Chemical Kinetic Simulations Research Articles

N2O molecular tagging velocimetry

A new seeded velocity measurement technique, N2O molecular tagging velocimetry (MTV), is developed to measure velocity in wind tunnels by photochemically creating an NO tag line. Nitrous oxide “laughing gas” is seeded into the air flow. A 193 nm ArF excimer laser dissociates the N2O to O(1D) that subsequently reacts with N2O to form NO. O2 fluorescence induced by the ArF laser “writes” the original position of the NO line. After a time delay, the shifted NO line is “read” by a 226-nm laser sheet and the velocity is determined by time-of-flight. At standard atmospheric conditions with 4% N2O in air, ∼1000 ppm of NO is photochemically created in an air jet based on experiment and simulation. Chemical kinetic simulations predict 800–1200 ppm of NO for 190–750 K at 1 atm and 850–1000 ppm of NO for 0.25–1 atm at 190 K. Decreasing the gas pressure (or increasing the temperature) increases the NO ppm level. The presence of humid air has no significant effect on NO formation. The very short NO formation time (<10 ns) makes the N2O MTV method amenable to low- and high-speed air flow measurements. The N2O MTV technique is demonstrated in air jet to measure its velocity profile. The N2O MTV method should work in other gas flows as well (e.g., helium) since the NO tag line is created by chemical reaction of N2O with O(1D) from N2O photodissociation and thus does not depend on the bulk gas composition.

Tabulated chemistry approaches for laminar flames: Evaluation of flame-prolongation of ILDM and flamelet methods

The present study considers the performance of tabulation methods for numerical simulation of complex chemical kinetics in laminar combusting flows and compares their predictions to results obtained by direct calculation. Two tabulation methods are considered: the Flame Prolongation of Intrinsic low-dimensional manifold (FPI) method and Steady Laminar Flamelet Model (SLFM). The FPI method is of current interest as it is a potentially unifying approach capable of dealing with both premixed and non-premixed flames for gaseous fuels. SLFM tabulation methods are popular for non-premixed flames and form a good basis for comparing the performance of the FPI approach. The performance of each method is also evaluated by comparing the results to the direct simulation of the laminar flames using two chemical kinetic schemes: simplified chemistry involving five species and one reaction and detailed chemistry involving 53 species and 325 reaction steps. As part of the evaluation process, the computational cost of each method is also assessed. The laminar flames considered in this study include: freely propagating laminar premixed flames, a two-dimensional axisymmetric methane–air opposed-jet diffusion flame, and a two-dimensional axisymmetric methane–air co-flow diffusion flame. Both tabulation methods are implemented in a parallel adaptive mesh refinement (AMR) framework for solving the complete set of governing partial differential equations. These equations are solved using a fully-coupled finite-volume formulation on body-fitted multi-block quadrilateral mesh. Significant improvements in terms of reduced computational requirements, as measured by both storage and processing time, are demonstrated for the tabulated methods.

Chemical Kinetic Study of Nitrogen Oxides Formation Trends in Biodiesel Combustion

The use of biodiesel in conventional diesel engines results in increasedNOxemissions; this presents a barrier to the widespread use of biodiesel. The origins of this phenomenon were investigated using the chemical kinetics simulation tool: CHEMKIN-2 and the CFD KIVA3V code, which was modified to account for the physical properties of biodiesel and to incorporate semidetailed mechanisms for its combustion and the formation of emissions. Parametric ϕ-T maps and 3D engine simulations were used to assess the impact of using oxygen-containing fuels on the rate of NO formation. It was found that using oxygen-containing fuels allows more O2molecules to present in the engine cylinder during the combustion of biodiesel, and this may be the cause of the observed increase in NO emissions.

A Study of HCCI Combustion Using Spectroscopic Measurements and Chemical Kinetic Simulations: Effects of Fuel Composition, Engine Speed and Cylinder Pressure on Low-temperature Oxidation Reactions and Autoignition

A Study of HCCI Combustion Using Spectroscopic Measurements and Chemical Kinetic Simulations: Effects of Fuel Composition, Engine Speed and Cylinder Pressure on Low-temperature Oxidation Reactions and Autoignition

The effect of CO 2/H 2O on the formation of soot particles in the homogeneous environment of a rapid compression facility

Previous investigations show that soot particle volume fraction and number density were significantly reduced by exhaust gas recirculation (EGR) diluents CO 2 and H 2O. However, these investigations were often convoluted by their experimental flame configurations and primarily focused on soot volume fraction rather than soot inception. To isolate the effects on soot inception and the corresponding chemistry, the current study measured the reactivity of CO 2 (up to 9.5% volume fraction) for both C 2H 2 (1.00% volume fraction) and CH 4 (1.85% volume fraction) fuels in homogeneous mixtures. Computed effect of H 2O on these and other fuels are also presented. Experiments were performed at high temperature (1640 K and 1770 K) and high equivalence ratios ( Φ = 55 and 75) to understand the effect of CO 2 on polycyclic aromatic hydrocarbons (PAH) and formation of nascent soot particles with negligible oxygen influence. Experimental results show that CO 2 enhanced the soot inception rate when added to C 2H 2 but had an undetectable affect on CH 4. Gas chromatography confirmed that CO 2 increases CO mole fraction and reduces C 2H 2 fuel concentration. Chemical kinetic simulations showed that the C 2H 2 was being converted to soot precursors. CO 2 enhanced the soot inception rate for C 2H 2 by producing OH radicals. Images of nascent soot particles produced in the presence of CO 2 were used to determine the size of PAH molecules in the particles and particle morphology. Both attributes were similar to particles formed without CO 2. CO 2 had little impact on the long reaction pathway from CH 4 to PAH molecules because H and CH 3 radicals propagated these reactions more readily than OH radicals.

Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS- α method

Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic α (FIS α) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway.

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation

BackgroundThe yeast Saccharomyces cerevisiae responds to amino acid starvation by inducing the transcription factor Gcn4. This is mainly mediated via a translational control mechanism dependent upon the translation initiation eIF2·GTP·Met-tRNAiMet ternary complex, and the four short upstream open reading frames (uORFs) in its 5' mRNA leader. These uORFs act to attenuate GCN4 mRNA translation under normal conditions. During amino acid starvation, levels of ternary complex are reduced. This overcomes the GCN4 translation attenuation effect via a scanning/reinitiation control mechanism dependent upon uORF spacing.ResultsUsing published experimental data, we have developed and validated a probabilistic formulation of GCN4 translation using the Chemical Master Equation (Model 1). Model 1 explains GCN4 translation's nonlinear dependency upon uORF placements, and predicts that an as yet unidentified factor, which was proposed to regulate GCN4 translation under some conditions, only has pronounced effects upon GCN4 translation when intercistronic distances are unnaturally short. A simpler Model 2 that does not include this unidentified factor could well represent the regulation of a natural GCN4 mRNA. Using parameter values optimised for this algebraic Model 2, we performed stochastic simulations by Gillespie algorithm to investigate the distribution of ribosomes in different sections of GCN4 mRNA under distinct conditions. Our simulations demonstrated that ribosomal loading in the 5'-untranslated region is mainly determined by the ratio between the rates of 5'-initiation and ribosome scanning, but was not significantly affected by rate of ternary complex binding. Importantly, the translation rate for codons starved of cognate tRNAs is predicted to be the most significant contributor to the changes in ribosomal loading in the coding region under repressing and derepressing conditions.ConclusionsOur integrated probabilistic Models 1 and 2 explained GCN4 translation and helped to elucidate the role of a yet unidentified factor. The ensuing stochastic simulations evaluated different factors that may impact on the translation of GCN4 mRNA, and integrated translation status with ribosomal density.

SIMULATION VERSUS DESIGN: TWO CASE STUDIES IN CHEMICAL REACTION KINETICS AND RADIATIVE HEAT TRANSFER

This paper describes two instructional modules pertaining to engineering design education and developed via two design approaches. The first module concerns itself with experimental simulation of chemical reaction kinetics using the analogy with the free-fall of a non-viscous liquid in ducts of various shapes. The second module is concerned with computer simulation of heat exchange via thermal radiation in a 3-D enclosure with nontrivial features. Both modules involve a series of case studies to enhance students understanding of the engineering concepts under consideration and to expose them to the power of both experimental and computer designs.

Implementation of Net-Event Monte Carlo algorithm in chemical kinetics simulation software of complex isothermal reacting systems

Many stochastic methods are available for kinetic simulation of a spatially homogeneous chemical or biochemical reacting system. These methods become time costing for very complex systems with huge mechanism as in combustion reactions or even with moderate mechanism with stiffness. In this work, a new algorithm based on Net-Event Kinetic Monte Carlo (NEKMC) method is implemented to improve the Kinetic Monte Carlo (KMC) method of simulation by reducing the calculation time. A set of N reversible reactions, in a given mechanism, is considered as 2N elementary reactions in the KMC method, but in the NEKMC method just N reactions are considered. For each reversible reaction, the net-probability can be calculated by using the absolute value of the difference between the rates of the forward and the reverse reaction. By doing this, the number of events is divided by two and should reduce consequently the calculation time. This new method (NEKMC) is described and tested on complex systems and speediness of the program is compared for this method to the old one (KMC).

Implicit Second Order Weak Taylor Tau-Leaping Methods for the Stochastic Simulation of Chemical Kinetics

For biochemical systems, when some chemical species are represented by small numbers of molecules, discrete and stochastic approaches are more appropriate than continuous and deterministic approaches. The stochastic simulation algorithm (SSA), proposed by Gillespie, is a cardinal simulation method for the chemical kinetics. Because the SSA simulates every reaction event, the amount of the computational time is huge when models have many reaction channels and species. Therefore there have been many alternative algorithms whose goal is to improve the computational efficiency of the SSA. In this paper we use stochastic Taylor expansions to propose implicit second order weak Taylor tau-leaping methods for the stochastic simulation of chemical kinetics. These methods are motivated by the theory of weakly convergent discretizations of stochastic differential equations. Three different schemes of the second order weak Taylor tau-leaping methods are numerically tested to demonstrate the performance with accuracy.

Simulating Kinetic Processes in Time and Space on a Lattice

We have developed a chemical kinetics simulation that can be used as both an educational and research tool. The simulator is designed as an accessible, open-source project that can be run on a laptop with a student-friendly interface. The application can potentially be scaled to run in parallel for large simulations. The simulation has been successfully used in a classroom setting for teaching basic electrochemical properties. We have shown that this can be used for simulating fundamental molecular and chemical processes and even simplified models of predator–prey interactions. By giving the simulated entities spatial extent in the lattice, the particles do not interpenetrate, and clusters of particles can spatially exclude one another. Our simulation demonstrates that spatial inhomogeneity leads to different results than those that are obtained by using standard ordinary differential equation models, as previously reported.

A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA)

We present a simple algorithm for the simulation of stiff, discrete-space, continuous-time Markov processes. The algorithm is based on the concept of flow averaging for the integration of stiff ordinary and stochastic differential equations and ultimately leads to a straightforward variation of the the well-known stochastic simulation algorithm (SSA). The speedup that can be achieved by the present algorithm [flow averaging integrator SSA (FLAVOR-SSA)] over the classical SSA comes naturally at the expense of its accuracy. The error of the proposed method exhibits a cutoff phenomenon as a function of its speed-up, allowing for optimal tuning. Two numerical examples from chemical kinetics are provided to illustrate the efficiency of the method.

ChemKinetics: Fundamental Chemical Kinetics Principles and Analysis by Computer Simulation

The ChemKinetics software is a chemical kinetics simulator and tutorial package that incorporates simple first-order irreversible, first-order reversible, first-order parallel, first-order consecutive, simple second-order, and general second-order irreversible processes.

Forward, tangent linear, and adjoint Runge–Kutta methods for stiff chemical kinetic simulations

This paper investigates numerical methods for direct decoupled sensitivity and discrete adjoint sensitivity analysis of stiff systems based on implicit Runge–Kutta schemes. Efficient implementations of tangent linear and adjoint schemes are discussed for two families of methods: fully implicit three-stage Runge–Kutta and singly diagonally-implicit Runge–Kutta. High computational efficiency is attained by exploiting the sparsity patterns of the Jacobian and Hessian. Numerical experiments with a large chemical system used in atmospheric chemistry illustrate the power of the stiff Runge–Kutta integrators and their tangent linear and discrete adjoint models. Through the integration with the Kinetic PreProcessor KPP–2.2 these numerical techniques become readily available to a wide community interested in the simulation of chemical kinetic systems.

Isobutane ignition delay time measurements at high pressure and detailed chemical kinetic simulations

Isobutane ignition delay time measurements at high pressure and detailed chemical kinetic simulations

Integrated gas dynamic computational modelling and thermodynamic combustion diagnostics of multicylinder four-stroke spark ignition engine using compressed natural gas as a fuel

A comprehensive computational simulation model has been developed to describe the performance, efficiency and emission characteristics of the four-stroke multi-cylinder spark ignition engine which uses compressed natural gas as a fuel. This model performs an integrated simulation of thermodynamic, gas dynamic, and chemical kinetics of the whole engine system coupling with intake and exhaust manifolds. The thermodynamic combustion process is modelled by using the turbulent flame propagation process with a two-zone chamber (burned and unburned). Gas dynamics in the manifold system are modelled by using unsteady compressible hyperbolic partial differential equations. These equations contain heat transfer, friction, area change in pipe and empirical constants, which are used to determine boundary conditions at pipe junctions, valves and open ends. These equations are transferred into a set of ordinary differential equations by applying the method of characteristics and are solved by the finite difference method. Regarding exhaust emissions, nitric oxide concentrations have been predicted by using the rate kinetic model in the power cycle and along the exhaust pipes. Carbon monoxide is computed under the chemical equilibrium condition and then the empirical adjustment is made for kinetic behaviours based upon experimental results. Finally, predicted results of this model have been compared with experimental results and are found to be compatible. The parametric studies have been conducted with the equivalence ratio and the engine RPM, to predict engine performance. Also, the variations of pressure, temperature, and gas compositions in the exhaust system have been studied.

N-Butane: Ignition delay measurements at high pressure and detailed chemical kinetic simulations

Ignition delay time measurements were recorded at equivalence ratios of 0.3, 0.5, 1, and 2 for n-butane at pressures of approximately 1, 10, 20, 30 and 45 atm at temperatures from 690 to 1430 K in both a rapid compression machine and in a shock tube. A detailed chemical kinetic model consisting of 1328 reactions involving 230 species was constructed and used to validate the delay times. Moreover, this mechanism has been used to simulate previously published ignition delay times at atmospheric and higher pressure. Arrhenius-type ignition delay correlations were developed for temperatures greater than 1025 K which relate ignition delay time to temperature and concentration of the mixture. Furthermore, a detailed sensitivity analysis and a reaction pathway analysis were performed to give further insight to the chemistry at various conditions. When compared to existing data from the literature, the model performs quite well, and in several instances the conditions of earlier experiments were duplicated in the laboratory with overall good agreement. To the authors’ knowledge, the present paper presents the most comprehensive set of ignition delay time experiments and kinetic model validation for n-butane oxidation in air.

Structures and burning velocity of biomass derived gas flames

Biomass derived gases produced via gasification, pyrolysis, and fermentation are carbon neutral alternative fuels that can be used in gas turbines, furnaces, and piston engines. To make use of these environmentally friendly but energy density low fuels the combustion characteristics of these fuels have to be fully understood. In this study the structure and laminar burning velocity of biomass derived gas flames are investigated using detailed chemical kinetic simulations. The studied gaseous fuels are the air-blown gasification gas, co-firing of gasification gas with methane, pyrolysis gases, landfill gases, and syngas, a mixture of carbon monoxide and hydrogen. The simulated burning velocities of reference fuel mixtures using two widely used chemical kinetic mechanisms, GRI Mech 3.0 and the San Diego mechanism, are compared with the experimental data to explore the uncertainties and scattering of the simulation data. The different chemical kinetic mechanisms are shown to give a reasonable agreement with each other and with experimental data, with a discrepancy within 7% over most of the conditions. The results show that the structures of typical landfill gas flames and co-firing of methane/gasification gas flames share essential similarity with methane flames. The reaction zones of these flames consist of a thin inner layer and a relatively thick CO/H-2 oxidation layer. In the inner layer hydrocarbon fuel (methane) is converted through chain reactions to intermediates such as CH3, CH2O, CO, H-2, etc. The structures of gasification gas flames, pyrolysis gas flames, syngas flames share similarity with the oxidization layer of the methane/air flames. Overall, the chemical reactions of all biomass derived gas flames occur in thin zones of the order of less than 1 mm. The thickness of all BDG gas flames is inversely proportional to their respective laminar burning velocity. The laminar burning velocities of landfill gases are found to increase linearly with the mole fraction of methane in the mixtures, whereas for gasification gas, syngas and pyrolysis gas where hydrogen is present, the laminar burning velocities scale linearly with the mole fraction of hydrogen. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved. (Less)

Mixing and flame structures inferred from OH-PLIF for conventional and low-temperature diesel engine combustion

The structure of first- and second-stage combustion is investigated in a heavy-duty, single-cylinder optical engine using chemiluminescence imaging, Mie-scatter imaging of liquid-fuel, and OH planar laser-induced fluorescence (OH-PLIF) along with calculations of fluorescence quenching. Three different diesel combustion modes are studied: conventional non-diluted high-temperature combustion (HTC) with either (1) short or (2) long ignition delay, and (3) highly diluted low-temperature combustion (LTC) with early fuel injection. For the short ignition delay HTC condition, the OH fluorescence images show that second-stage combustion occurs mainly on the fuel jet periphery in a thickness of about 1 mm. For the long ignition delay HTC condition, the second-stage combustion zone on the jet periphery is thicker (5–6 mm). For the early-injection LTC condition, the second-stage combustion is even thicker (20–25 mm) and occurs only in the down-stream regions of the jet. The relationship between OH concentration and OH-PLIF intensity over a range of equivalence ratios is estimated from quenching calculations using collider species concentrations predicted by chemical kinetics simulations of combustion. The calculations show that both OH concentration and OH-PLIF intensity peak near stoichiometric mixtures and fall by an order of magnitude or more for equivalence ratios less than 0.2–0.4 and greater than 1.4–1.6. Using the OH fluorescence quenching predictions together with OH-PLIF images, quantitative boundaries for mixing are established for the three engine combustion modes.