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Results for “kinetic modeling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

From Escherichia coli mutant 13 C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction. The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect of perturbations in metabolite concentrations and reaction fluxes in response to genetic and environmental perturbation that are beyond the scope of stoichiometric models. In this study, we develop a two-step computational pipeline for the rapid parameterization of kinetic models of metabolic networks using a curated metabolic model and available 13 C-labeling distributions under multiple genetic and environmental perturbations. The first step involves the elucidation of all intracellular fluxes in a core model of E. coli containing 74 reactions and 61 metabolites using 13 C-Metabolic Flux Analysis ( 13 C-MFA). Here, fluxes corresponding to the mid-exponential growth phase are elucidated for seven single gene deletion mutants from upper glycolysis, pentose phosphate pathway and the Entner-Doudoroff pathway. The computed flux ranges are then used to parameterize the same (i.e., k-ecoli74) core kinetic model for E. coli with 55 substrate-level regulations using the newly developed K-FIT parameterization algorithm. The K-FIT algorithm employs a combination of equation decomposition and iterative solution techniques to evaluate steady-state fluxes in response to genetic perturbations. k-ecoli74 predicted 86% of flux values for strains used during fitting within a single standard deviation of 13 C-MFA estimated values. By performing both tasks using the same network, errors associated with lack of congruity between the two networks are avoided, allowing for seamless integration of data with model building. Product yield predictions and comparison with previously developed kinetic models indicate shifts in flux ranges and the presence or absence of mutant strains delivering flux towards pathways of interest from training data significantly impact predictive capabilities. Using this workflow, the impact of completeness of fluxomic datasets and the importance of specific genetic perturbations on uncertainties in kinetic parameter estimation are evaluated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models

Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. Here, we transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Fully Kinetic versus Reduced-kinetic Modeling of Collisionless Plasma Turbulence

We report the results of a direct comparison between different kinetic models of collisionless plasma turbulence in two spatial dimensions. The models considered include a first-principles fully kinetic (FK) description, two widely used reduced models (gyrokinetic (GK) and hybrid-kinetic (HK) with fluid electrons), and a novel reduced gyrokinetic approach (KREHM). Two different ion beta (β{sub i}) regimes are considered: 0.1 and 0.5. For β{sub i}=0.5, good agreement between the GK and FK models is found at scales ranging from the ion to the electron gyroradius, thus providing firm evidence for a kinetic Alfvén cascade scenario. In the same range, the HK model produces shallower spectral slopes, presumably due to the lack of electron Landau damping. For β{sub i}=0.1, a detailed analysis of spectral ratios reveals a slight disagreement between the GK and FK descriptions at kinetic scales, even though kinetic Alfvén fluctuations likely still play a significant role. The discrepancy can be traced back to scales above the ion gyroradius, where the FK and HK results seem to suggest the presence of fast magnetosonic and ion Bernstein modes in both plasma beta regimes, but with a more notable deviation from GK in the low-beta case. The identified practical limits and strengths of reduced-kinetic approximations, compared here against the FK model on a case-by-case basis, may provide valuable insight into the main kinetic effects at play in turbulent collisionless plasmas, such as the solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Isomeric effects on the reactivity of branched alkenes: An experimental and kinetic modeling study of methylbutenes

Here, a detailed experimental study of the low-to-intermediate temperature combustion of methylbutene isomers, i.e., branched C 5 alkenes, has been undertaken with multiple experimental facilities. Ignition delay times were measured at equivalence ratios 0.5–2.0, 685–1020 K and up to 45 bar condition from two rapid compression machines and showed slight deviation from an Arrhenius behavior for all three isomers, while their reactivity order differs as temperature changes. Sampled intermediates formed during the oxidation process of mixtures at 900–1150 K and 0.82 bar from a flow reactor and at 730 K and 20 bar from a rapid compression machine were analyzed using gas chromatography techniques. Trends in the formation and consumption of sampled intermediates were modeled using a kinetic model developed in this work for all three isomers. Rate of production and sensitivity analyses emphasize the role of double bond-specific reactions governing the global reactivity of these fuels. Additional studies of the addition reactions of HO 2 radicals to the double bond and to allylic radicals may improve the model performance.

2-Methyl-1-butene↗
DOE OSTI2016

Kinetic model for the collisionless sheath of a collisional plasma

Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. These predictions are contrasted here with direct kinetic simulations, showing good agreement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Kinetic Modeling of Secondary Organic Aerosol in a Weather-Chemistry Model: Parameterizations, Processes, and Predictions for GOAmazon

Secondary organic aerosol (SOA) forms and evolves in the atmosphere through many pathways and processes, over diverse spatial and time scales. Hence, there is a need to represent these widely-varying kinetic processes in large-scale atmospheric models to allow for accurate predictions of the abundance, properties, and impacts of SOA. In this work, we integrated a kinetic, process-level model (simpleSOM-MOSAIC) into a weather-chemistry model (WRF-Chem) to simulate the oxidation chemistry and microphysics of atmospheric SOA. simpleSOM-MOSAIC simulates multigenerational gas-phase chemistry, autoxidation reactions, heterogeneous oxidation, oligomerization, and phase-state-influenced gas/particle partitioning of SOA. As a case study, the integrated WRF-Chem-simpleSOM-MOSAIC (WC-SSM) model was used to simulate the photochemical evolution downwind of a large city (Manaus, Brazil) in the Amazon and, in turn, study the anthropogenic and biogenic interactions in an otherwise pristine environment. Consistent with previous work, we found that OA was enhanced by up to a factor of four in the urban plume due to elevated hydroxyl radical (OH) concentrations, relative to the background, and that this OA was dominated by SOA from biogenic precursors (80%). Further, in addition to accurately simulating the OA enhancement in the urban plume, the model reproduced the magnitude of the OA oxygen-to-carbon (O:C) ratio and broadly tracked the evolution of the aerosol size distribution. Our work highlights the importance of including an integrated, kinetic representation of SOA processes in an atmospheric model

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

An experimental and chemical kinetic modeling study of 4-butoxyheptane combustion

Here, the combustion kinetics of a novel oxygenated bioblendstock for diesel, 4-butoxyheptane (4-BH), was investigated experimentally using a flow reactor and a heated, high-pressure shock tube. The flow reactor experiments employed oxygen as the oxidizer and helium as the diluent with oxidation conducted at atmospheric pressure and 10 bar for temperatures from 400 to 1000 K at 20-K intervals. The fuel, oxidizer, and diluent flow rates were varied at different temperatures to maintain a constant initial fuel mole fraction of 1000 ppm, with stoichiometric equivalence ratio, and a residence time of 2.0 s. The reacted gas was fed to two separate GC systems that could qualitatively and quantitatively detect product species. Additionally, real fuel-air ignition delay time (IDT) data were collected using a heated, high-pressure shock-tube facility. Fuel lean (φ = 0.5) and stoichiometric (φ = 1.0) mixtures were investigated at 10 atm as well as at 30 atm for the fuel lean case for temperatures between 847 and 1259 K. A detailed chemical kinetics mechanism was developed to model the product distribution from the flow reactor and IDTs from the shock tube. The proposed model was able to predict the double NTC behavior in flow reactor experiments reasonably well. Model predictions at low temperatures were observed to be highly sensitive to the rate constants of ketohydroperoxide (KHP) decomposition in the case of the OOH group in α position which were modeled based on existing literature studies on ethers. It was noted that in the absence of theoretical or experimental studies, the rate constants for KHP decomposition used in the literature were empirically set. Additional studies are required to address the gap in model prediction obtained in this study and to reduce the uncertainty in kinetics models for ether oxidation. Predicted product concentrations and IDTs showed some quantitative agreement with experimental data, but the overall reactivity of the IDTs is underpredicted. Additionally, significant deviation is observed for the IDT results at 10 atm for the stoichiometric case with minor deviations for the other cases. The reaction pathways to the missing products were then further analyzed theoretically through quantum-mechanical calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A kinetic model for stress generation in thin films grown from energetic vapor fluxes

We have developed a kinetic model for residual stress generation in thin films grown from energetic vapor fluxes, encountered, e.g., during sputter deposition. The new analytical model considers sub-surface point defects created by atomic peening, along with processes treated in already existing stress models for non-energetic deposition, i.e., thermally activated diffusion processes at the surface and the grain boundary. According to the new model, ballistically induced sub-surface defects can get incorporated as excess atoms at the grain boundary, remain trapped in the bulk, or annihilate at the free surface, resulting in a complex dependence of the steady-state stress on the grain size, the growth rate, as well as the energetics of the incoming particle flux. We compare calculations from the model with in situ stress measurements performed on a series of Mo films sputter-deposited at different conditions and having different grain sizes. The model is able to reproduce the observed increase of compressive stress with increasing growth rate, behavior that is the opposite of what is typically seen under non-energetic growth conditions. On a grander scale, this study is a step towards obtaining a comprehensive understanding of stress generation and evolution in vapor deposited polycrystalline thin films.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Continuum kinetic modeling of the tokamak plasma edge

The first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalous radial transport.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Styrene Thermal Decomposition and Its Reaction with Acetylene under Shock Tube Pyrolysis Conditions: an Experimental and Kinetic Modeling Study

Styrene is an important compound for polymer production and a key intermediate in gas-phase kinetics of polycyclic aromatic hydrocarbons (PAHs). For the first time, the pyrolysis of styrene with and without the presence of acetylene is investigated in a single-pulse shock tube coupled to gas chromatography and mass spectrometry. For each reaction system, quantitative speciation profiles are probed within the temperature range of 1100-1730 K, nominal pressure of 20 bar, and reaction duration of similar to 4 ms. A kinetic model is built to simulate the results. The model explains how styrene is consumed under high-pressure pyrolytic conditions, how the secondary chemistry of intermediate products affect subsequent PAH formation, and how acetylene addition alters the reaction pathways. Throughout the temperature range, styrene breakdown is dominated by the bimolecular interaction between styrene and hydrogen atom, which produces benzene+vinyl or phenyl and ethylene through the stabilization of 2-phenylethyl and its subsequent dissociation. As a result, large amounts of phenyl accumulate, which react with styrene to form C14H12 species while simultaneously releasing H atoms through addition/elimination reactions. The reactivity of fuel consumption is preserved by the regeneration of H atoms as chain carriers. Several C14H10 compounds are formed as a result of the following breakdown of the C14H12 isomers, particularly stilbene, 1,1-diphenyl ethylene, and 9-methyl-9H-fluorene. The presence of acetylene as a co-reactant with styrene allows the Hydrogen-Abstraction-Acetylene-Addition (HACA) pathway to proceed from phenyl radical to enhance the production of phenylacetylene at very low temperatures and acenaphthylene. This hinders the formation of C14H12 isomers, exclusive products from pure styrene dissociation by competing with the styrene+phenyl routes.

Kinetic Modeling↗
DOE OSTI2025

Kinetic Model of Photochemical Nitrogen Reduction [SWR-25-97]

The code in this repository was used to model the kinetics of photochemical nitrogen reduction. Each directory represents a manuscript. The directory titled Dahl_CRPS_2025 contains the code used to fit the kinetic models presented in the manuscript titled, "Pre-steady-state kinetics of nanocrystal:molybdenum nitrogenase biohybrids reveals hole-scavenging efficiency is critical to achieving N2 reduction" by Peter J. Dahl, Lauren M. Pellows, Zhi-Yong Yang, Lance C. Seefeldt, John W. Peters, Gordana Dukovic, David W. Mulder, and Paul W. King. Molybdenum (Mo) nitrogenase is a two-component enzyme complex that catalyzes the reduction of dinitrogen to ammonia and protons to hydrogen gas. We have shown that electrons for dinitrogen reduction can be delivered photochemically to the catalytic MoFe protein component by CdS nanocrystals. In this study, we used electron paramagnetic resonance spectroscopy to measure the transient populations of catalytic intermediates. We fit the populations with a pre-steady-state kinetic model which allowed us to distinguish between productive and non-productive reaction pathways and extract the rate constants for the reaction. Our results demonstrated that the rate of catalytic electron delivery into MoFe protein increased with the concentration of sacrificial electron donor. This enabled electron delivery to exceed the rate of hydride protonation, a relaxation pathway which competes with N2 binding. Thus, managing the balance between electron transfer and hole transfer reactions is required to achieve a kinetic regime that favors N2 reduction.

Dahl, Peter [National Renewable Energy Laboratory ↗