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. FENIX couples various MOOSE capabilities such as heat transfer, thermomechanics, thermal hydraulics, electromagnetics, and plasma kinetics with the MOOSE-based applications Cardinal (neutronics) and TMAP8 (tritium transport). During the webinar, we will present FENIX and discuss how its modularity, openness, software quality assurance processes, and licensing approach supports effective collaborations, including public-private partnerships.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Protonic nickelate device networks for spatiotemporal neuromorphic computing

Computation in biological neural circuits arises from the interplay of nonlinear temporal responses and spatially distributed dynamic network interactions. Replicating this richness in hardware has remained challenging, as most neuromorphic devices emulate only isolated neuron- or synapse-like functions. Here we introduce an integrated neuromorphic computing platform in which both nonlinear spatiotemporal processing and programmable memory are realized within a single perovskite nickelate material system. By engineering symmetric and asymmetric hydrogenated NdNiO 3 junction devices on the same wafer, we combine ultrafast, proton-mediated transient dynamics with stable multilevel resistance states. Networks of symmetric NdNiO 3 junctions exhibit emergent spatial interactions mediated by proton redistribution, while each node simultaneously provides short-term temporal memory, enabling nanosecond-scale operation with an energy cost of ~0.2 nJ per input. When interfaced with asymmetric output units serving as reconfigurable long-term weights, these networks allow both feature transformation and linear classification in the same material system. Leveraging these emergent interactions, the platform enables real-time pattern recognition and achieves high accuracy in spoken digit classification and early seizure detection, outperforming temporal-only or uncoupled architectures. These results position protonic nickelates as a compact, energy-efficient, CMOS-compatible platform that integrates processing and memory for scalable intelligent hardware.

Electrical and electronic engineering↗
DOE OSTI2021

Progressive growth of the solid–electrolyte interphase towards the Si anode interior causes capacity fading

The solid–electrolyte interphase (SEI), a layer formed on the electrode surface, is essential for electrochemical reactions in batteries and critically governs the battery stability. Active materials, especially those with extremely high energy density, such as silicon (Si), often inevitably undergo a large volume swing upon ion insertion and extraction, raising a critical question as to how the SEI interactively responds to and evolves with the material and consequently controls the cycling stability of the battery. Here, by integrating sensitive elemental tomography, an advanced algorithm and cryogenic scanning transmission electron microscopy, we unveil, in three dimensions, a correlated structural and chemical evolution of Si and SEI. Furthermore, corroborated with a chemomechanical model, we demonstrate progressive electrolyte permeation and SEI growth along the percolation channel of the nanovoids due to vacancy injection and condensation during the delithiation process. Consequently, the Si–SEI spatial configuration evolves from the classic ‘core–shell’ structure in the first few cycles to a ‘plum-pudding’ structure following extended cycling, featuring the engulfing of Si domains by the SEI, which leads to the disruption of electron conduction pathways and formation of dead Si, contributing to capacity loss. The spatially coupled interactive evolution model of SEI and active materials, in principle, applies to a broad class of high-capacity electrode materials, leading to a critical insight for remedying the fading of high-capacity electrodes.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling

Tree growth and survival are dependent on their ability to perceive signals, integrate them, and trigger timely and fitted molecular and growth responses. While ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems, little is known about how and to what extent it helps trees cope with environmental changes. We hypothesized that the presence of Laccaria bicolor influences abiotic cue perception by Populus trichocarpa and the ensuing signaling cascade. We submitted ectomycorrhizal or non-ectomycorrhizal P. trichocarpa cuttings to short-term cessation of watering or ozone fumigation to focus on signaling networks before the onset of any physiological damage. Poplar gene expression, metabolite levels, and hormone levels were measured in several organs (roots, leaves, mycorrhizas) and integrated into networks. We discriminated the signal responses modified or maintained by ectomycorrhization. Ectomycorrhizas buffered hormonal changes in response to short-term environmental variations systemically prepared the root system for further fungal colonization and alleviated part of the root abscisic acid (ABA) signaling. Furthermore, the presence of ectomycorrhizas in the roots also modified the leaf multi-omics landscape and ozone responses, most likely through rewiring of the molecular drivers of photosynthesis and the calcium signaling pathway. In conclusion, P. trichocarpa-L. bicolor symbiosis results in a systemic remodeling of the host's signaling networks in response to abiotic changes. In addition, ectomycorrhizal, hormonal, metabolic, and transcriptomic blueprints are maintained in response to abiotic cues, suggesting that ectomycorrhizas are less responsive than non-mycorrhizal roots to abiotic challenges.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Modeling laser interactions with aluminum and tantalum targets using a hybrid atomistic-continuum model

A hybrid atomistic-continuum method can model the microstructure evolution of metals subjected to laser irradiation. This method combines classical molecular dynamics (MD) simulations with the two-temperature model (TTM) to account for the laser energy absorption and heat diffusion behavior. Accurate prediction of the temperature evolution in the combined MD-TTM method requires reliable accuracy in electron heat capacity, electron thermal conductivity, and electron–phonon coupling factor across the temperatures generated. This study uses the electronic density of states (DOS) obtained from first-principle calculations. The calculated electron temperature-dependent parameters are used in MD-TTM simulations to study the laser metal interactions in FCC and BCC metals and the phenomenon of laser shock loading and melting. This study uses FCC Al and BCC Ta as model systems to demonstrate this capability. When subjected to short pulsed laser shocks, the dynamic failure behavior predicted using temperature-dependent parameters is compared with the experimentally reported single-crystal and nanocrystalline Al and Ta systems. The MD-TTM simulations also investigate laser ablation and melting behavior of Ta to compare with the ablation threshold reported experimentally. In conclusion, this manuscript demonstrates that integrating the temperature-dependent parameters into MD-TTM simulations leads to the accurate modeling of the laser–metal interaction and allows the prediction of the kinetics of the solid–liquid interface.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Exchange correlation potentials from full configuration interaction in a Slater orbital basis

Ryabinkin–Kohut–Staroverov (RKS) theory builds a bridge between wave function theory and density functional theory by using quantities from the former to produce accurate exchange-correlation potentials needed by the latter. In this work, the RKS method is developed and tested alongside Slater atomic orbital basis functions for the first time. To evaluate this approach, full configuration interaction computations in the Slater orbital basis are employed to give quality input to RKS, allowing full correlation to be present along with correct nuclei cusps and asymptotic decay of the wavefunction. SlaterRKS is shown to be an efficient algorithm to arrive at exchange-correlation potentials without unphysical artifacts in moderately-sized basis sets. Furthermore, enforcement of the nuclear cusp conditions will be shown to be vital for the success of the Slater-basis RKS method. As a result, examples of weakly and strongly correlated molecular systems will demonstrate the main features of SlaterRKS.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Superdiffusion resilience in Heisenberg chains with two-dimensional interactions on a quantum processor

Superdiffusive spin transport in the one-dimensional (1D) Heisenberg model is a key theoretical discovery in nonequilibrium quantum many-body physics. Although extensively studied in 1D systems, the breakdown and sustenance of superdiffusion in two-dimensional (2D) lattices with integrability-breaking terms, as found in real materials, remains an open question. To address this, we develop a toy model that extends the 1D Heisenberg model with a representative set of 2D interaction types and tunable strengths. Our model exhibits varying degrees of superdiffusion breakdown depending on the interaction type, spanning ballistic to diffusive regimes. We establish and justify a hierarchy of 2D interactions based on their resilience against superdiffusion breakdown: Heisenberg >𝑋⁢𝑋 > Ising. This precise control over the superdiffusive behavior also enables rigorous benchmarking of quantum hardware, and our simulations on IBM's Heron devices confirm the hardware's ability to accurately capture these many-body nonequilibrium phenomena. Overall, our results are relevant not only to simulating superdiffusion in real materials, such as the 1D Heisenberg compound KCuF3, which contains modest nonintegrable 2D terms, but also to extending superdiffusive behavior to larger 2D qubit lattices and other 2D materials.

Alagarsamy Manikandan, Keerthi Kumaran [ORNL]↗
DOE OSTI2026

Web-based Preprocessing and Visualization of 3D FIB Tomography Data for Nuclear Fuel Characterization

Three-dimensional (3D) focused ion beam (FIB) tomography enables reconstruction of internal nuclear fuel features that can't be fully evaluated through surface imaging alone. This capability supports characterization of fuel constituents and defects under thermal and irradiation conditions relevant to microreactor development. However, large tomography datasets can create data-handling, loading, and visualization challenges, especially when image-stack preparation and file conversion must be completed with separate tools. The Computational Ultraspatial Tomography Toolkit for High-Resolution Object Analysis Tools (CUTTRHOAT) is an open-source web application being developed to display FIB tomography datasets available through the Nuclear Research Data System (NRDS). The current alpha version requires prepared HDF5 datasets and has limited integrated data-preparation capabilities. This project improves CUTTHROAT by adding dataset-folder selection, automatic input detection, dataset scanning, missing-slice identification, blank-slice insertion, and image-stack-to-HDF5 conversion. Two applications will be compared: the baseline CUTTHROAT alpha workflow and the updated application containing the integrated data-handling and preprocessing functions. Evaluation will consider dataset detection accuracy, conversion success, loading time, rendering responsiveness, application stability, and user interaction. Preliminary results demonstrate successful loading of existing HDF5 files and converted image stacks, while testing also identified performance reductions caused by excessive blank-slice generation. The updated workflow reduces reliance on external preparation tools and supports more direct movement from image stacks to color-code 3D visualization. Future work includes refining missing-slice handling, integrating additional preprocessing functions, like a denoising feature, parsing TIFF metadata for automatic voxel scaling, and adding manual X, Y, and Z voxel-spacing inputs for PNG and JPEG.

36 - MATERIALS SCIENCE↗
DOE OSTI2026

Cooperative Agreement To Analyze variabiLity, change and predictabilitY in the earth SysTem (CATALYST)

CATALYST proposes to perform foundational coordinated research in a team-oriented collaborative effort aimed at advancing a robust understanding of modes of Earth system variability and change using models, observations and process studies. The proposed research will address the DOE/BER mission by exploring the limits to predictability, identifying fundamental underlying mechanisms, quantifying interactions among modes of variability, and discovering tipping points in the Earth system to understand the current and future impacts of these phenomena on regional and global climate. Four fundamental gaps are identified in our knowledge of the Earth system: 1) What are the limits to predictability on various timescales? 2) What are the interactions among modes of Earth system variability? 3) How may modes of Earth system variability change in response to changes in external forcing, and what are the tipping points involved with those changes? 4) How are high impact events connected to modes of Earth system variability and how may they change in the future? Related to those gaps in our knowledge, we formulate four research objectives to address those gaps using a combination of Earth system models (ESMs) and machine learning (ML) methods. Research Objective 1 (RO1) addresses the first gap above and proposes to understand modes of variability and their limits of predictability on subseasonal to decadal timescales using ESMs and ML. Research Objective 2 (RO2) addresses the second gap and proposes to use a hierarchy of models to understand relevant processes and feedbacks related to how modes of variability interact with each other. Research Objective 3 (RO3) is designed to study the third gap and proposes to examine the role of external forcings in changes of modes of Earth system variability and their interactions, and the likelihood and predictability of tipping points and irreversible changes. Research Objective 4 (RO4) will address the fourth gap and proposes to use high resolution ESMs, regionally refined models (RRMs), and ML methods to investigate the relationships between high impact events (e.g. flash droughts and precipitation extremes, atmospheric rivers (ARs), tropical cyclones (TCs), storm surge/sea level rise), the synoptic systems that produce them, and their changes related to modes of Earth system variability. The research will involve the use of the Community Earth System Model (CESM), Energy Exascale Earth System Model (E3SM), CMIP multi-model data sets, a hierarchy of simpler models, and numerous observational data sets. In the course of the proposed research, CATALYST will contribute to metrics and diagnostics that will be integrated in Coordinated Model Evaluation Capabilities (CMEC), particularly with regards to the Quasi-biennial Oscillation (QBO) and its interactions with the Madden-Julian Oscillation (MJO), high atmospheric pressure blocking, and new precipitation metrics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled‐Coil Patches and Patterns

Abstract DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence‐specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well‐defined micron‐scale structures through hierarchical self‐assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled‐coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher‐order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled‐coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA‐based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5‐10‐fold increase in bending stiffness. The results provide a foundation for stimulus‐responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.

59 BASIC BIOLOGICAL SCIENCES↗
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↗