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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Coupled SAM/Griffin Model of a Reference Fluoride-Salt-Cooled High-Temperature Reactor for Multi-Physics Simulations

A multi-physics coupled simulation model of a reference pebble bed fluoride-salt-cooled high-temperature reactor (PB-FHR) has been developed with SAM and Griffin computer codes for transient safety analysis. The reference problem of a prototypical reactor design serves as the foundation for the U.S. NRC (Nuclear Regulatory Commission) to verify the adequacy of computer codes and evaluation models for specific reactor types. In this work, the previously developed SAM model for PB-FHR primary loop has been updated for the coupled simulation. The updated SAM PB-FHR model includes a 2-D axial symmetric core region and external core components in 0-D/1-D. In addition to the primary loop, a detailed model of the RCCS (reactor cavity cooling system) is added. The 2-D and 1-D domains are tightly coupled using the single-solve approach developed in SAM. In the pebble bed region, the SAM multiscale explicit pebble model is applied to calculate the pebble and TRISO fuel kernel temperatures. The Griffin model used in this work is based on a model developed at Idaho National Laboratory in collaboration with the U.S. NRC. The Griffin neutronics model and SAM thermal hydraulics model is coupled with the Comprehensive Reactor Analysis Bundle (CRAB or alternately BlueCRAB) application. Both steady-state and transient scenarios are simulated to demonstrate the model's suitability for multi-physics simulations of PB-FHR transients.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

Procedure for the Computational Models created for the DOE/NRC Collaboration for Criticality Safety Support for Commercial-Scale HALEU Fuel Cycles Project (DNCSH)

This procedure outlines the application models developed as part of the US Department of Energy (DOE) and Nuclear Regulatory Commission (NRC) collaboration for criticality safety support for commercial scale HALEU fuel cycle and transportation (DNCSH) project, an effort authorized by the US Congress. The project is a joint effort among the DOE, NRC, numerous national laboratories, and private enterprises with project management from Oak Ridge National Laboratory.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Nuclear Materials Packaging, Transportation, and Systems Analysis Group Software Quality Assurance Plan: ANSYS Mechanical Finite Element Analysis Software Version 2023R1

ANSYS Inc. develops and markets engineering simulation software and services used in the aerospace, automotive, manufacturing, electronics, biomedical, energy, defense, and many other industries. ANSYS is dedicated to engineering simulation and is the world’s leading software provider. ANSYS was founded in 1970 and is headquartered in Canonsburg, Pennsylvania. ANSYS provides an engineering analysis tool combining structural, thermal, computational fluid dynamics, acoustic, and electromagnetic simulation capabilities. ANSYS has two main programs, which use the same solvers: (1) Mechanical APDL (ANSYS Design Parametric Language), a Fortran-based coding platform, and (2) ANSYS Workbench, which uses a graphical user interface to aid in finite element analysis implementation. This plan covers both APDL and Workbench. The ANSYS computer program is a large-scale, multipurpose finite element program that can be used to solve several classes of engineering analyses. The analysis capabilities of ANSYS include the ability to solve static and dynamic structural analyses, steady-state and transient heat transfer problems, mode-frequency and buckling eigenvalue problems, static or time-varying magnetic analyses, and various types of field and coupled-field applications. The program contains many special features that allow nonlinearities or secondary effects such as plasticity, large strain, hyperelasticity, creep, swelling, large deflections, contact, stress stiffening, temperature dependency, material anisotropy, and radiation to be included in the solution. As ANSYS has been developed, other special capabilities such as substructuring, submodeling, random vibration, kinetostatics, kinetodynamics, free convection fluid analysis, acoustics, magnetics, piezoelectrics, coupled-field analysis, and design optimization have been added to the program. These capabilities contribute further to making ANSYS a multipurpose analysis tool for varied engineering disciplines. The ANSYS program has been in commercial use for over 50 years and has been used extensively in the aerospace, automotive, construction, electronic, energy services, manufacturing, nuclear, plastics, oil, and steel industries. Additionally, many consulting firms and hundreds of universities have used ANSYS for analysis, research, and educational purposes. ANSYS is recognized worldwide as one of the most widely used and capable programs of its type. Ansys design analysis software is the first created within a quality system with ISO 9001 certification, the internationally accepted quality standard. Product development, testing, maintenance and support processes also meet the United States Nuclear Regulatory Commission's quality requirements, as they have for nearly four decades. The Quality Assurance Service Agreement is suitable for the customers working in the nuclear industry who need to meet specific federal regulations including 10CRF50 Appendix B and provisions of 10CFR21. ANSYS has retained its original International Organization for Standardization (ISO) 9001 accreditation certificate since1995-05-04, It’s current certificate is valid until 2027-05-29.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Data Center Cybersecurity, Supply Chain Risk Management, and Emerging Regulation Cohort Summary: Takeaways and Action Plans

This report summarizes the outcomes of the Data Center Cohort under the Department of Energy’s Technical Assistance for Digital Assurance (TADA) initiative, aimed at enhancing grid resilience through cybersecurity, supply chain risk management (SCRM), and Cyber-Informed Engineering (CIE). The cohort engaged 17 organizations across utilities, data center operators, vendors, and technology providers in three sessions combining presentations, discussions, and exercises. Key topics included AI-driven load behavior, cybersecurity vulnerabilities in UPS/BESS and cooling systems, governance gaps at utility–data center boundaries, and supply chain integrity. Five cross-cutting themes emerged: interconnection architecture vulnerabilities, fragmented governance, AI-driven stability risks, lack of regulatory frameworks, and long-term supply chain concerns. Actionable recommendations were developed, including implementing DMZ segmentation, formalizing vendor access agreements, designing AI workload limits, and advancing standards through NERC and state-level programs. These strategies aim to strengthen resilience, clarify responsibilities, and ensure secure integration of data centers into the grid.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS1996

Evaluating Fatigue in Operational Settings: The NASA Ames Fatigue Countermeasures Program

In response to a 1980 Congressional request, NASA Ames initiated a program to examine fatigue in flight operations. The Program objectives are to examine fatigue, sleep loss, and circadian disruption in flight operations, determine the effects of these factors on flight crew performance, and the development of fatigue countermeasures. The NASA Ames Fatigue Countermeasures Program conducts controlled laboratory experiments, full-mission flight simulations, and field studies. A range of subjective, behavioral, performance, physiological, and environmental measures are used depending on study objectives. The Program has developed substantial expertise in gathering data during actual flight operations and in other work settings. This has required the development of ambulatory and other measures that can be carried throughout the world and used at 41,000 feet in aircraft cockpits. The NASA Ames Fatigue Countermeasures Program has examined fatigue in shorthaul, longhaul, overnight cargo, and helicopter operations. A recent study of planned cockpit rest periods demonstrated the effectiveness of a brief inflight nap to improve pilot performance and alertness. This study involved inflight reaction time/vigilance performance testing and EEG/EOG measures of physiological alertness. The NASA Ames Fatigue Countermeasures Program has applied scientific findings to the development of education and training materials on fatigue countermeasures, input to federal regulatory activities on pilot flight, duty, and rest requirements, and support of National Transportation Safety Board accident investigations. Current activities are examining fatigue in nonaugmented longhaul flights, regional/commuter flight operations, corporate/business aviation, and psychophysiological variables related to performance.

Rosekind, Mark R.↗
NASA NTRS2007

Pharmacovigilance in Space: Stability Payload Compliance Procedures

Pharmacovigilance is the science of, and activities relating to the detection, assessment, understanding, and prevention of drug-related problems. Over the lase decade, pharmacovigilance activities have contributed to the development of numerous technological and conventional advances focused on medication safety and regulatory intervention. The topics discussed include: 1) Proactive Pharmacovigilance; 2) A New Frontier; 3) Research Activities; 4) Project Purpose; 5) Methods; 6) Flight Stability Kit Components; 7) Experimental Conditions; 8) Research Project Logistics; 9) Research Plan; 10) Pharmaceutical Stability Research Project Pharmacovigilance Aspects; 11) Security / Control; 12) Packaging/Containment Actions; 13) Shelf-Life Assessments; 14) Stability Assessment Parameters; 15) Chemical Content Analysis; 16) Preliminary Results; 17) Temperature/Humidity; 18) Changes in PHysical and Chemical Assessment Parameters; 19) Observations; and 20) Conclusions.

Daniels, Vernie R.↗
NASA NTRS2015

Nuclear Thermal Propulsion Development Risks

There are clear advantages of development of a Nuclear Thermal Propulsion (NTP) for a crewed mission to Mars. NTP for in-space propulsion enables more ambitious space missions by providing high thrust at high specific impulse ((is) approximately 900 sec) that is 2 times the best theoretical performance possible for chemical rockets. Missions can be optimized for maximum payload capability to take more payload with reduced total mass to orbit; saving cost on reduction of the number of launch vehicles needed. Or missions can be optimized to minimize trip time significantly to reduce the deep space radiation exposure to the crew. NTR propulsion technology is a game changer for space exploration to Mars and beyond. However, 'NUCLEAR' is a word that is feared and vilified by some groups and the hostility towards development of any nuclear systems can meet great opposition by the public as well as from national leaders and people in authority. The public often associates the 'nuclear' word with weapons of mass destruction. The development NTP is at risk due to unwarranted public fears and clear honest communication of nuclear safety will be critical to the success of the development of the NTP technology. Reducing cost to NTP development is critical to its acceptance and funding. In the past, highly inflated cost estimates of a full-scale development nuclear engine due to Category I nuclear security requirements and costly regulatory requirements have put the NTP technology as a low priority. Innovative approaches utilizing low enriched uranium (LEU). Even though NTP can be a small source of radiation to the crew, NTP can facilitate significant reduction of crew exposure to solar and cosmic radiation by reducing trip times by 3-4 months. Current Human Mars Mission (HMM) trajectories with conventional propulsion systems and fuel-efficient transfer orbits exceed astronaut radiation exposure limits. Utilizing extra propellant from one additional SLS launch and available energy in the NTP fuel, HMM radiation exposure can be reduced significantly.

Kim, Tony↗
DOE OSTI2023

Biofuel Air Emissions Analysis

U.S. has goals to produce 3 billion gallons of sustainable aviation fuel (SAF) annually by 2030, increasing to 35 billion gallons by 2050 to decarbonize the aviation sector. Meeting these production targets will require large number of biorefineries to be set up. However, ability to comply with federal air quality standards is prerequisite to being issued a construction permit. Negotiating the permitting process for a new biorefinery can be quite onerous and cost the investors significant time and money. Although there can be numerous reasons for delayed biorefinery construction, air permitting is fraught with pitfalls because the permitting process relies on precedence, which the future SAF biorefineries lack. NREL's Biofuel Air Emissions Analysis project is unique and innovative in terms of the tools, approaches, and analyses provided. NREL is the only national laboratory that is actively working at the intersection of Federal air quality regulations, emissions and air quality analysis across the supply chain, and process design. This project is focused on providing much needed data and analyses that address biorefinery air permitting. This project develops models and quantitative analyses and measures progress towards meeting air quality regulatory requirements. These models and methods are applied to analyze air permitting related to wastewater sludge to biofuel conversion pathways using hydrothermal liquefaction (HTL), impacts of HTL pathway on local and regional air quality including an assessment of health and equity impacts. In addition to filling research gaps, this project also disseminates the findings to the relevant stakeholders at BETO, other national labs, and regulatory agencies.

air quality↗
DOE OSTI2025

Considerations for Thermal Annealing of Zr-Alloy Cladding During Dry Storage

In January 2025, the U.S. Department of Energy (DOE) sponsored a technical workshop with fuel vendors that provided a forum for increased collaboration on backend fuel cycle research. The workshop reviewed observations of thermal annealing of irradiated zirconium alloys in simulated dry storage conditions and discussed implications to the industry’s interest in reducing wet storage to optimize operational flexibility and the expected trend of increasing discharge burnup (and decay heats), which could lead to an increase in dry storage temperatures. One approach to accommodate increased decay heats in dry storage is to increase the regulatory temperature limit during dry storage, which is now 400°C. However, this could lead to thermal annealing of the cladding, which will tend to increase creep rates, creep strains, and ductility while decreasing yield strength. These considerations are compounded by bonding between the pellet and cladding at high burnup, which results in the pellet carrying more load during fuel rod deformations, especially in bending, which is the dominant deformation phenomenon in canister drop analyses. Because the U.S. Nuclear Regulatory Commission (NRC) recommends yield strength as a primary failure criterion for accident analyses in storage and transportation, particularly for canister drop scenarios, the purpose of the workshop was to develop options for alternative failure criterion that could replace yield strength in canister drop analyses. Topics discussed were (1) the regulatory framework, (2) the effect of thermal annealing on microhardness and tensile properties of cladding materials, (3) the effect of thermal annealing on fuel rod failure during bending, bending fatigue, and pinch loading, and (4) an alternative failure criterion for canister drop analyses. This paper provides a summary of the key discussions and outcomes of the workshop

Cantonwine, Paul [ORNL] (ORCID:0009000522247033)↗
DOE OSTI2024

Advancements in Multiphysics Microdepletion Analysis of an eVinci TM -like Microreactor Leveraging OpenMC-CRAB Workflow

Nuclear microreactors (MRs) are a class of nuclear reactor technology, characterized by reduced dimensions, modular design, and reduced power output in contrast to conventional Light Water Reactors (LWRs). MRs are proposed for supplying electricity and eventual process heat to remote locations, such as military installations and disaster-affected areas. Current research work sponsored by the US Department of Energy Microreactor Program (MRP) is devoted to the development of novel modeling and simulation tools to better support MR vendors and regulatory bodies. Notably, the NRC is projected to utilize the CRAB multiphysics software driver for executing both design and beyond-design-basis accident analyses. Furthermore, the NRC has been utilizing the MELCOR code to calculate mechanistic source terms during accidents. Since MELCOR relies on isotopic inventory and reactor temperature/power profiles under accident conditions, which theoretically can be derived from CRAB, the goal is to establish a comprehensive CRAB-MELCOR computational framework. Past work was focused on testing and demonstrating CRAB's capability to generate results that can be used to inform mechanistic source term calculations in MELCOR. In particular, a computational workflow leveraging OpenMC-generated microscopic cross sections and CRAB was first applied to perform multiphysics microscopic depletion calculation followed by an accident scenario for a stylized microreactor problem. In fiscal year 2024, the research work has been focused on applying the OpenMC-CRAB workflow, which was first tested in fiscal year 2023, to a realistic 3D heat-pipe cooled MR problem representative of the eVinci TM design. The latter computational problem was developed with inputs from WEC to conserve selected neutronic and thermal characteristics of the eVinci TM design without releasing proprietary data. The results of this simulation, encompassing isotopic inventory, power density distribution, and kinetic parameters, will inform both MELCOR and the WEC-developed FATE code for mechanistic source terms calculations. The results from the two codes will then be compared for code verification purposes. This report contains the design characteristics of the realist heat pipe cooled microreactor developed as a use-case for the verification exercise, and the current results for the multiphysics microscopic depletion performed with the OpenMC-CRAB workflow. The results include eigenvalue as a function of time, power distribution at EOL, in addition to nuclides inventory's time evolution and spatial distribution. Finally, we report improvements to the workflow efficiency achieved through a collaboration with the NEAMS programs. Through this collaborative effort, we were able to strongly decrease the computational time for the multiphysics microdepletion calculation (i.e., from 17.4 hours to 5.7 hours on 280 processors) in addition to simplifying the interface to generate isotopics spatial distribution utilizable by FATE and MELCOR. Future work, including the improvement of the current microscopic cross-sections' library and the simulation of an accident scenario at EOL, is also discussed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1996

A mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis

The phytohormone auxin controls processes such as cell elongation, root hair development and root branching. Tropisms, growth curvatures triggered by gravity, light and touch, are also auxin-mediated responses. Auxin is synthesized in the shoot apex and transported through the stem, but the molecular mechanism of auxin transport is not well understood. Naphthylphthalamic acid (NPA) and other inhibitors of auxin transport block tropic curvature responses and inhibit root and shoot elongation. We have isolated a novel Arabidopsis thaliana mutant designated roots curl in NPA (rcn1). Mutant seedlings exhibit altered responses to NPA in root curling and hypocotyl elongation. Auxin efflux in mutant seedlings displays increased sensitivity to NPA. The rcn1 mutation was transferred-DNA (T-DNA) tagged and sequences flanking the T-DNA insert were cloned. Analysis of the RCN1 cDNA reveals that the T-DNA insertion disrupts a gene for the regulatory A subunit of protein phosphatase 2A (PP2A-A). The RCN1 gene rescues the rcn1 mutant phenotype and also complements the temperature-sensitive phenotype of the Saccharomyces cerevisiae PP2A-A mutation, tpd3-1. These data implicate protein phosphatase 2A in the regulation of auxin transport in Arabidopsis.

Non-NASA Center↗
DOE OSTI2021

Planning Near-Term Tasks for the Development of Advanced Reactor Mechanistic Source Term Modeling and Simulation Tools

To assist both the advanced reactor industry and U.S. Nuclear Regulatory Commission (NRC) in the pursuit of reactor design and licensing, the U.S. Department of Energy (DOE) Nuclear Energy Advanced Modeling and Simulation (NEAMS) program has established a mechanistic source term (MST) research project under the auspices of the Application Drivers technical area. The MST research project is a collaboration between Argonne National Laboratory (Argonne) and Sandia National Laboratories (SNL) with a high-level objective to coordinate the development of comprehensive advanced reactor MST mod/sim capabilities to support risk-informed design and licensing decisions. As part of this effort, an MST mod/sim development pathway was developed in FY21, which outlines the high-level objectives and near-term tasks necessary to achieve the project objectives. Since publication of the development pathway, Argonne and SNL have been addressing the “near-term tasks” outlined in the report. The current provides a status update of the progress achieved in the fourth quarter of FY21. The report structure follows that of ref and is divided by advanced reactor type: High temperature gas reactor (HTGR), molten salt reactor (MSR) including fluoride salt-cooled high temperature reactor (FHR), and sodium fast reactor (SFR). Each section reviews the near-term tasks associated with the reactor type, current progress, and future plans. The near-term tasks associated with consequence modeling are reviewed in an upcoming work by SNL.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Characterization factors and other air quality impact metrics: Case study for PM 2.5 -emitting area sources from biofuel feedstock supply

In this paper, we develop a framework and metrics for estimating the impact of emission sources on regulatory compliance and human health for applications in air quality planning and life cycle impact assessment (LCIA). Our framework is based on a pollutant's characterization factor (CF) and three new metrics: Available Regulatory Capacity for Incremental Emissions (ARCIE), Source CF Ratio, and Activity Health Impact (AHI) Ratio. ARCIE can be used to assess whether a receptor location has capacity to accommodate additional source emissions while complying with regulatory limits. We present CF as a midpoint indicator of health impacts per unit mass of emitted pollutant. Source CF Ratio enables comparison of potential new-source locations based on human health impacts. The AHI Ratio estimates the health impacts of a pollutant in relation to the utilization of the source for each unit of product or service. These metrics can be applied to any pollutant, energy source sector (e.g., agriculture, electricity), source type (point, line, area), and spatial modeling domain (nation, state, city, region). We demonstrate these metrics through a case study of fine particulate (PM 2.5 ) emissions from U.S. corn stover harvesting and local processing at various scales, representing steps in the biofuel production process. We model PM 2.5 formation in the atmosphere using a novel reduced-complexity chemical transport model called the Intervention Model for Air Pollution (InMAP). Through this case study, we present the first area-source PM 2.5 CFs that address the recommendations of several LCIA studies to establish spatially explicit CFs specific to an energy source sector or type. Overall, the framework developed in this work provides multiple new ways to consider the potential impacts of air emissions through spatially differentiated metrics.

09 BIOMASS FUELS↗
DOE OSTI2025

The Monolithic Heat Pipe Microreactor Reference Plant Model Updates

This work presents the latest improvements to, and investigations performed with, the generic monolithic heat-pipe-cooled microreactor reference plant model for the United States Nuclear Regulatory Commission. This model serves as the foundation for the future detailed design evaluation models based on license applications. This model has been developed with the Comprehensive Reactor Analysis Bundle (BlueCRAB) and its specifications are based on open literature publications for the eVinci™ design . BlueCRAB is the U.S. Nuclear Regulatory Commission non-light-water reactor analysis system based on MOOSE, the Multiphysics Object-Oriented Simulation Environment framework, which can couple the Griffin, BISON, and Sockeye applications to resolve the various physics that are essential for the safety analysis of this type of reactor system. The core specifications include tristructural isotropic fuel, graphite monolith, graphite reflectors, and drums composed of graphite and B 4 C.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data

Single-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands of individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed to address this problem. Here, we present an expanded benchmarking study of eleven recent network inference methods on seven published scRNA-seq datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that, while most methods have a modest recovery of experimentally derived interactions based on global metrics such as Area Under the Precision Recall curve, methods are able to capture targets of regulators that are relevant to the system under study. Among the top performing methods that use only expression were SCENIC, PIDC, MERLIN or Correlation. Addition of prior biological knowledge and the estimation of transcription factor activities resulted in the best overall performance with the Inferelator and MERLIN methods that use prior knowledge outperforming methods that use expression alone. We found that imputation for network inference did not improve network inference accuracy and could be detrimental. Comparisons of inferred networks for comparable bulk conditions showed that the networks inferred from scRNA-seq datasets are often better or at par with the networks inferred from bulk datasets. Our analysis should be beneficial in selecting methods for network inference. At the same time, this highlights the need for improved methods and better gold standards for regulatory network inference from scRNAseq datasets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Regulatory Treatment of Low Frequency External Events under a Risk-Informed Performance-Based Licensing Pathway

Significant efforts are underway to develop and implement a risk-informed performance-based licensing framework for advanced reactors built on the establishment of an affirmative safety case. Such approaches offer the benefits of increased flexibility regarding key design and licensing decisions based on a detailed assessment and understanding of plant risk. These methods include the comprehensive analysis of scenarios that have historically been addressed through conservative and deterministic licensing analysis approaches, such as the evaluation of event sequences at frequencies of occurrence beyond the design basis. While the detailed analysis of low frequency events provides insights that can help justify alternative treatments to past conservatism, the findings are dependent on the quality and confidence associated with the analyses. The assessment of external hazards presents a unique challenge, as their potential frequency of occurrence, especially of large magnitude events, is inherently uncertain given the long return periods in question. The current project seeks to further explore the regulatory treatment of low frequency external events as part of a risk-informed performance-based framework. The goals are to identify the benefits and challenges of such approaches for advanced reactor vendors and to aid in the development of consistent and appropriate methodologies. As part of this effort, the current report summarizes initial project findings, with a focus on the evaluation of the seismic hazard. This includes an exploration of the implementation of a risk-informed performance-based approach through an example analysis. Based on the identified challenges associated with the probabilistic treatment of low frequency event sequences, additional performance-based methods were explored as complementary tools for demonstrating regulatory compliance. The report highlights key challenges and opportunities associated with the methods and outlines recommendations and future activities to assist with their implementation.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

59 BASIC BIOLOGICAL SCIENCES↗