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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The phylogenetic roots of addiction: compulsive drug seeking, natural and drug-sensitive reward, and the acquisition of learned habits

Our rational faculties permit us humans to maximize the utility of our actions. We perform a fundamental type of cost-benefit analysis in which we frame a problem, assign values to the different paths, and then choose from among a set of available options, the course that promises the most favorable outcome. So why then does addiction appear to be so impervious to the associated costs, so unaffected by undesired consequences, and ultimately so resistant to cognitive oversight? The answer may likely be found in the fact that the drivers for compulsive drug seeking and drug taking are located in affective brain circuits, circuits that are structured and patterned by learning with repeated activation. These deep processes exhibit significant resistance to control by our cognitive faculties. The general consensus is that addiction arises from mechanisms that overvalue the magnitude of reward, discount the associated risks, and thereby bias individuals towards compulsive pursuit of addictive drugs. Behavioral disruption and dependence appear to arise at the intersection of a number of connected but separate phenomena: expectations for the occurrence of specific events, behaviors that seek encounters with them, the ability to notice and learn nonrandom, co-occurring conditions, the prediction and valuation of consequences, the forming of enduring memories, and the drivers of focused behavior through compulsion, habits, and acquired routines. It is important to recognize that each one of these individual faculties are present and well developed across the entire phylogenetic tree of bilateral metazoans. The goal of this special volume is dedicated to exploring the degree to which inherent elements can account for addiction and addiction-associated phenomena. In much of the literature on addiction, the underlying processes are often viewed as distinctly mammalian, arising, in part, from the strong cognitive capacities of this taxon. Some phenomena may even be regarded to exist only in primates, or even solely in humans. This supposition arises from the fact that studies are conducted almost exclusively in mammals and primates, while evolutionary antecedents of the behavior are rarely considered. A more comprehensive perspective that examines drug reward and reinforcement in a wider range of organisms demonstrates that many of the component traits are actually well developed across the greater metazoan lineage, and they may well predate the emergence of a mammalian clade by a wide margin. The collection of papers assembled here supports the notion that the capacity to associate cues and quences has not arisen in mammals de novo. Rather, the neural mechanisms for detecting contingencies and for predicting future outcomes are very deeply rooted across broad phylogenetic divisions. Our understanding of an ability to associate paired events has been enriched by work in invertebrate preparations in both classical and operant conditioning scenarios [Cook and Carew, 1986, 1989a, 1989b]. The ability to learn allows us to connect cues and behavioral actions to their associated consequences. Pavlovian conditioning enriches surrounding cues with predictive value. Outcomes with positive valence generate appetitive responses and approach to the associated cues, while those perceived as aversive bring cue avoidance and withdrawal. Humans are not the only life forms capable of such short- and long-term modulations of behavior

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Circular Economy for Lithium-Ion Batteries Used in Mobile and Stationary Energy Storage: Drivers, Barriers, Enablers, and U.S. Policy Considerations

As large-format battery energy storage (BES) capacity increases in the United States, so will the volume of spent lithium-ion batteries (LiBs) (Bade 2019). Estimates based on a 10-year lifetime assumption found that the volume of LiBs that have reached the end of their utility for electric vehicle (EV) applications could total two million units (four million metric tons) annually by 2040 in the United States (Richa et al. 2014; Ai and Borucki 2018). Although there is currently no publicly available decommissioning or end-of-life (EoL) projection for stationary BES systems, the U.S. energy storage market is expected to grow from an annual deployment of 523 megawatts in 2013 to 7.3 gigawatts in 2025 (Wood MacKenzie and ESA 2020; Wesoff 2020). Despite potential secondary market opportunities and the potential benefits associated with the reuse/recovery of LiB material, anecdotal evidence suggests that in the United States most decommissioned LiBs from EVs are landfilled or otherwise disposed of (Steward et al. 2019; Salim et al. 2019; CPUC 2019; DTSC 2019d; NREL 2019b; Jacoby 2019; DOE 2019). The reuse of large-format LiBs is not at commercial scale and to date consists of only a handful of U.S.-led pilot projects. Similarly, less than 5% of LiBs from EVs are sent to recycling facilities in the United States (Steward et al. 2019; Jacoby 2019; America Made 2019; Patel 2017). As awareness of current practices grows, and the demand for critical LiB materials increases, U.S. industry stakeholders, regulators, and policymakers are starting to (1) consider solutions to drive and enable environmentally sustainable materials management decisions and behaviors and (2) identify barriers to a circular economy for LiBs (Figure 1). Circular economy principles (Figure 1) attempt to transition from a “take-make-consume-dispose” linear economic system to a circular system that allows for the long life, high performance, and the reuse/recovery of products and materials (Ellen MacArthur Foundation 2016). We begin this report by summarizing drivers, barriers, and enablers to a circular economy for LiBs used in mobile and stationary BES systems in the United States. We then report on our analysis of federal and state regulatory considerations that may impact the reuse/recovery and disposal of LiBs, and potential civil and criminal liabilities associated with noncompliance. We conclude by highlighting state policies and initiatives in the United States that expressly address reuse/recovery and disposal of large-format LiBs. Our results are based on legal and literature-based research and interviews with mobile and stationary BES industry stakeholders, regulators, and policymakers. While this report addresses stationary BES, as well as mobile BES, much of the information and experience with LiB decommissioning and EoL material management is derived from the increasing management of spent EV LiBs in the United States.

25 ENERGY STORAGE↗
DOE OSTI2021

Use of X-Ray Fluorescence Microscopy for Studies on Research Models of Hepatocellular Carcinoma

Introduction: TheraSphere ® microspheres containing yttrium 90 Y are among many radioembolization agents used clinically to reduce liver tumor burden, and their effects on cancer volume reduction are well-established. At the same time, concerns about off target tissue injury often limit their use. Deeper investigation into tissue distribution and long-term impact of these microspheres could inform us about additional ways to use them in practice. Methods: Healthy rat liver and rabbit liver tumor samples from animals treated with TheraSpheres were sectioned and their elemental maps were generated by X-ray fluorescence microscopy (XFM) at the Advanced Photon Source (APS) synchrotron at Argonne National Laboratory (ANL). Results: Elemental imaging allowed us to identify the presence and distribution of TheraSpheres in animal tissues without the need for additional sample manipulation or staining. Ionizing radiation produced by 90 Y radioactive contaminants present in these microspheres makes processing TheraSphere treated samples complex. Accumulation of microspheres in macrophages was observed. Conclusions: This is the first study that used XFM to evaluate the location of microspheres and radionuclides in animal liver and tumor samples introduced through radioembolization. XFM has shown promise in expanding our understanding of radioembolization and could be used for investigation of human patient samples in the future.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Gasification of Coal and Biomass: The Route to Net-Negative-Carbon Power and Hydrogen

One promising process that is a candidate for meeting the goals of the US Department of Energy’s 21st Century Power Plant initiative is to gasify a mixture of coal and biomass to yield a syngas, which can have CO2 removed and then be used to produce hydrogen as well as an off-gas that can be used to flexibly produce power. This concept would overall be carbon net-negative and readily meet the 21st Century Power Plant initiative targets of smaller scale MW generation, high ramp rates and turndown, feedstock flexibility, and high efficiency—at a reasonable cost. Moreover, adding the large-scale production of “ultra-green” hydrogen yields a system tailored for the coming hydrogen economy, providing long-term energy storage and an attractive co-product for sale. The objective of the work being led by the Electric Power Research Institute, Inc. (EPRI), with support by Bechtel Corporation (Bechtel), Gas Technology Institute (GTI), Hamilton Mauer International, Inc. (HMI), Nebraska Public Power District (NPPD), NexantECA, Inc. (Nexant), and Wärtsilä, is to perform a front-end design and engineering (FEED) study on an oxygen-blown gasification system coupled with water-gas shift, pre-combustion CO2 capture, and pressure-swing adsorption working off a coal/biomass mix to yield high-purity hydrogen and a fuel off-gas that can generate power. Several designs are being considered that will be capable of producing 50 MW net from a flexible generator, over 8500 kg/hr of hydrogen, and net-negative CO2 emissions, at an efficiency of 50% net HHV. The plant would be hosted at an NPPD site, where opportunities for enhanced oil recovery and sequestration have been investigated and the need for low-carbon power and hydrogen is imminent. The principal biomass to be used is corn stover—prevalent in Nebraska where the plant will be located—mixed with Powder River Basin (PRB) coal, necessitating a gasifier that can use this feedstock and be flexible to allow other types. Waste plastics will also be reviewed for use. Two oxygen-blown gasifiers have been identified as candidates that have done testing with biomass including corn stover: the GTI gasifier—a high-pressure, fluidized-bed type—and HMI’s, a lower pressure moving-bed type. Both have relative advantages that were investigated in the Phase I design study, with a resultant down select of one system for which the FEED will be performed in Phase II. The technical tasks for the project are: • Design Development: Completion of design activities necessary to provide inputs for the FEED study. Multiple design cases will be assessed with the selection of the optimal one for the FEED. • Investment Case Preparation: Development of the draft investment case for the proposed process with business cases performed for the proposed host site and two other locations. • Host Site Selection: Evaluation of the two potential host sites within NPPD’s portfolio to select the preferred candidate based on technical, economic, and environmental considerations. • Environmental Information Volume (EIV) Development: Completion of the EIV for the host site. • FEED Study: Completion of a FEED study based on the design selected in Phase I. A Greenhouse Gas Life Cycle Analysis will also be performed for the process. • Update Investment Case: Finalization of the investment case based on findings from the FEED. The advantages of the proposed project are significant. Having an engaged U.S. power utility willing to provide a host site that will produce energy from coal plus a deep and experienced team is critical; the process meets all the goals of DOE’s 21st Century Power Plant initiative at an estimated total plant cost of ~$880M and a production cost of hydrogen of ~$2/kg-H2 while producing net-negative carbon power. If developed, this process has real commercial potential in the United States—supported by EPRI’s initial review of the considerable interest from selected U.S. utilities—and elsewhere around the globe. The process has fewer environmental hurdles compared to other concepts, lowering regulatory and protest risks—providing a pathway to preserving the viability of a critical indigenous energy source by transforming its use to match a changing world. This presentation outlines the motivation for the effort, summarizes project plans, work completed to date, results of the Phase I effort and, and detailed work scope for the remainder of the project in the Phase II FEED effort.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2022

Gasification of Coal and Biomass: The Route to Net-Negative-Carbon Power and Hydrogen

One promising process that is a candidate for meeting the goals of the US Department of Energy’s 21st Century Power Plant initiative is to gasify a mixture of coal and biomass to yield a syngas, which can have CO2 removed and then be used to produce hydrogen as well as an off-gas that can be used to flexibly produce power. This concept would overall be carbon net-negative and readily meet the 21st Century Power Plant initiative targets of smaller scale MW generation, high ramp rates and turndown, feedstock flexibility, and high efficiency—at a reasonable cost. Moreover, adding the large-scale production of “ultra-green” hydrogen yields a system tailored for the coming hydrogen economy, providing long-term energy storage and an attractive co-product for sale. The objective of the work being led by the Electric Power Research Institute, Inc. (EPRI), with support by Bechtel Corporation (Bechtel), Gas Technology Institute (GTI), Hamilton Mauer International, Inc. (HMI), Nebraska Public Power District (NPPD), NexantECA, Inc. (Nexant), and Wärtsilä, is to perform a front-end design and engineering (FEED) study on an oxygen-blown gasification system coupled with water-gas shift, pre-combustion CO2 capture, and pressure-swing adsorption working off a coal/biomass mix to yield high-purity hydrogen and a fuel off-gas that can generate power. Several designs are being considered that will be capable of producing 50 MW net from a flexible generator, over 8500 kg/hr of hydrogen, and net-negative CO2 emissions, at an efficiency of 50% net HHV. The plant would be hosted at an NPPD site, where opportunities for enhanced oil recovery and sequestration have been investigated and the need for low-carbon power and hydrogen is imminent. The principal biomass to be used is corn stover—prevalent in Nebraska where the plant will be located—mixed with Powder River Basin (PRB) coal, necessitating a gasifier that can use this feedstock and be flexible to allow other types. Waste plastics will also be reviewed for use. Two oxygen-blown gasifiers have been identified as candidates that have done testing with biomass including corn stover: the GTI gasifier—a high-pressure, fluidized-bed type—and HMI’s, a lower pressure moving-bed type. Both have relative advantages that are being investigated in the Phase I design study, with a resultant down select of one system for which the FEED will be performed in Phase II. The technical tasks for the proposed project are: • Design Development: Completion of design activities necessary to provide inputs for the FEED study. Multiple design cases will be assessed with the selection of the optimal one for the FEED. • Investment Case Preparation: Development of the draft investment case for the proposed process with business cases performed for the proposed host site and two other locations. • Host Site Selection: Evaluation of the two potential host sites within NPPD’s portfolio to select the preferred candidate based on technical, economic, and environmental considerations. • Environmental Information Volume (EIV) Development: Completion of the EIV for the host site. • FEED Study: Completion of a FEED study based on the design selected in Phase I. A Greenhouse Gas Life Cycle Analysis will also be performed for the process. • Update Investment Case: Finalization of the investment case based on findings from the FEED. The advantages of the proposed project are significant. Having an engaged U.S. power utility willing to provide a host site that will produce energy from coal plus a deep and experienced team is critical; the process meets all the goals of DOE’s 21st Century Power Plant initiative at an estimated total plant cost of ~$880M and a production cost of hydrogen of ~$2/kg-H2 while producing net-negative carbon power. If developed, this process has real commercial potential in the United States—supported by EPRI’s initial review of the considerable interest from selected U.S. utilities—and elsewhere around the globe. The process has fewer environmental hurdles compared to other concepts, lowering regulatory and protest risks—providing a pathway to preserving the viability of a critical indigenous energy source by transforming its use to match a changing world. This presentation will outline the motivation for the effort, summarize project plans, work completed to date, results of the Design Development task, and detailed work scope for the remainder of the project.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Bamboo Bio-composite Truck/Trailer Decking

Bamboo is one of the fastest growing plants in the world. Massively productive, bamboo will maintain that productivity with limited inputs and minimal management resulting in predictable volume and operating margins and with low overhead. The goal of this project was to develop a bamboo bio-composite trailer decking product that replaces apitong, is lighter weight, stronger and luminescent. The collaboration partners, Fontaine, Resource Fiber and IACMI, worked closely to develop the bamboo bio-composite decking to Fontaine Trailer’s (end-user) specifications. The various technological objectives were (a) To conduct a comprehensive Design of Experiments study for bamboo composites to understand the structure-property relationships for different resin composites and bamboo forms (strips, woven, bulk etc); (b) To establish the nail pull out characteristics of trailer deck geometry bamboo composite form. The nail pull out is a critical test in trailer decks; (c) To design, process and prototype select number of trailer decking planks for Fontaine evaluation; and (d) To conduct life cycle analysis to conduct energy calculations from the various conversion steps of the bamboo from crop to product. The project meets DOE/IACMI metrics of reduced embodied energy, lightweighting and lowering the cost of the end product. It also offers a green solution to a value-added application, i.e. trailer decking. The development goals and benefits of bamboo composite decking included: A. Decreased weight when compared to Apitong and Gen 1, thereby reducing operating costs and petroleum usage due to increased miles per gallon. B. Flexibility to allow camber design into trailers. C. Luminescence to increase safety during low light and dark conditions. D. Composite material to maximize use of bamboo bio-composites as substitute for petroleum-based composites. E. Embedded layer(s) of conditioned bamboo for added strength and stability. F. Improved safety over Apitong by temporary cargo indentation in planks for better stability. G. Cradle-to-cradle design so end-of-life becomes beginning-of-life for other products. Resource Fiber’s bamboo biocomposite trailer decking passed nail pullout tests as compared to apitong (incumbent), was lighter weight than apitong, and used less embodied energy particularly when bamboo is sourced domestically. The planks were optimized in the lab setting to the extent possible and successfully installed on the trailer at Fontaine for field testing. Despite the process not being fully optimized due to through-heat and tooling limitations within the budget constraints, the prototype decking withstood 400 cycles of reverse fatigue loading of a 107,000 lb Caterpillar 349F which was extreme conditions of field testing by Fontaine Trailer. Resource Fiber plans to outsource production of a next round of planks with a commercial pultrusion processor, then to do a re-test with Fontaine Trailers. Tooling specific to the part is required. Long-term commercial plans are to continue outsourcing production while supplying bamboo fiber and mats. Commercial markets include heavy haul trailers, military trailers, and decking for marine, industrial and residential use.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Coupled Aerodynamic and Hydrodynamic Hybrid Simulation of Floating Offshore Wind Turbines

The development and innovation of floating offshore wind energy in the U.S. requires detailed high-fidelity observations and measurements of turbine and platform loading due to wind, waves, and currents. However, full-scale and quasi-full-scale experiments require significant financial and temporal investments for construction, experimental testing, and long-term field campaigns. To support the commercial advancement of the offshore wind energy industry, specialized wind tunnel and wave basin experimental facilities are critical to be able to test FOWT designs at small scale under controlled conditions prior to full-scale deployment. Oregon State University (OSU) is internationally known as a leader in water and energy research, development, and testing. The O.H. Hinsdale Wave Research Laboratory (HWRL) and the Wallace Energy Systems and Renewables Facility (WESRF) at OSU have extensive experience building, modeling, monitoring, controlling, and actuating scaled systems. Experiments on wave-structure interaction have been performed at the HWRL since its establishment in 1972. Studies have included the interaction of waves with coastal structures (breakwaters, seawalls, buildings, cylinders, bridges, fixed foundations of offshore wind turbines, etc.) and with floating structures (e.g., wave energy converters, maneuvering of vessels, etc.). Hinsdale is actively used by marine energy technology developers, both for private testing and OSU-collaborative research projects. However, despite the availability of several large-scale facilities for hydrodynamic testing (at OSU and elsewhere in the U.S.), existing experimental laboratories are generally limited in their ability to accurately generate combined wind and wave conditions. The simulation of both wind and waves in experimental testing is complicated due to a number of constraints, including: [i] incompatible similitude laws governing the wind and waves for scaled experiments, [ii] producing accurate wind over a large enough control volume via fans, and [iii] generating wind that reasonably represents the atmospheric boundary layer in existing wave basins/flumes. Hence, physical test data providing insight into the simultaneous wave- and wind-structure response of floating offshore wind components can be difficult to generate. Given the aforementioned challenges in classic hydrodynamic experiments, the motivation of this project is to establish a real-time hybrid simulation (RTHS) approach that can apply aero- and hydro-dynamic loading by augmenting wave-only experimental facilities with virtual aerodynamic forces through numerical models representing the remaining dynamic forces. RTHS is a physical-numerical approach that partitions a prototype system into physical and numerical sub-assemblies that interact with each other through actuators and sensors in real time. In coupling physical and numerical models, the hybrid simulation approach applied herein is ideal for problems with: (1) structures subjected to different scaling laws, such as floating offshore wind turbines subjected to combined aero/hydro-dynamic loading, (2) structures that are too large or complex to be tested entirely in a laboratory setting, such as deep-water mooring applications, and (3) component testing, where the behavior of a portion of the assembly is uncertain but still interacts with other portions of the structure, such as testing the fatigue life of turbine blades. Few U.S. experimental facilities are able to test simultaneous aero- and hydro-dynamic loading and none can accurately produce aero/hydro-dynamic response on scaled FOWT models due to conflicting similitude laws between the wind (commonly Reynolds) and the waves (commonly Froude). To aid in accelerating the development of the U.S. floating offshore industry, there is a significant need to develop a flexible, modular framework that can expand the capacities of existing wave-only laboratories. The project goal is to demonstrate a hydrodynamic real-time hybrid simulation (hydro-RTHS) framework that couples numerical wind and physical waves acting on a FOWT, thus representing simultaneous aero/hydro-dynamic loading. The FOWT is partitioned into a full-scale numerical sub-assembly associated with the aerodynamics and a model-scale physical sub-assembly associated with the hydrodynamics. The numerical-physical partition associated with hydro-RTHS mitigates scaling constraints by supplying different scaling laws to the physical and numerical sub-assemblies. Herein, length, force, and time are scaled and exchanged between the sub-assemblies using Froude scaling to represent the open-channel flow in the physical sub-assembly. Other similitude laws could also be utilized depending on the problem definition. It is envisioned that the ability to model FOWTs under waves and wind, with mitigation of similitude distortions, would result in reduced development costs (currently, FOWT concept development is performed with full-size pro- totypes at enormous expense and risk) and increase the reliability of the FOWT industry (since extreme wave and wind conditions and contingency events can be tested safely in a controlled environment).

16 TIDAL AND WAVE POWER↗
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↗