Search NASA⌕ Search

SEARCH · Search NASA

Results for “flux growth”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

From Inside Out: How the Buried Interface, Shell Defects, and Surface Chemistry Conspire to Determine Optical Performance in Nonblinking Giant Quantum Dots

“Giant” or core/thick‐shell quantum dots (gQDs) are an important class of solid‐state quantum emitter characterized by strongly suppressed blinking and photobleaching under ambient conditions, and reduced nonradiative Auger processes. Together, these qualities provide distinguishing and useful functionality as single‐ and ensemble‐photon sources. For many applications, operation at elevated temperatures and under intense photon flux is desired, but performance is strongly dependent on the synthetic method employed for thick‐shell growth. Here, a comprehensive analysis of gQD structural properties “from the inside out” as a function of shell‐growth method is reported: successive ionic layer adsorption and reaction (SILAR) and high‐temperature continuous injection (HT‐CI), or sequential combinations of the two. Key correlations across synthesis methods, structural features (interfacial alloying, stacking‐fault density and surface‐ligand identity), and performance metrics (quantum yield, single‐gQD photoluminescence under thermal/photo stress, charging behavior and quantum‐optical properties) are identified. Surprisingly, it is found that interfacial alloying is the strongest indicator of gQD stability under stress, but this parameter is not the determining factor for Auger suppression. Furthermore, quantum yield is strongly influenced by surface chemistry and can approach unity even in the case of high shell‐defect density, while introduction of zinc‐blende stacking faults increases the likelihood that a gQD exhibits charged‐state emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Two-fluid and kinetic transport physics of Kelvin–Helmholtz instabilities in nonuniform low-beta plasmas

Hall-magnetohydrodynamic (Hall-MHD) theory, two-fluid simulations, and kinetic simulations are used in this work to investigate the cross-field transport properties of Kelvin–Helmholtz instabilities in nonuniform low-beta collisionless plasmas. Hall-MHD analysis shows how the linear properties of the instability are modified by density gradients and magnetization. High-order accurate two-fluid and kinetic simulations, with complete dynamics of finite-mass electrons and ions, are applied to a suite of parameter cases to systematically assess the effects of diamagnetic drift, magnetization, charge separation, and finite Larmor motion. Initialization of exact two-species kinetic equilibria facilitates the study of isolated physical effects and enables detailed cross-comparisons between two-fluid and kinetic simulations, including for cases where ion gyroradii are comparable to gradient scale lengths. For nonuniform plasmas with significant space charge, the results of two-fluid and kinetic simulations are found to disagree with Hall-MHD predictions. Kelvin–Helmholtz instability growth rates, per unit shear, are shown to be smaller when ion diamagnetic drift and $E \times B$ drift are parallel and larger when the two drifts are antiparallel. The effect is attributed to polarization drift in the shear layer, which leads to redistribution of charge, alters the electric field that drives plasma advection, and consequently modifies growth rates. Instability-induced mass transport for different parameters is characterized in terms of the flux across the shear layer and a simplified diffusion model. Distribution functions from kinetic simulations are shown to deviate substantially from Maxwellian reconstructions, indicating the importance of kinetic physics during the nonlinear phase of the instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Flow-shear destabilization of multiscale electron turbulence

The impact of sheared ${\mathbf{E} \hskip -1pt \times \hskip -1pt \mathbf{B}}$ flow on multiscale turbulence is studied with nonlinear gyrokinetic simulations. Simulations are based on DIII-D-like, high-confinement mode (H-mode) pedestal parameters in the regime of low ion temperature gradient drive, where there is a broad spectrum of electron temperature gradient (ETG)-driven turbulence. It is found that ${\mathbf{E} \hskip -1pt \times \hskip -1pt \mathbf{B}}$ shear can have a significant effect on ETG-driven electron transport, with an unexpected transition from a turbulence stabilization regime at moderate to large shearing rates $γ_E$ to a novel turbulence destabilization regime at low levels of $γ_E$. In the turbulence stabilization regime, the electron energy flux decreases monotonically with $γ_E$, even when $γ_E$ is small compared to electron mode growth rates. The stabilizing effect comes dominantly from the electron, not ion, gyrokinetic equation. In the novel destabilization regime, reduction of zonal energy results from the interaction of $γ_E$-modulated nonlinear drive in the zonal ion gyrokinetic equation, increasing the electron transport over a broad range of shearing rates. Finally, neither of these effects has been observed in previous electron-scale simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Verification and validation of linear gyrokinetic and kinetic-MHD simulations for internal kink instability in DIII-D tokamak

Here, verification and linear validation of the internal kink instability in tokamak have been performed for both gyrokinetic (GTC) and kinetic-MHD codes (GAM-solver, M3D-C1-K, NOVA, XTOR-K). Using realistic magnetic geometry and plasma profiles from the same equilibrium reconstruction of the DIII-D shot #141216, these codes exhibit excellent agreement for the growth rate and mode structure of the internal kink mode when all kinetic effects are suppressed. The simulated radial mode structures, obtained from linear simulations, are in reasonable agreement with the normalised electron cyclotron emission measurement after adjusting, within the experimental uncertainty, the safety factor q = 1 flux-surface location in the equilibrium reconstruction. Compressible magnetic perturbations strongly destabilize the kink, while poloidal variations of the equilibrium current density reduce the growth rate of the kink. Furthermore, kinetic effects of thermal ions are found to decrease the kink growth rate in kinetic-MHD simulations, but increase the kink growth rate in gyrokinetic simulations, due to the additional drive of the ion temperature gradient and parallel electric field. Kinetic thermal electrons are found to have negligible effects on the internal kink instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Magnetic anisotropy in single-crystalline antiferromagnetic Mn 2 Au

Multiple recent studies have identified the metallic antiferromagnet Mn 2 ⁢Au to be a candidate for spintronic applications due to apparent in-plane anisotropy, preserved magnetic properties above room temperature, and current-induced Néel vector switching. Crystal growth is complicated by the fact that Mn 2 ⁢Au melts incongruently. We present a bismuth flux method to grow millimeter-scale bulk single crystals of Mn 2 ⁢Au in order to examine the intrinsic anisotropic electrical and magnetic properties. Flux quenching experiments reveal that the Mn 2 ⁢Au crystals precipitate below 550°⁢C, about 100⁢°⁢C below the decomposition temperature of Mn 2 ⁢Au. Bulk Mn 2 ⁢Au crystals have a room-temperature resistivity of 16–19 µ⁢Ωcm and a residual resistivity ratio of 41. Mn 2 ⁢Au crystals have a dimensionless susceptibility on the order of 10 –4 (SI units), comparable to calculated and experimental reports on powder samples. Single-crystal neutron diffraction confirms the in-plane magnetic structure. The tetragonal symmetry of Mn 2 ⁢Au constrains the ab-plane magnetic susceptibility to be constant, meaning that χ 100 =χ 110 in the low-field limit, below any spin-flop transition. We find that three measured magnetic susceptibilities χ 100 , χ 110 , and χ 001 are the same order of magnitude and agree with the calculated prediction, meaning the low-field susceptibility of Mn 2 ⁢Au is quite isotropic, despite clear differences in ab-plane and ac-plane magnetocrystalline anisotropy. Mn 2 ⁢Au is calculated to have an extremely high in-plane spin-flop field above 30 T, which is much larger than that of another in-plane antiferromagnet, Fe 2 ⁢As (less than 1 T). Finally, the subtle anisotropy of intrinsic susceptibilities may lead to dominating effects from shape, crystalline texture, strain, and defects in devices that attempt spin readout in Mn 2⁢ Au.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

CHARACTERIZING AND CONTROLLING RECOVERY AND RECRYSTALLIZATION IN NIOBIUM FOR IMPROVED SRF CAVITY PERFORMANCE

Crystal defects, such as dislocations and low-angle boundaries, provide sources of magnetic flux trapping in the Nb materials used for superconducting radio frequency (SRF) resonating cavities. Improving the performance of SRF cavities, as measured through the quality factor, requires reducing these defects. SRF cavity production involves deformation processing, such as rolling and forming, and strategic annealing heat treatments. The resulting microstructures can be recovered, recrystallized, or both. Because recovery leaves many defects that can trap flux, recrystallization should improve cavity performance. Thus, processing schedules that produce complete recrystallization without excessive grain growth need to be designed. Solutions to this problem require understanding physical metallurgy and differentiating between recovered and recrystallized regions of microstructure. Backscattered electron microscopy techniques are applied to this end. We demonstrate that the conditions required to produce fully recrystallized microstructures depend on Nb impurity content, suggesting that processing schedules may need to be adjusted by material heat or lot. We also demonstrate that processing can be used to control growth of recrystallized grains to maintain mechanical strength in fully recrystallized materials. Forming cavities from cold-rolled Nb sheet material may provide strategic new routes to obtain microstructures that improve SRF cavity performance.

Taleff, E. [The University of Texas at Austin]↗
DOE OSTI2022

Evaluating alternative ebullition models for predicting peatland methane emission and its pathways via data–model fusion

Abstract. Understanding the dynamics of peatland methane (CH4) emissions and quantifying sources of uncertainty in estimating peatland CH4 emissions are critical for mitigating climate change. The relative contributions of CH4 emission pathways through ebullition, plant-mediated transport, and diffusion, together with their different transport rates and vulnerability to oxidation, determine the quantity of CH4 to be oxidized before leaving the soil. Notwithstanding their importance, the relative contributions of the emission pathways are highly uncertain. In particular, the ebullition process is more uncertain and can lead to large uncertainties in modeled CH4 emissions. To improve model simulations of CH4 emission and its pathways, we evaluated two model structures: (1) the ebullition bubble growth volume threshold approach (EBG) and (2) the modified ebullition concentration threshold approach (ECT) using CH4 flux and concentration data collected in a peatland in northern Minnesota, USA. When model parameters were constrained using observed CH4 fluxes, the CH4 emissions simulated by the EBG approach (RMSE = 0.53) had a better agreement with observations than the ECT approach (RMSE = 0.61). Further, the EBG approach simulated a smaller contribution from ebullition but more frequent ebullition events than the ECT approach. The EBG approach yielded greatly improved simulations of pore water CH4 concentrations, especially in the deep soil layers, compared to the ECT approach. When constraining the EBG model with both CH4 flux and concentration data in model–data fusion, uncertainty of the modeled CH4 concentration profiles was reduced by 78 % to 86 % in comparison to constraints based on CH4 flux data alone. The improved model capability was attributed to the well-constrained parameters regulating the CH4 production and emission pathways. Our results suggest that the EBG modeling approach better characterizes CH4 emission and underlying mechanisms. Moreover, to achieve the best model results both CH4 flux and concentration data are required to constrain model parameterization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Runaway electron deconfinement in SPARC and DIII-D by a passive 3D coil

The operation of a 3D coil—passively driven by the current quench (CQ) loop voltage—for the deconfinement of runaway electrons (REs) is modeled for disruption scenarios in the SPARC and DIII-D tokamaks. Nonlinear magnetohydrodynamic (MHD) modeling is carried out with the NIMROD code including time-dependent magnetic field boundary conditions to simulate the effect of the coil. Further modeling in some cases uses the ASCOT5 code to calculate advection and diffusion coefficients for REs based on the NIMROD-calculated fields, and the DREAM code to compute the runaway evolution in the presence of these transport coefficients. Compared with similar modeling in Tinguely et al (2021 Nucl. Fusion 61 124003), considerably more conservative assumptions are made with the ASCOT5 results, zeroing low levels of transport, particularly in regions in which closed flux surfaces have reformed. Of three coil geometries considered in SPARC, only the n = 1 coil is found to have sufficient resonant components to suppress the runaway current growth. Without the new conservative transport assumptions, full suppression of the RE current is maintained when the thermal quench MHD is included in the simulation or when the RE current is limited to 250kA, but when transport in closed flux regions is fully suppressed, these scenarios allow RE beams on the order of 1–2 MA to appear. Additional modeling is performed to consider the effects of the close ideal wall. In DIII-D, the CQ is modeled for both limited and diverted equilibrium shapes. In the limited shape, the onset of stochasticity is found to be insensitive to the coil current amplitude and governed largely by the evolution of the safety-factor profile. In both devices, prediction of the q-profile evolution is seen to be critical to predicting the later time effects of the coil.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Boundary Layer Climatology at ARM Southern Great Plains

Operational since 1992, the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site in Oklahoma, USA, has become a reference research site for meteorological studies. Because of an open data policy the ARM data are used by researchers all over the world. In this report, we review the long-term climatology of the atmospheric boundary layer, the SGP instrumentation, the site and some site-specific atmospheric conditions, which potentially affect wind turbines in the region. Because the atmospheric boundary layer is bounded and influenced by the land surface, observations of surface radiation components and heat fluxes are crucial to understanding land–atmosphere interactions. The entrainment of air, updrafts, downdrafts, and boundary layer height characteristics is needed for understanding the structure and growth of the atmospheric boundary layer. Therefore, measurements from both ground surface in situ and remote-sensing observations at the SGP site provide an overall climatology and their interactions from ground surface up to the boundary layer. Measurements from a 60 m meteorological tower, surface flux stations, disdrometers, soil temperature and moisture flux plates, coherent Doppler lidar, Raman lidar, radiosondes, and satellite data at the SGP central facility were analyzed. All the measurements were generally made within a few square kilometers of each other at the central facility. This report focuses on data from January 2010 to June 2020 at the SGP central facility. The various sections describe the ARM SGP site and surrounding wind turbines; in situ and remotesensing instrumentation used in the report; mathematical equations to analyze fluxes, turbulence, and other boundary layer parameters; a climatological analysis of surface winds, fluxes and thermodynamic parameters for several years; an analysis of observed winds in the framework of Monin-Obukhov Similarity Theory (MOST); an analysis of the boundary layer winds and direction from a Doppler lidar; multi-year turbulence estimates through the boundary layer from a Doppler lidar; atmospheric boundary layer water vapor and relative humidity profiles from Raman lidar; cloud base height and boundary layer height from multiple sensors and satellite data; and finally site-specific atmospheric conditions, such as nocturnal low-level jets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Status of h-BN quasi-bulk crystals and high efficiency neutron detectors

III-nitrides have fomented a revolution in the lighting industry and are poised to make a huge impact in the field of power electronics. In the III-nitride family, the crystal growth and use of hexagonal BN (h-BN) as an ultrawide bandgap (UWBG) semiconductor are much less developed. Bulk crystals of h-BN produced by the high-temperature/high-pressure and the metal flux solution methods possess very high crystalline and optical qualities but are impractical to serve as substrates or for device implementation as their sizes are typically in millimeters. The development of crystal growth technologies for producing thick epitaxial films (or quasi-bulk or semi-bulk crystals) in large wafer sizes with high crystalline quality is a prerequisite for utilizing h-BN as an UWBG electronic material. Compared to traditional III-nitrides, BN has another unique application as solid-state neutron detectors, which however, also require the development of quasi-bulk crystals to provide high detection efficiencies because the theoretical efficiency (ηi) relates to the detector thickness (d) by ηi=1−e−dλ, where λ denotes the thermal neutron absorption length which is 47 μm (237 μm) for 10B-enriched (natural) h-BN. We provide an overview and recent progress toward the development of h-BN quasi-bulk crystals via hydride vapor phase epitaxy (HVPE) growth and the attainment of thermal neutron detectors based on 100 μm thick 10B-enriched h-BN with a record efficiency of 60%. The thermal neutron detection efficiency was shown to enhance at elevated temperatures. Benchmarking the crystalline and optical qualities of h-BN quasi-bulk crystals with the state-of-the-art mm-sized bulk crystal flakes and 0.5 μm thick epitaxial films identified that reducing the density of native defects such as vacancies remains the most critical task for h-BN quasi-bulk crystal growth by HVPE.

Physics↗
DOE OSTI2022

Grain boundary transport through thermally grown alumina scales on NiAl

The oxidation resistance of Ni-based alloys is typically improved by additions of elements segregating to grain boundaries, contributing to reducing scale growth, and improving scale adherence. To develop a mechanistic understanding of doping, outward Al and inward O fluxes through the scale formed on β-NiAl with Ti, Y, and Ti+Y additions were characterized for oxidation at 1200°C and times up to 100h. Doped alloys exhibited varying reductions in oxidation rates and Al and O fluxes affecting scale grain morphologies. In conclusion, Ti+Y co-doping further reduced the outward Al and inward O transport compared to doping with Ti or Y alone.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Energy transport analysis of NSTX plasmas with the TGLF turbulent and NEO neoclassical transport models

This work presents a study of plasma transport at low aspect ratio on the National Spherical Torus Experiment tokamak, where the turbulent and neoclassical energy fluxes calculated by the quasilinear Trapped Gyro Landau Fluid (TGLF) model and the multi species drift-kinetic Neoclassical solver (NEO) are validated against experimental data. The turbulent energy transport of two plasma discharges, one in the L-mode confinement regime and another in the H-mode regime, is dominated by electrostatic drift-wave instabilities, while the ion heat transport has a significant neoclassical contribution. The data analysis workflow is described in detail to understand how the variations of mapping and fitting of experimental data affect the power balance solution and subsequent flux-matching plasma profile predictions with the TGYRO solver. On average, the predicted plasma profiles are consistent with experimental data. However, the solutions are sensitive to various input parameters, including boundary conditions, and the electron-ion coupling. Linear gyrokinetic stability analysis demonstrates close agreement of the real frequencies of unstable modes between TGLF and CGYRO gyrokinetic simulations, but higher growth rates are predicted by TGLF, especially for the H-mode case. Estimates of the low-k modes' contributions to the total flux are consistent with linear stability analysis and the E × B suppression of turbulence in TGLF simulations with the SAT1 saturation model, while the SAT2 saturation model over-predicts the low-k modes' contribution in the H-mode case. Moreover, the results with SAT1 model are consistent with power balance analysis, which indicates only neoclassical ion energy fluxes inside ρ < 0.4 in the L-mode case and $\rho \unicode{x2A7D} 0.7$ in the H-mode case. The presence of multi-scale turbulence and ion-scale driven zonal flow mixing effects are also observed in TGLF scans of the electron turbulent heat flux over a range of temperature gradients and the electron-ion temperature ratio, which could explain the strong model sensitivity to variations of input parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Arabidopsis lipins mediate lipid droplet biogenesis to protect cells from lipotoxicity

Lipin proteins, a family of phosphatidic acid phosphatases (PAHs), are key regulators of lipid metabolism, storage, and homeostasis across eukaryotes. While Arabidopsis (Arabidopsis thaliana) lipins function in lipid biosynthesis and gene regulation, their roles in lipid droplet (LD) biogenesis and lipid homeostasis remain largely unknown. Here, we show that double knockout of two PAH genes (PAH1/2) results in impaired LD biogenesis, accelerated triacylglycerol (TAG) hydrolysis, and lipid imbalance. pah1/2 mutant leaves exhibited a marked reduction in TAG levels and a significant decrease in LD size, while the rates of TAG and diacylglycerol (DAG) synthesis remained largely unchanged. In seeds, PAH1/2 disruption minimally affected TAG content but significantly reduced LD size. Fatty acid feeding experiments demonstrated impaired LD formation and increased lipotoxicity in pah1/2 leaves and seedlings. Furthermore, knockout of PAH1/2 in mutants with enhanced fatty acid flux through phosphatidylcholine (PC) led to severe reductions in leaf TAG levels, despite increases in TAG synthesis rates, indicating accelerated TAG turnover. Phosphatidic acid, free fatty acids, and PC accumulated, leading to massive proliferation of endoplasmic reticulum membranes and severe growth and developmental defects. These findings demonstrate evolutionarily conserved roles for PAH1/2 in LD biogenesis, membrane lipid homeostasis, and cellular protection against lipotoxicity, particularly under conditions of elevated fatty acid flux.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

New Compounds and Phase Selection of Nickel Sulfides via Oxidation State Control in Molten Hydroxides

Molten salts are promising reaction media candidates for the discovery of novel materials; however, they offer little control over oxidation state compared to aqueous solutions. Here, we demonstrated that when two hydroxides are mixed, their melts become fluxes with tunable solubility, which are surprisingly powerful solvents for ternary chalcogenides and offer effective paths for crystal growth to new compounds. We report that precise control of the oxidation state of Ni is achievable in mixed molten LiOH/KOH to grow single crystals of all known ternary K-Ni-S compounds. It is also possible to access several new phases, including a new polytope of β-K 2 Ni 3 S 4 , as well as low-valence KNi 4 S 2 and K 4 Ni 9 S 11 . KNi 4 S 2 is a two-dimensional low-valence nickel-rich sulfide, and β-K 2 Ni 3 S 4 has a hexagonal lattice. Moreover, using KNi 4 S 2 as a template, we obtained a new layered binary Ni 2 S by topotactic deintercalation of K. The new binary Ni 2 S has a van der Waals gap and can function as a new host layer for intercalation chemistry, as demonstrated by the intercalation of LiOH between its layers. The oxidation states of low-valence KNi 4 S 2 and Ni 2 S were studied using X-ray absorption spectroscopy and X-ray photoelectron spectroscopy. Density functional theory calculations showed large antibonding interactions at the Fermi level for both KNi 4 S 2 and Ni 2 S 2 corresponding to the flat-bands with large Ni-d$_{x^2}$$_{y^2}$ character.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Self-regulated growth of candidate topological superconducting parkerite by molecular beam epitaxy

Ternary chalcogenides, such as parkerites and shandites, are a broad class of materials exhibiting a rich diversity of transport and magnetic behavior and an array of topological phases, including Weyl and Dirac nodes. However, they remain largely unexplored as high-quality epitaxial thin films. Here, we report the self-regulated growth of thin films of the strong spin–orbit coupled superconductor Pd 3 Bi 2 Se 2 on SrTiO 3 by molecular beam epitaxy. Films are found to grow in a self-regulated fashion, where, in excess Se, the temperature and relative flux ratio of Pd to Bi control the formation of Pd 3 Bi 2 Se 2 due to the combined volatility of Bi, Se, and Bi–Se bonded phases. The resulting films are shown to be of high structural quality, and the stoichiometry is independent of the Pd:Bi and Se flux ratio and exhibits a superconducting transition temperature of 800 mK and a critical field of 17.7 ± 0.5 mT, as probed by transport and magnetometry. Understanding and navigating the growth of the chemically and structurally diverse classes of ternary chalcogenides open a vast space for discovering new phenomena and enabling new applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Establishing Validation Sites for Field-Level Emissions Quantification from Grain Sorghum in Southern Great Plains

Establish publicly available open-source, high-resolution datasets of greenhouse gas (GHG) emissions, meteorology, soil, and vegetation to support testing and validation of emerging biofuel production monitoring technologies. The project team deployed latest technologies to collect “Gold Standard” data for field- level fluxes of CO 2 , N 2 O, CH 4 and H 2 O in grain sorghum production systems in Texas, Oklahoma, and Kansas. The Oklahoma State University led SMARTFARM was initiated on Oct 1, 2020, due to COVID-19 pandemic delay. We installed closed-path dual laser Eddy Covariance (EC) flux measurement system along with a well-established open-path EC system for simultaneously measuring field-level fluxes of CO 2 , N 2 O, CH 4 , and H2O. The eddy flux data are combined with sub-acre soil moisture and temperature measurements, plant and soil analysis data (nutrient, composition, carbon, growth, and phenology), spatial surveys of soil EC, and pH. Grain sorghum crop was managed including planting and harvesting by producers. All teams recruited postdocs and students for the project and submitted purchase orders for field equipment. The team has developed a draft impact sheet and finalized the advisory board for the project.

09 BIOMASS FUELS↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

13 C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions

Carbon dioxide-fixing acetogenic bacteria (acetogens) utilizing the Wood-Ljungdahl Pathway (WLP) play an important role in CO 2 fixation in the biosphere and in the development of biological processes – alone or in cocultures, under both autotrophic and mixotrophic conditions – for production of chemicals and fuels. To date, limited work has been reported in experimentally validating and quantifying reaction fluxes of their core metabolic pathways. Here, the core metabolic model of the acetogen Clostridium ljungdahlii was interrogated using 13 C-metabolic flux analysis ( 13 C-MFA), which required the development of a new defined culture medium. Autotrophic, heterotrophic, and mixotrophic growth in defined medium was possible by adding 1 mM methionine to replace yeast extract. Our 13 C-MFA found an incomplete TCA cycle and inactive core pathways/reactions, notably those of the oxidative pentose phosphate pathway, Entner-Doudoroff pathway, and malate dehydrogenase. 13 C-MFA during mixotrophic growth using the parallel tracers [1– 13 C]fructose, [1,2– 13 C]fructose, [1,2,3– 13 C]fructose, and [U– 13 C]asparagine found that externally supplied CO 2 contributed the majority of carbon consumed. All internally-produced CO 2 from the catabolism of asparagine and fructose was consumed by the WLP. While glycolysis of fructose was active, it was not a major contributor to overall production of ATP, NADH, and acetyl-CoA. Gluconeogenic reactions were active despite the availability of organic carbon. Asparagine was catabolized equally via conversion to threonine and subsequent cleavage to produce acetaldehyde and glycine, and via deamination to fumarate and then the anaplerotic conversion of malate to pyruvate. Both pathways for asparagine catabolism produced acetyl-CoA, either directly via pyruvate or indirectly via the WLP. Cofactor stoichiometry based on our data predicted an essentially zero flux through the ferredoxin-dependent transhydrogenase (Nfn) reaction. Instead, nearly all of NADPH generated from the hydrogenase reaction was consumed by the WLP. Reduced ferredoxin produced by the hydrogenase reaction and glycolysis was mostly used for ATP generation via the RNF/ATPase system, with the remainder consumed by the WLP. NADH produced by RNF/ATPase was entirely consumed via the WLP.

13C metabolic flux analysis↗