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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Whole‐tree nonstructural carbohydrate storage and seasonal dynamics in five temperate species

Summary Despite the importance of nonstructural carbohydrates ( NSC ) for growth and survival in woody plants, we know little about whole‐tree NSC storage. The conventional theory suggests that NSC reserves will increase over the growing season and decrease over the dormant season. Here, we compare storage in five temperate tree species to determine the size and seasonal fluctuation of whole‐tree total NSC pools as well as the contribution of individual organs. NSC concentrations in the branches, stemwood, and roots of 24 trees were measured across 12 months. We then scaled up concentrations to the whole‐tree and ecosystem levels using allometric equations and forest stand inventory data. While whole‐tree total NSC pools followed the conventional theory, sugar pools peaked in the dormant season and starch pools in the growing season. Seasonal depletion of total NSC s was minimal at the whole‐tree level, but substantial at the organ level, particularly in branches. Surprisingly, roots were not the major storage organ as branches stored comparable amounts of starch throughout the year, and root reserves were not used to support springtime growth. Scaling up NSC concentrations to the ecosystem level, we find that commonly used, process‐based ecosystem and land surface models all overpredict NSC storage.

Furze, Morgan E.↗
DOE OSTI2013

Dismantling the nuclear research reactor Thetis

The research reactor Thetis, in service since 1967 and stopped in 2003, is part of the laboratories of the institution of nuclear science of the University of Ghent. The reactor, of the pool-type, was used as a neutron-source for the production of radio-isotopes and for activation analyses. The reactor is situated in a water pool with inner diameter of 3 m. and a depth of 7.5 m. The reactor core is situated 5.3 m under water level. Besides the reactor, the pool contains pneumatic loops, handling tools, graphite blocks for neutron moderation and other experimental equipment. The building houses storage rooms for fissile material and sources, a pneumatic circuit for transportation of samples, primary and secondary cooling circuits, water cleaning resin circuits, a ventilation system and other necessary devices. Because of the experimental character of the reactor, laboratories with glove boxes and other tools were needed and are included in the dismantling program. The building is in 3 levels with a crawl-space. The ground-floor contains the ventilation installation, the purification circuits with tanks, cooling circuits and pneumatic transport system. On the first floor, around the reactor hall, the control-room, visiting area, end-station for pneumatic transport, waste-storage room, fuel storage room and the labs are located. The second floor contains a few laboratories and end stations of the two high speed transfer tubes. The lowest level of the pool is situated under ground level. The reactor has been operated at a power of 150 kW and had a max operating power of 250 kW. Belgoprocess has been selected to decommission the reactor, the labs, storage halls and associated circuits to free release the building for conventional reuse and for the removal of all its internals as legal defined. Besides the dose-rate risk and contamination risk, there is also an asbestos risk of contamination. During construction of the installation, asbestos-containing materials were used, which must be removed in controlled conditions. The ventilation system is considered free from nuclear contamination but it contains asbestos. This paper covers the organization of the dismantling work, the technical execution aspect and conclusions already known (dismantling is ongoing as this is written). (authors)

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2024

Optimizing Transmission of Acoustic Signals to Monitor Internal Conditions of Canisters for Dry Storage of Commercial Spent Nuclear Fuel

Safe storage of spent nuclear fuel (SNF) is critical to the nuclear fuel cycle and the future of nuclear energy. In the United States, SNF is stored primarily via two methods regulated by the U.S. Nuclear Regulatory Commission: wet storage in SNF pools and dry storage in dry cask storage systems (DCSSs). After about five years of cooling in spent fuel pools, the fuel assemblies are transferred into DCSSs, and the systems are filled with helium and sealed by welding. Deterioration of conditions inside of a DCSS is reflected in changes in the internal gas properties; this motivates the development of acoustic techniques to monitor internal gas properties, over extended storage periods, using sensors mounted on the exterior of the storage packages. However, a major challenge in collecting acoustic signals is the impedance mismatch between the steel canister shell and the gas. Only a small fraction of the ultrasonic signal can be transmitted through the gas medium. This paper documents experimental studies conducted on a full-scale canister mock-up to capture the gas-borne signals. Damping materials were pasted on the outside, and blocking and unblocking tests were conducted to identify the gas-borne signal. The results show that the excitation frequency plays an important role in maximizing the gas-borne signals. The gas-borne signal was successfully detected at around the theoretical time-of-flight. A high signal-to-noise ratio was achieved in the measurements. Next, the acoustic impedance matching layers were introduced, and the gas signal was drastically improved compared with that using no AIM layers.

Spent nuclear fuel (SNF), Canisters, Internal cond↗
DOE OSTI2016

The impact of system matrix dimension on small FOV SPECT reconstruction with truncated projections

Purpose: A dedicated cardiac hybrid single photon emission computed tomography (SPECT)/CT scanner that uses cadmium zinc telluride detectors and multiple pinhole collimators for stationary acquisition offers many advantages. However, the impact of the reconstruction system matrix (SM) dimension on the reconstructed image quality from truncated projections and 19 angular samples acquired on this scanner has not been extensively investigated. In this study, the authors aimed to investigate the impact of the dimensions of SM and the use of body contour derived from adjunctive CT imaging as an object support in reconstruction on this scanner, in relation to background extracardiac activity. Methods: The authors first simulated a generic SPECT/CT system to image four NCAT phantoms with various levels of extracardiac activity and compared the reconstructions using SM in different dimensions and with/without body contour as a support for quantitative evaluations. The authors then compared the reconstructions of 18 patient studies, which were acquired on a GE Discovery NM570c scanner following injection of different radiotracers, including {sup 99m}Tc-Tetrofosmin and {sup 123}I-mIBG, comparing the scanner’s default SM that incompletely covers the body with a large SM that incorporates a patient specific full body contour. Results: The simulation studies showed that the reconstructions using a SM that only partially covers the body yielded artifacts on the edge of the field of view (FOV), overestimation of activity and increased nonuniformity in the blood pool for the phantoms with higher relative levels of extracardiac activity. However, the impact on the quantitative accuracy in the high activity region, such as the myocardium, was subtle. On the other hand, an excessively large SM that enclosed the entire body alleviated the artifacts and reduced overestimation in the blood pool, but yielded slight underestimation in myocardium and defect regions. The reconstruction using the larger SM with body contour yielded the most quantitatively accurate results in all the regions of interest for a range of uptake levels in the extracardiac regions. In patient studies, the SM incorporating patient specific body contour minimized extracardiac artifacts, yielded similar myocardial activity, lower blood pool activity, and subsequently improved myocardium-to-blood pool contrast (p < 0.0001) by an average of 7% (range 0%–18%) across all the patients, compared to the reconstructions using the scanner’s default SM. Conclusions: Their results demonstrate that using a large SM that incorporates a CT derived body contour in the reconstruction could improve quantitative accuracy within the FOV for clinical studies with high extracardiac activity.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2019

Electrical and Optical Characteristics of Si-Nanoparticle Films Deposited onto Substrates by High-Voltage Electrospraying from Ethanol Sols

The optical and electrical characteristics of films consisting of nanocrystalline silicon (nc-Si) deposited onto substrates by the high-voltage electrospraying of nc-Si sols in ethanol are investigated. It is found that the interaction of ethanol droplets carrying Si nanoparticles with a corona-discharge electric field leads to the polymerization of ethanol and the formation of a polymer layer on the Si-nanoparticle surface. A high-voltage facility for depositing the films using an additional focusing electrode allows one to change the geometry of the electric field and intensity in the region of the ethanol droplet flow. As a result, nc-Si films with qualitatively different properties of the polymer on the nanoparticle surface are formed, specifically, nc-Si-A and nc-Si-B, obtained without a focusing electrode and with it, respectively. Upon annealing at temperatures of up to 400°С, the optical band gap E{sub g} of the nc-Si-A films increases from ~1.9 to ~2.2 eV, while the E{sub g} value of the nc-Si-B films remains constant and amounts to 1.85 eV. The constant E{sub g} value of the nc-Si-B films is explained by the properties of the polymer on the Si-nanoparticle surface and the more effective blocking of oxygen penetration from the surrounding environment upon annealing at temperatures of up to 400°C than in the case of a polymer in nc-Si-A films. The temperature dependences of the dark and photoinduced conductivity of nc-Si-A films are approximated with good accuracy by two activation-type exponential functions and the dark activation energies are ~0.75 and 0.1 eV, respectively. The conductivity of the nc-Si-A films noticeably decreases under irradiation of the samples at wavelengths of 460–470 nm. The temperature dependences of the conductivity of the nc-Si-B films are approximated with good accuracy by exponential functions with activation energies of 0.73 (in the dark) and 0.59 eV (under photoexcitation). In contrast to the case of nc-Si-A films, the photoconductivity of nc-Si-B films grows more than fourfold relative to the dark conductivity under analogous illumination. The nc-Si-B films are photoactive and sandwich-like Al/nc-Si-B/Al structures can generate a voltage. The dark conductivity and photoconductivity of the nc-Si-A films in the voltage range of V > 2 V are determined by the two-center Poole–Frenkel effect; the concentration of the centers affecting the Poole–Frenkel conductivity is ~3 × 10{sup 17} cm{sup –3}. In nc-Si-B films in the voltage range of 2–5 V, electron transport is determined by space-charge-limited currents and, at high voltages, by the two-center Poole–Frenkel effect. The concentration of traps contributing to the space-charge-limited currents is ~4 × 10{sup 16} cm{sup –3}. The concentration of Poole–Frenkel centers affecting the conductivity decreases according to the activation law with an activation energy of 0.7 eV from 3 × 10{sup 16} to 2 × 10{sup 14} cm{sup –3} with a decrease in temperature from 120°C to 40°C.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

A Simple Lagrangian Parcel Model for the Initiation of Summer-time Mesoscale Convective Systems over the Central United States

Mesoscale convective systems (MCSs) account for more than 50% of summertime precipitation over the central United States and have a significant impact on local weather and hydrologic cycle. It is hypothesized that the inadequate treatment of MCSs is responsible for the long-standing warm and dry bias over the central United States in coarse-resolution general circulation model (GCM) simulations. In particular, a better understanding of MCS initiation is still lacking. Here a single-column Lagrangian parcel model is first developed to simulate the basic features of a rising parcel. This simple model demonstrates the collective effects of boundary layer moistening and dynamical lifting in triggering convective initiation and reproduces successfully its early afternoon peak with surface equivalent potential temperature as a controlling factor. It also predicts that convection is harder to trigger in the future climate under global warming, consistent with the results from convection-permitting regional climate simulations. Then, a multicolumn model that includes an array of single-column models aligned in the east–west direction and incorporates idealized cold pool interaction mechanisms is developed. The multicolumn model captures readily the cold pool–induced upscale growth feature in MCS genesis from initially scattered convection that is organized into a mesoscale cluster in a few hours. It also highlights the crucial role of lifting effects due to cold pool collision and spreading, subsidence effect, and gust front propagation speed in controlling the final size of mesoscale clusters and cold pool regions. This simple model should be useful for understanding fundamental mechanisms of MCS initiation and providing guidance for improving MCS simulations in GCMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for "Metabolic Engineering Strategies to Produce Medium-Chain Oleochemicals via Acyl-ACP:CoA Transacylase Activity"

Microbial lipid metabolism is an attractive route for producing oleochemicals. The predominant strategy centers on heterologous thioesterases to synthesize desired chain-length fatty acids. To convert acids to oleochemicals (e.g., fatty alcohols, ketones), the narrowed fatty acid pool needs to be reactivated as coenzyme A thioesters at cost of one ATP per reactivation – an expense that could be saved if the acyl-chain was directly transferred from ACP- to CoA-thioester. Here, we demonstrate such an alternative acyl-transferase strategy by heterologous expression of PhaG, an enzyme first identified in Pseudomonads, that transfers 3-hydroxy acyl-chains between acyl-carrier protein and coenzyme A thioester forms for creating polyhydroxyalkanoate monomers. We use it to create a pool of acyl-CoA’s that can be redirected to oleochemical products. Through bioprospecting, mutagenesis, and metabolic engineering, we develop three strains of Escherichia coli capable of producing over 1 g/L of medium-chain free fatty acids, fatty alcohols, and methyl ketones.

Bioproducts↗
DOE OSTI2011

Hydrocarbon characterization experiments in fully turbulent fires : results and data analysis.

As the capabilities of numerical simulations increase, decision makers are increasingly relying upon simulations rather than experiments to assess risks across a wide variety of accident scenarios including fires. There are still, however, many aspects of fires that are either not well understood or are difficult to treat from first principles due to the computational expense. For a simulation to be truly predictive and to provide decision makers with information which can be reliably used for risk assessment the remaining physical processes must be studied and suitable models developed for the effects of the physics. The model for the fuel evaporation rate in a liquid fuel pool fire is significant because in well-ventilated fires the evaporation rate largely controls the total heat release rate from the fire. This report describes a set of fuel regression rates experiments to provide data for the development and validation of models. The experiments were performed with fires in the fully turbulent scale range (> 1 m diameter) and with a number of hydrocarbon fuels ranging from lightly sooting to heavily sooting. The importance of spectral absorption in the liquid fuels and the vapor dome above the pool was investigated and the total heat flux to the pool surface was measured. The importance of convection within the liquid fuel was assessed by restricting large scale liquid motion in some tests. These data sets provide a sound, experimentally proven basis for assessing how much of the liquid fuel needs to be modeled to enable a predictive simulation of a fuel fire given the couplings between evaporation of fuel from the pool and the heat release from the fire which drives the evaporation.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

In-Device Delay: Introduction to Obscurant Physcial Protection System

The Office of Radiological Security (ORS) In-Device Delay (IDD) program has undertaken a project to research and develop a novel protection system for industrial irradiators that contain high-activity Co-60 sources. Based on adversary testing conducted by ORS, it is was determined that to successfully accomplish the theft of the target material, the adversary will require visual contact of the sources and source rack located at the bottom of the pool. Therefore, if a means of obscuring or visually hiding the sources in the pool can be achieved (while adhering to facility operations, safety, and regulatory requirements), then illicit source theft will be significantly hindered. This project aims to develop a low-cost, non-propriety obscurant that, when an adversary action is detected, the obscurant will be deployed into the pool quickly, rendering visual observation of the source problematic; however, this obscurant will not otherwise disturb the sources, source rack, and filtration system. The obscurant will remain in the pool until removed by another process.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

Sodium Fire Collaborative Study Progress CNWG Fiscal Year 2021

This report discusses the progress on the collaboration between Sandia National Laboratories (Sandia) and Japan Atomic Energy Agency (JAEA) on the sodium fire research in fiscal year (FY) 2021 and is a continuation of the FY2020 progress report. In this report, we only report the changes made to the current sodium pool fire model in MELCOR. We modified and corrected many control functions to enhance the current model from the FY2020 report. This year’s enhancements relate to better agreement of the suspended aerosol measurement from JAEA’s F7 series tests. Staff from Sandia and JAEA conducted the validation studies of the sodium pool fire model in MELCOR. To validate this pool fire model with the latest enhancement, JAEA sodium pool fire experiments (F7-1 and F7-2) were used. The results of the calculation, including the code-to-code comparisons are discussed as well as suggestions for further model improvement. Finally, recommendations are made for new MELCOR simulations for FY2022.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Sodium Fire Collaborative Study Progress (CNWG Fiscal Year 2022)

This report discusses the progress on the collaboration between Sandia National Laboratories (Sandia) and Japan Atomic Energy Agency (JAEA) on the sodium fire research in fiscal year (FY) 2022 and is a continuation of the FY 2021 progress report. We only report the changes made to the current sodium pool fire model in MELCOR. We modified and corrected many control functions to enhance the fraction of oxygen consumed that reacts to form monoxide (FO2) parameter in the current model from the FY2021 report. This year's enhancements relate to better agreement of the suspended aerosol measurement from JAEA's F7 series tests. Staff from Sandia and JAEA conducted the validation studies of the sodium pool fire model in MELCOR. To validate this pool fire model with the latest enhancement, JAEA sodium pool fire experiments (F7-1 and F7-2) were used. The results of the calculation, including the code-to-code comparisons are discussed as well as suggestions for further model improvement. Finally, recommendations are made for new MELCOR simulations for FY 2023.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Using root and soil traits to forecast woody encroachment dynamics in mesic grassland

Grasslands are a widespread and globally important biome providing key ecosystem services including C storage and regulation of the water cycle. Grasslands face multiple threats, including changes in drought intensity and woody encroachment - a process that results in increased woody plant abundance corresponding with decreased herbaceous plant abundance. The combination of reduced soil moisture and shifts in plant dominance from herbaceous to woody are likely to alter C pools in the soil profile. We currently do not have the capacity to predict either the magnitude or rates of change in these C pools. In order to predict changes in grassland vegetation structure and the associated impacts on C cycling requires greater understanding of changes in soil C pools at multiple soil depths, and the responses of these pools to changes in precipitation. To support and perform this parameterization of Land Surface Models, we performed detailed investigations of root (anatomical and physiological) and soil traits (microbial function) at varying soil depths, to capture the belowground impacts of changing dominant plant growth forms (grasses to shrubs) and the impacts of frequent drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Differential Organic Carbon Mineralization Responses to Soil Moisture in Three Different Soil Orders Under Mixed Forested System: Supporting Data

This data contains data from 90-day long incubation study which aimed to look at the soil moisture-texture relationship on soil organic carbon (SOC) cycling. Soils were collected from three distinct soil textures from mixed forests in 2017: sandy (Georgia, 2017-05-01), loamy (Missouri, 2017-06-14) and clayey (Texas, December 2017) were incubated at different soil moisture levels (air-dried, 25% water holding capacity (WHC), 50% WHC, 100% WHC and 175% WHC) at room temperature for a period of 90 days. Files contain microbial respiration, active and slow SOC pools, and their respective mineralization rates, extractable organic carbon (C), and C-acquiring extracellular enzymes. Findings from these data were used in Singh et al. (2021). This study aimed to examine the interactive effect of soil moisture and texture on SOC mineralization. Soil samples of three distinct textures (sandy, loamy, and clayey) were collected from mixed forests of Georgia, Missouri, and Texas, respectively. Soil cores of 5 cm diameter were collected from numerous random locations at each site from 0-15 cm depth after scraping the litter layer and mixed thoroughly to obtain a composite sample per site. Three additional soil cores were collected to determine the WHC using pressure plate extractors. Soil samples were composited, and triplicate soil samples were incubated in mason jars for a period of 90 days at room temperature under different moisture regimes: air dried, 25% WHC, 50% WHC, at WHC and 100% saturation. Soil respiration was measured weekly, and destructive sampling was conducted at 1, 15, 60, and 90 days to determine extractable organic C, C acquiring enzyme activity, and active and slow SOC pools with their respective mineralization rates. The C acquiring enzyme activity was the total activity of α-glucosidase, β-glucosidase, cellobiohydrolase, and β-xylosidase enzymes. Gas samples for microbial respiration measurements were collected from headspace of incubation jars through the sampling ports on the lids and then analyzed using a Shimadzu Gas Chromatograph (GC-2014). Prior to sampling, the vials were evacuated. Blank correction was also done by collecting gas samples from empty incubation jars. Double pool exponential decay model was used in SigmaPlot to determine the active and slow SOC pools and their mineralization rates (Farrar et al., 2012; Jagadamma et al., 2014). The C-acquiring extracellular enzymes were measured using the microplate method by German et al., (2011). Microbial community structure was determined using the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) analyses (Buyer and Sasser, 2012). This dataset has seven data files provided in comma-separate (*.csv) format. Additional metadata are provided: seven data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

Carbon acquiring enzyme activity↗
DOE OSTI2023

Simulations for Planning of Liquid Hydrogen Spill Test

In order to better understand the complex pooling and vaporization of a liquid hydrogen spill, Sandia National Laboratories is conducting a highly instrumented, controlled experiment inside their Shock Tube Facility. Simulations were run before the experiment to help with the planning of experimental conditions, including sensor placement and cross wind velocity. This paper describes the modeling used in this planning process and its main conclusions. Sierra Suite’s Fuego, an in-house computational fluid dynamics code, was used to simulate a RANS model of a liquid hydrogen spill with five crosswind velocities: 0.45, 0.89, 1.34, 1.79, and 2.24 m/s. Two pool sizes were considered: a diameter of 0.85 m and a diameter of 1.7. A grid resolution study was completed on the smaller pool size with a 1.34 m/s crosswind. A comparison of the length and height of the plume of flammable hydrogen vaporizing from the pool shows that the plume becomes longer and remains closer to the ground with increasing wind speed. The plume reaches the top of the facility only in the 0.45 m/s case. From these results, we concluded that it will be best for the spacing and location of the concentration sensors to be reconfigured for each wind speed during the experiment.

08 HYDROGEN↗
DOE OSTI2024

In Situ Prediction of Microstructure and Mechanical Properties in Laser-Remelted Al-Si Alloys: Towards Enhanced Additive Manufacturing

Laser surface remelting of aluminum alloys has emerged as a promising technique to enhance mechanical properties through refined microstructures. This process involves rapid cooling rates ranging from 10 3 to 10 8 °C/s, which increase solid solubility within aluminum alloys, shifting their eutectic composition to a larger value of silicon content. Consequently, the resulting microstructure combines a strengthened aluminum matrix with silicon fibers. This study focuses on the laser scanning of Al-Si aluminum alloy to reduce the size of aluminum matrix spacings and transform fibrous silicon particles from micrometer to nanometer dimensions. Analysis revealed that the eutectic structure contained 17.55% silicon by weight, surpassing the equilibrium eutectic composition of 12.6% silicon. Microstructure dimensions within the molten zones, termed ‘melt pools’, were extensively examined using Scanning Electron Microscopy (SEM) at intervals of approximately 20 μm from the surface. A notable increase in hardness, exceeding 50% compared to the base plate, was observed in the melt pool regions. Thus, it is exemplified that laser surface remelting introduces a novel strengthening mechanism in the alloy. Moreover, this study develops an in situ method for predicting melt pool properties and dimensions. A predictive model is proposed, correlating energy density and spectral signals emitted during laser remelting with mechanical properties and melt pool dimensions. This method significantly reduces characterization time from days to seconds, offering a streamlined approach for future studies in additive manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis

Abstract. The nitrogen (N) cycle has the potential to regulate climate change through its influence on carbon (C) sequestration. Although extensive research has explored whether or not progressive N limitation (PNL) occurs under CO2 enrichment, a comprehensive assessment of the processes that regulate PNL is still lacking. Here, we quantitatively synthesized the responses of all major processes and pools in the terrestrial N cycle with meta-analysis of CO2 experimental data available in the literature. The results showed that CO2 enrichment significantly increased N sequestration in the plant and litter pools but not in the soil pool, partially supporting one of the basic assumptions in the PNL hypothesis that elevated CO2 results in more N sequestered in organic pools. However, CO2 enrichment significantly increased the N influx via biological N fixation and the loss via N2O emission, but decreased the N efflux via leaching. In addition, no general diminished CO2 fertilization effect on plant growth was observed over time up to the longest experiment of 13 years. Overall, our analyses suggest that the extra N supply by the increased biological N fixation and decreased leaching may potentially alleviate PNL under elevated CO2 conditions in spite of the increases in plant N sequestration and N2O emission. Moreover, our syntheses indicate that CO2 enrichment increases soil ammonium (NH4+) to nitrate (NO3−) ratio. The changed NH4+/NO3− ratio and subsequent biological processes may result in changes in soil microenvironments, above-belowground community structures and associated interactions, which could potentially affect the terrestrial biogeochemical cycles. In addition, our data synthesis suggests that more long-term studies, especially in regions other than temperate ones, are needed for comprehensive assessments of the PNL hypothesis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

FUN-BioCROP model with litter decomposition parameters derived from the LIDET dataset

This repository contains the code and data necessary to run the FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms, and Protection) model with litter decomposition parameters derived from a modified Monte Carlo simulation that used the Long-term Intersite Decomposition Experiment Team dataset. Related publication:Juice, S.M., Ridgeway, J.R., Hartman, M.D., Parton, W.J., Berardi, D.M., Sulman, B.N., Allen, K.E., & Brzostek, E.R. Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Description of Files: FUNBioCROP_LIDET Study.Rmd R code with FUN-BioCROP model that can be run with 10 different sets of parameters for litter decomposition (Baseline, LIDET, or eight other best parameter sets identified in the modified Monte Carlo simulation. CORPSE Functions_Bioenergy_V2.R Code with CORPSE model functions, called by FUNBioCROP_LIDET Study.Rmd Model Input Data: bulk.csv, bulk_till.csv, rhizo.csv, rhizo_till.csv, litter.csv Initial C and N (kg C or N/m2) pool values for each soil compartment, final values from spin up. All five files have the same columns: (Column - Description - Units) uFastC - Unprotected fast decomposing carbon - kg carbon/m2 uSlowC - Unprotected slow decomposing carbon - kg carbon/m2 uNecroC - Unprotected necromass carbon - kg carbon/m2 pFastC - Protected fast decomposing carbon - kg carbon/m2 pSlowC - Protected slow decomposing carbon - kg carbon/m2 pNecroC - Protected necromass carbon - kg carbon/m2 livingMicrobeC - Carbon in living microbial biomass - kg carbon/m2 uFastN - Unprotected fast decomposing nitrogen - kg nitrogen/m2 uSlowN - Unprotected slow decomposing nitrogen - kg nitrogen/m2 uNecroN - Unprotected necromass nitrogen - kg nitrogen/m2 pFastN - Protected fast decomposing nitrogen - kg nitrogen/m2 pSlowN - Protected slow decomposing nitrogen - kg nitrogen/m2 pNecroN - Protected necromass nitrogen - kg nitrogen/m2 inorganicN - Inorganic nitrogen - kg nitrogen/m2 CO2 - Carbon in carbon dioxide - kg carbon/m2 livingMicrobeN - Nitrogen in living microbial biomass - kg nitrogen/m2 Model Input Data: FluxTower_AvgSoilT.csv: Average daily soil temperature (oC) at 10 cm depth at University of Illinois Urbana-Champaign (UIUC) Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: FluxTower_AvgSoilVWC.csv: Average daily soil volumetric water content (VWC) at 10 cm depth at UIUC Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: input_CCS_LIDET Study.csv: This file has daily data to run FUN-BioCROP (Column - Description - Units): yr - calendar year - year doy - day of year (1 to 365) (no leap year) - day anpp - aboveground NPP (DayCent) - kg C/m2/day bnpp - belowground NPP (DayCent) - kg C/m2/day aglivc - live aboveground biomass carbon (DayCent) - kg C/m2 bglivcj - live juvenile fine root biomass carbon (DayCent) - kg C/m2 bglivcm - live mature fine root biomass carbon (DayCent) - kg C/m2 aglivn - live aboveground biomass nitrogen (DayCent) - kg N/m2 bglivnj - live juvenile fine root biomass nitrogen (DayCent) - kg N/m2 bglivnm - live mature fine root biomass nitrogen (DayCent) - kg N/m2 nyr - simulation year - year cult - indicates a cultivation event (0 or 1) crop - indicates a new crop (0 or 1) fert - indicates a fertilizer event (0 or 1) frst - indicates the first day of the growing season (0 or 1) harv - indicates a harvest event (0 or 1) last - indicates the end of the growing season (0 or 1) croptype - crop type (0=none; 1=alfalfa; 2=corn; 3=grass clover pasture; 4=soybean; 5=wheat) cropsrl - crop specific root length - mm/g root cultrhizmix - fraction of rhizosphere mixed with bulk soil during cultivation (0.0-1.0) - fraction cultlitmix - fraction of litter mixed with bulk soil during cultivation (0.0-1.0) - fraction harvremov - fraction of above ground biomass removed during harvest (0.0-1.0) - fraction fertamt - fertilization amount - g N/m2 lifehist - plant life history (0 = annual, 1 = perennial) froot_turnover_c - amount of C in fine root turnover - kg C/m2 froot_turnover_n - amount of N in fine root turnover - kg N/m2 agrd_turnover_c - amount of C in aboveground biomass turnover - kg C/m2 agrd_turnover_n - amount of N in aboveground biomass turnover - kg N/m2 leaf_litter_fastfrac - Fast decomposing fraction of leaf litter (0.0-1.0) - fraction root_litter_fastfrac - Fast decomposing fraction of root litter (0.0-1.0) - fraction root_diameter - root diameter - mm root_length - root length - mm root/m2 rhizo_frac - fraction of total soil volume that is rhizosphere (0.0 - 1.0) - fraction date - date in format YYYY-MM-DD Instructions: Save the model code ("FUN-BioCROP_LIDET Study.Rmd") and accompanything files (data streams and CORPSE function code) in the same folder. In model code "Chunk 3: Load CORPSE Data Streams" set the working directory (setwd) to the folder with the files saved in step #1. In "Chunk 5: Define LIDET parameter sets" select the litter decomposition parameter set to be used in the run, and comment out all other sets. If changing any parameter values, edit them in "Chunk 6: Load parameters." Run all chunks up to and including "Chunk 10: Prepare Data for Export." In "Chunk 11: Export Output Data" edit data frames for export and filenames, as necessary. "Chunk 12: Graph Total Soil C" makes a figure of C remaining over the model run period. Description of each model chunk (in file FUN-BioCROP_LIDET Study.Rmd): Chunk 1: Remove all functions, clear memory. Removes all functions from R environment, clears the memory. Chunk 2: Load Packages. Loads packages necessary to run the code. Chunk 3: Load CORPSE Data Streams. Sets the working directory and loads the data files necessary to run CORPSE. Chunk 4: Load CORPSE Functions. Loads the R script with CORPSE functions from the working directory, "CORPSE Functions_Bioenergy_V2.R". Chunk 5: Define LIDET parameter sets. Has ten different parameter sets for litter decomposition tested in this study: Baseline parameters, LIDET parameters, and the other 8 best performing parameter sets identified in the modified Monte Carlo. To run the model, all but one parameter set must be commented out. Chunk 6: Load Parameters. Loads all fixed parameters to run the model. Data frame with definitions of parameters is in the CORPSE function script "CORPSE Functions_Bioenergy_V2.R" Chunk 7: Prepare Data Streams. Takes data streams loaded in Chunk 3 and puts them in the format necessary to run the model. The model is coded to run at least two sites at a time, so if only one site is being run it must be run in duplicate. Individual data tables of daily values are created in this chunk from the input data file. Chunk 8: Set Initial Conditions. Creates data tables of soil C and N pools for each soil compartment (rhizo_till, rhizo, bulk_till, bulk, litter) and loads initial values into the data tables. Creates lists for each soil compartment to hold model output. Chunk 9: Load FUN Data and Set Up Matrices. Uses DayCent data to calculate FUN input data: root and leaf N demand, total N demand, plant CN, leaf N available for retranslocation, and litter production. Creates matrices for FUN model outputs. Chunk 10: Run Model. Runs the model. Chunk 11: Prepare Data for Export. Combines data from each day saved as lists into data frames for each soil compartment. Adds values from all soil compartments together to calculate total soil values, creates separate data frames for each soil C and N pool (e.g., protected slow C) for the total soil value. Adds different C and N pools together to calculate total soil C and N for all layers. Creates data frame of ratio of protected to unprotected SOC. Organizes FUN data for export. Chunk 12: Export Results. Exports CSV files of model results to the working directory. Chunk 13: Graph Total Soil C. Makes figure of C remaining over time. Related Links: Original FUN-BioCROP model: https://github.com/BrzostekEcologyLab/FUN-BioCROP LIDET dataset: https://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=TD023

Juice, Stephanie↗