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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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NASA NTRS2008

Overview of the NASA Subsonic Rotary Wing Aeronautics Research Program in Rotorcraft Crashworthiness

This paper provides an overview of rotorcraft crashworthiness research being conducted at NASA Langley Research Center under sponsorship of the Subsonic Rotary Wing (SRW) Aeronautics Program. The research is focused in two areas: development of an externally deployable energy attenuating concept and improved prediction of rotorcraft crashworthiness. The deployable energy absorber (DEA) is a composite honeycomb structure, with a unique flexible hinge design that allows the honeycomb to be packaged and remain flat until needed for deployment. The capabilities of the DEA have been demonstrated through component crush tests and vertical drop tests of a retrofitted fuselage section onto different surfaces or terrain. The research on improved prediction of rotorcraft crashworthiness is focused in several areas including simulating occupant responses and injury risk assessment, predicting multi-terrain impact, and utilizing probabilistic analysis methods. A final task is to perform a system-integrated simulation of a full-scale helicopter crash test onto a rigid surface. A brief description of each research task is provided along with a summary of recent accomplishments.

Jackson, Karen E.↗

NASA NTRS2009

Overview of the NASA Subsonic Rotary Wing Aeronautics Research Program in Rotorcraft Crashworthiness

Jackson, Karen E.↗

NASA NTRS2010

Tropospheric Airborne Meteorological Data Reporting (TAMDAR) Sensor Validation and Verification on National Oceanographic and Atmospheric Administration (NOAA) Lockheed WP-3D Aircraft

As part of the National Aeronautics and Space Administration's Aviation Safety and Security Program, the Tropospheric Airborne Meteorological Data Reporting project (TAMDAR) developed a low-cost sensor for aircraft flying in the lower troposphere. This activity was a joint effort with support from Federal Aviation Administration, National Oceanic and Atmospheric Administration, and industry. This paper reports the TAMDAR sensor performance validation and verification, as flown on board NOAA Lockheed WP-3D aircraft. These flight tests were conducted to assess the performance of the TAMDAR sensor for measurements of temperature, relative humidity, and wind parameters. The ultimate goal was to develop a small low-cost sensor, collect useful meteorological data, downlink the data in near real time, and use the data to improve weather forecasts. The envisioned system will initially be used on regional and package carrier aircraft. The ultimate users of the data are National Centers for Environmental Prediction forecast modelers. Other users include air traffic controllers, flight service stations, and airline weather centers. NASA worked with an industry partner to develop the sensor. Prototype sensors were subjected to numerous tests in ground and flight facilities. As a result of these earlier tests, many design improvements were made to the sensor. The results of tests on a final version of the sensor are the subject of this report. The sensor is capable of measuring temperature, relative humidity, pressure, and icing. It can compute pressure altitude, indicated air speed, true air speed, ice presence, wind speed and direction, and eddy dissipation rate. Summary results from the flight test are presented along with corroborative data from aircraft instruments.

Tsoucalas, George↗

DOE OSTI2024

Large eddy simulation of a pressurized reactive fluid–particle system: single-particle dynamics analysis

Pressurized oxy-combustion (POC) is a promising candidate to reduce carbon emissions in power generation. Designing an effective burner plays a vital role in developing new combustion technologies. Because of the high pressure, the volume fraction of particles in a pressurized oxy-combustor could be higher than that in the conventional combustor, therefore, the particle dynamics in the pressurized vessel need to be evaluated accordingly. The present computational work is to predict the influence of the particle size and particle injection location on the particle trajectory. The Stokes number based on turbulence fluctuation, St, is adopted to evaluate the impact of the gas phase on the particulate phase. A large eddy simulation (LES) with the environment pressure of 15 bar and the thermal input of the fuel particle of 100 kWth has been performed by means of the commercial CFD package. It is shown that that in this pressurized environment St << 1 for the 25 µm particles, St ~ 1 for the 100 µm particles, while for the particles exceeding 200 µm St >> 1. The trajectories of the sampling particles from the LES results support this conclusion: the particles less than 100 µm tend to be uniformly distributed in the space while the particles exceeding 200 µm tend to concentrate in the combustor.

Li, Lei↗

NASA NTRSDate not supplied

Solar Cruiser TRAC Boom Development

The TRAC boom studied is a 30 meter, high-aspect ratio and highly nonlinear structural element planned for the NASA Solar Cruiser spacecraft where it would serve as the solar sail’s skeletal system designed to deploy the packaged reflective sail membrane as well as support operational sail tension loads for flight. Key design drivers for this boom are understanding and characterizing load-deformation behavior and quantifying buckling performance–under flight conditions (zero gravity). Knowing that the full-scale solar sail system cannot be feasibly tested for flight conditions under Earth’s gravity, a building block approach is methodically followed to verify finite element analysis (FEA) predictions and to evolve the finite element model (FEM) accordingly, beginning with the lowest level complexity to match global elastic behavior to the highest level complexity to bound theoretical responses under conservative expected flight conditions. Although the testing campaign for the TRAC boom has not developed yet to produce a full-scale test data point that loads the boom to failure, the fidelity of simulations have evolved with success and warrant further interest and work on this high-aspect ratio, but highly stable, deployable structural boom.

Lee Nguyen↗

DOE OSTI2015

Measurements and non-local thermodynamic equilibrium modeling of mid-Z plasma emission

The x-ray yields from laser-irradiated thin foils of iron, copper, zinc, and germanium have been measured in the soft and multi-keV x-ray ranges at the OMEGA laser at the Laboratory for Laser Energetics. The incident laser power had a pre-pulse to enhance the x-ray emission of a 1 ns flat-top main pulse. The experimental results have been compared with post-shot simulations performed with the two-dimensional radiation-hydrodynamics code FCI2. A new non-local thermodynamic equilibrium model, NOO-RAD, have been incorporated into FCI2. In this approach, the plasma ionization state is in-line calculated by the atomic physics NOHEL package. In the soft x-ray bands, both simulations using RADIOM [M. Busquet, Phys. Fluids B 5, 4191 (1993)] and NOO-RAD clearly over-predict the powers and energies measured by a broad-band spectrometer. In one case (the iron foil), the discrepancy between the measured and simulated x-ray output is nevertheless significantly reduced when NOO-RAD is used in the simulations. In the multi-keV x-ray bands, the simulations display a strong sensitivity to the coupling between the electron thermal conductivity and the NLTE models, and for some particular combinations of these, provide a close match to the measured emission. The comparison between the measured and simulated H-like to He-like line-intensity ratios deduced from high-resolution spectra indicates higher experimental electron temperatures were achieved, compared to the simulated ones. Measurements of the plasma conditions have been achieved using the Thomson-scattering diagnostic. The electron temperatures are found to range from 3 to 5 keV at the end of the laser pulse and are greater than predicted by the simulations. The measured flow velocities are in reasonable agreement with the calculated ones. This last finding gives us confidence in our numerical predictions for the plasma parameters, which are over that time mainly determined by hydrodynamics, such as the mass densities and the ion temperatures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Classroom aerosol dispersion modeling: experimental assessment of a low-cost flow simulation tool

The purpose of this study was to assess the utility of a low-cost flow simulation tool for an indoor air modeling application by comparing its outputs with the results of a physical experiment, as well as those from a more advanced computational fluid dynamics (CFD) software package. In this study, five aerosol dispersion tests were performed in two different classrooms by releasing a CO 2 tracer gas from six student locations. Resultant steady-state concentrations were monitored at 13 locations around the periphery of the room. Subsequently, the experiments were modeled using both a low-cost tool (SolidWorks Flow Simulation) and a more sophisticated tool (STAR-CCM+). Models were evaluated based on their ability to predict the experimentally measured concentrations at the 13 monitoring locations by calculating four performance parameters commonly used in the evaluation of dispersion models: fractional mean bias (FB), normalized mean-square error (NMSE), fraction of predicted value within a factor of two (FAC2), and normalized absolute difference (NAD). The more sophisticated model performed better in 15 of the 20 possible cases (five tests at four parameters each), with parameters meeting acceptance criteria in 19 of 20 cases. However, the lower-cost tool was only slightly worse, with parameters meeting acceptance criteria in 18 of 20 cases, and it performed better than the other tool in 3 of 20 cases. Because it provides useful results at a fraction of the monetary and training cost and is already widely accessible to many institutions, such a tool may be worthwhile for many indoor aerosol dispersion applications, especially for students or researchers just beginning CFD modeling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Rapid sampling of stochastic displacements in Brownian dynamics simulations

Here, we present a new method for sampling stochastic displacements in Brownian Dynamics (BD) simulations of colloidal scale particles. The method relies on a new formulation for Ewald summation of the Rotne-Prager-Yamakawa (RPY) tensor, which guarantees that the real-space and wave-space contributions to the tensor are independently symmetric and positive-definite for all possible particle configurations. Brownian displacements are drawn from a superposition of two independent samples: a wave-space (far-field or long-ranged) contribution, computed using techniques from fluctuating hydrodynamics and non-uniform fast Fourier transforms; and a real-space (near-field or short-ranged) correction, computed using a Krylov subspace method. The combined computational complexity of drawing these two independent samples scales linearly with the number of particles. The proposed method circumvents the super-linear scaling exhibited by all known iterative sampling methods applied directly to the RPY tensor that results from the power law growth of the condition number of tensor with the number of particles. For geometrically dense microstructures (fractal dimension equal three), the performance is independent of volume fraction, while for tenuous microstructures (fractal dimension less than three), such as gels and polymer solutions, the performance improves with decreasing volume fraction. This is in stark contrast with other related linear-scaling methods such as the force coupling method and the fluctuating immersed boundary method, for which performance degrades with decreasing volume fraction. Calculations for hard sphere dispersions and colloidal gels are illustrated and used to explore the role of microstructure on performance of the algorithm. In practice, the logarithmic part of the predicted scaling is not observed and the algorithm scales linearly for up to 4×10 6 particles, obtaining speed ups of over an order of magnitude over existing iterative methods, and making the cost of computing Brownian displacements comparable to the cost of computing deterministic displacements in BD simulations. Finally, a high-performance implementation employing non-uniform fast Fourier transforms implemented on graphics processing units and integrated with the software package HOOMD-blue is used for benchmarking.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Modeling of particle transport, neutrals and radiation in magnetically-confined plasmas with Aurora

In this work, we present Aurora, an open-source package for particle transport, neutrals and radiation modeling in magnetic confinement fusion plasmas. Aurora's modern multi-language interface enables simulations of 1.5D impurity transport within high-performance computing frameworks, particularly for the inference of particle transport coefficients. A user-friendly Python library allows simple interaction with atomic rates from the Atomic Data and Atomic Structure database as well as other sources. This enables a range of radiation predictions, both for power balance and spectroscopic analysis. We discuss here the superstaging approximation for complex ions, as a way to group charge states and reduce computational cost, demonstrating its wide applicability within the Aurora forward model and beyond. Aurora also facilitates neutral particle analysis, both from experimental spectroscopic data and other simulation codes. Leveraging Aurora's capabilities to interface SOLPS-ITER results, we demonstrate that charge exchange is unlikely to affect the total radiated power from the ITER core during high performance operation. Finally, we describe the ImpRad module in the one modeling framework for integrated task framework, developed to enable experimental analysis and transport inferences on multiple devices using Aurora.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

Application of an Online-Coupled Regional Climate Model, WRF-CAM5, over East Asia for Examination of Ice Nucleation Schemes: Part I. Comprehensive Model Evaluation and Trend Analysis for 2006 and 2011

Online-coupled climate and chemistry models are necessary to realistically represent the interactions between climate variables and chemical species and accurately simulate aerosol direct and indirect effects on cloud, precipitation, and radiation. In this Part I of a two-part paper, simulations from the Weather Research and Forecasting model coupled with the physics package of Community Atmosphere Model (WRF-CAM5) are conducted with the default heterogeneous ice nucleation parameterization over East Asia for two full years: 2006 and 2011. A comprehensive model evaluation is performed using satellite and surface observations. The model shows an overall acceptable performance for major meteorological variables at the surface and in the boundary layer, as well as column variables (e.g., precipitation, cloud fraction, precipitating water vapor, downward longwave and shortwave radiation). Moderate to large biases exist for cloud condensation nuclei over oceanic areas, cloud variables (e.g., cloud droplet number concentration, cloud liquid and ice water paths, cloud optical depth, longwave and shortwave cloud forcing). These biases indicate a need to improve the model treatments for cloud processes, especially cloud droplets and ice nucleation, as well as to reduce uncertainty in the satellite retrievals. The model simulates well the column abundances of chemical species except for column SO 2 but relatively poor for surface concentrations of several species such as CO, NO 2 , SO 2 , PM2.5, and PM10. Several reasons could contribute to the underestimation of major chemical species in East Asia including underestimations of anthropogenic emissions and natural dust emissions, uncertainties in the spatial and vertical distributions of the anthropogenic emissions, as well as biases in meteorological, radiative, and cloud predictions. Despite moderate to large biases in the chemical predictions, the model performance is generally consistent with or even better than that reported for East Asia with only a few exceptions. The model generally reproduces the observed seasonal variations and the difference between 2006 and 2011 for most variables or chemical species. Overall, these results demonstrate promising skills of WRF-CAM5 for long-term simulations at a regional scale and suggest several areas of potential improvements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Design of a Compact Dry Cooler With an Aluminum Heat Exchanger Core for a Supercritical CO2 Power Cycle Is Evaluated for a Concentrating Solar Power Application

Abstract As the supercritical CO2 power cycle develops and the component technologies mature, there is still a need to reduce the associated capital and operating costs to maintain a competitive levelized cost of electricity (LCOE) in order to enter the market. When considering concentrating solar power (CSP) coupled with an sCO2 power block and sensible thermal storage, the technology presents a clean source for utility-scale power generation to support baseload or peak-load electrical demand. However, the LCOE of the technology is still considered higher than the competing technologies and should be reduced to better compete in the market; 2030 targets for dispatchable solar plants are 5¢/kWh for baseload CSP and 10¢/kWh for peaker plants, as set by the United States Department of Energy. In response to this need, this study is targeting improvements in the power cycle precooler to reduce power block contribution to LCOE. This study considers a dry cooler, as CSP plants are sensitive to water consumption because many installations are slated for remote or arid locations where solar irradiance is very high, but water is scarce. Furthermore, the power block footprint for an sCO2 system is quite compact, especially as compared to a steam cycle. Therefore, there is interest in installing a more compact dry cooler that is proportional to the reduced footprint sCO2 power block, while conventional dry coolers are an order of magnitude larger. The competing goals of size, performance, and cost were considered in this study to develop a compact dry cooler that can easily be packaged with the power block, significantly reducing the installation and transport cost compared to the current state of the art, while maintaining or improving upon the heat transfer performance and impact on plant LCOE. This paper details the high-level findings of a large dry cooler sensitivity study for design point selection, design of the compact dry cooler, expected year-round performance for the dry cooler and the power cycle, and the predicted LCOE for a 30-year plant life. It was found that an aluminum heat exchanger core can be suitably designed to meet the pressure and temperature requirements for a precooler in an sCO2 recompression Brayton cycle. The dry cooler assembly was found to have improved heat transfer performance, allowing for increased cycle efficiencies and a reduced plant LCOE. When coupled with a centrifugal blower and compact transition duct, the dry cooler assembly was able to reduce the installation footprint by over 50%.

14 SOLAR ENERGY↗

DOE OSTI2021

pnnl/DPVPROT

Distributed photovoltaics protection software toolkit The code package includes several important functions for design and analysis of new grid protection schemes, for scenarios of distributed photovoltaic (DPV) generation approaching 100% of the peak feeder load, i.e., high-penetration DPV. Convert distribution feeder models, used by planning engineers, to electromagnetic transient (EMT) models that produce waveforms for advanced relay algorithms. Visualize the results of protection scheme operation. Tools to determine distance relay settings on distribution systems. Tools to predict the performance of time-domain, incremental distance relay algorithms

McDermott, Tom↗

DOE OSTI2023

Leaf Nitrogen, Leaf Mass Area, Leaf Water Content, Seward Peninsula, Alaska, 2017

Nitrogen and carbon content, leaf mass per area and leaf water content of leaves sampled from the NGEE Arctic Teller study site, Seward Peninsula, Alaska in 2017. Data is included for 13 species from the deciduous shrub, forb and graminoid plant functional types. See related dataset for leaf reflective spectra, sample photographs and dGPS locations. This data package includes leaf sample information and trait data (*.csv). Note that leaf nitrogen content analysis was performed on a subset of samples. Metadata files include data descriptions (_dd.csv) for tabular data and a key to species symbols used in data files. All included files are listed and described in NGA103_flmd.csv. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2015

Digital Astronaut Project Biomechanical Models: Biomechanical Modeling of Squat, Single-Leg Squat and Heel Raise Exercises on the Hybrid Ultimate Lifting Kit (HULK)

The NASA Digital Astronaut Project (DAP) implements well-vetted computational models to predict and assess spaceflight health and performance risks, and to enhance countermeasure development. The DAP Musculoskeletal Modeling effort is developing computational models to inform exercise countermeasure development and to predict physical performance capabilities after a length of time in space. For example, integrated exercise device-biomechanical models can determine localized loading, which will be used as input to muscle and bone adaptation models to estimate the effectiveness of the exercise countermeasure. In addition, simulations of mission tasks can be used to estimate the astronaut's ability to perform the task after exposure to microgravity and after using various exercise countermeasures. The software package OpenSim (Stanford University, Palo Alto, CA) (Ref. 1) is being used to create the DAP biomechanical models and its built-in muscle model is the starting point for the DAP muscle model. During Exploration missions, such as those to asteroids and Mars, astronauts will be exposed to reduced gravity for extended periods. Therefore, the crew must have access to exercise countermeasures that can maintain their musculoskeletal and aerobic health. Exploration vehicles may have very limited volume and power available to accommodate such capabilities, even more so than the International Space Station (ISS). The exercise devices flown on Exploration missions must be designed to provide sufficient load during the performance of various resistance and aerobic/anaerobic exercises while meeting potential additional requirements of limited mass, volume and power. Given that it is not practical to manufacture and test (ground, analog and/or flight) all candidate devices, nor is it always possible to obtain data such as localized muscle and bone loading empirically, computational modeling can estimate the localized loading during various exercise modalities performed on a given device to help formulate exercise prescriptions and other operational considerations. With this in mind, NASA's Digital Astronaut Project (DAP) is supporting the Advanced Exercise Concepts (AEC) Project, Exercise Physiology and Countermeasures (ExPC) laboratory and NSBRI-funded researchers by developing and implementing well-validated computational models of exercises with advanced exercise device concepts. This report focuses specifically on lower-body resistance exercises performed with the Hybrid Ultimate Lifting Kit (HULK) device as a deliverable to the AEC Project.

health↗

DOE OSTI2021

Analysis of ZPPR-15 experimental data for VTR software validation

As part of the Versatile Test Reactor (VTR) program, extensive validation work is being performed to demonstrate the fidelity of the Argonne Reactor Code (ARC) software package presently used for the core design studies. It is anticipated that this software will be also used for initial operations although additional software may be introduced at a later time to supplement or replace some components. The validation work was focused on accumulating reactor models that are consistent with the VTR and thus can be used to validate the accuracy of predictions made by the software used to design and operate the VTR. The U.S. does not have any active experimental facilities that can neutronically mockup the VTR core design. However, in the past, the U.S. had extensive experimental facilities for fast reactor neutronics. In that regard, the ZPPR-15 experiments carried out at ANL during the 1980s work best because the fuel form is closest to the VTR design, there is a considerable amount of processed data available for use, and existing staff are already familiar with the experimental machine and measurements. Because of previous collaborative work, many of the ZPPR-15 loadings of interest have already been processed into MCNP and preliminary ARC models, and a full uncertainty quantification has already been completed for many of the ZPPR-15 measurements. This manuscript covers the recent analysis work on the ZPPR-15 experiments and compares it with the experimental results. With respect to the ARC software components, this manuscript focuses on validation of the MC 2 , DIF3D and GAMSOR using the ZPPR-15 experimental data.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

Exploring the role of electronic structure on photo-catalytic behavior of carbon-nitride polymorphs

A fully self-consistent density-functional theory (DFT) with improved functionals is used herein to provide a comprehensive account of structural, electronic, and optical properties of C 3 N 4 polymorphs. Using our recently developed van Leeuwen-Baerends (vLB) corrected local-density approximation (LDA), we implemented LDA + vLB within full-potential N th -order muffin-tin orbital (FP-NMTO) method and show that it improves structural properties and band gaps compared to semi-local functionals (LDA/GGA). We demonstrate that the LDA + vLB predicts band-structure and work-function for well-studied 2D-graphene and bulk-Si in very good agreement with experiments, and more exact hybrid functional (HSE) calculations as implemented in the Quantum-Espresso (QE) package. The structural and electronic-structure (band gap) properties of C 3 N 4 polymorphs calculated using FP-NMTO-LDA + vLB is compared with more sophisticated hybrid-functional calculations. We also perform detailed investigation of photocatalytic behavior using QE-HSE method of C 3 N 4 polymorphs through work-function, band (valence and conduction) position with respect to water reduction and oxidation potential. Our results show $γ$-C 3 N 4 as the best candidate for photocatalysis among all the C 3 N 4 polymorphs but it is dynamically unstable at ‘zero’ pressure. We show that $γ$-C 3 N 4 can be stabilized under hydrostatic-pressure, which improves its photocatalytic behavior relative to water reduction and oxidation potentials.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Bounding the Chemistry Conditions in the HM Solvent Extraction Process Criticality Safety Analyses

An approach new to the H-Canyon facility criticality safety analysis has been performed using highly detailed models of the H-Modified (HM) process mixer settlers. The HM process uses tributyl phosphate (TBP) in organic n-paraffin to extract and purify uranium from used nuclear fuel. This occurs in two cycles of counter-current solvent extraction. The aqueous stream is a weak to moderate nitric acid and the feed stock is an aqueous stream. The first Cycle, consisting of two 16-stage banks (A and B-Banks) and one 12-stage bank (C-Bank), is a three step process that separates uranium from the fuel matrix, fission products, and most of the transuranic actinide content. The first Cycle aqueous product is concentrated, adjusted for acidity and fed to the second Cycle. The second Cycle, consisting of one 16-stage bank (D-Bank) and one 12-stage bank (E-Bank), is a two-step process that further purifies the uranium and removes to a great extent remaining actinides and fission products Each stage of the mixer settler banks is modeled as three unique compositions: the mixer as a combined composition of aqueous and organic components and the settler one aqueous and one organic component. This work addresses what is believed to be normal, credible abnormal, and beyond credible abnormal conditions for a particular postulated series of process parameter upsets. The level of detail and the source for the stage-wise compositions are both new and unique to criticality safety analyses of the HM process. Initial work was presented in Ref. 1 and has since been refined. A predictive chemistry model for flowsheet development has been used to solve the solvent extraction equations for the prescribed conditions and the output of that model was then transformed into compositions for each mixture in each stage. The remaining question upon which to achieve consensus is if the approach was appropriately conservative by concluding the chemistry is appropriately bounded. Computational modeling for criticality calculations was performed using KENO-VI in the SCALE 6.1 code package. Computational modeling of the chemistry was performed using the SEPHIS Modification 4 code.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

A standardized quantitative analysis strategy for stable isotope probing metagenomics

ABSTRACT Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg , an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, “who is eating what?” and “who is active?” within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism’s taxonomic identity and genome composition while providing quantitative estimates of the microorganism’s isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

54 ENVIRONMENTAL SCIENCES↗