Chemical Kinetics Simulator

Hinsberg, W. Houle, F. "Chemical Kinetics Simulation," http //www.almaden.ibm.com/st/computational science/ck/msim/7overview, (Accessed May 22, 2006). 

All of the individual steps in Scheme 15 have been observed and characterized independently, making this a particularly attractive case for kinetic simulations. This was done by use of the program Chemical Kinetics Simulator (IBM). Simulated traces reproduced the experimental data in every detail. This includes the rapid initial drop in absorbance at 290 nm and the smooth, remaining portion that obeyed second order kinetics. The rapid initial step generates the equilibrium amount of CraqOON02+, which throughout... 

TST, and/or MD simulations (the choice depends mainly on whether the process is activated or not). The creation of a database, a lookup table, or a map of transition probabilities for use in KMC simulation emerges as a powerful modeling approach in computational materials science and reaction arenas (Maroudas, 2001 Raimondeau et al., 2001). This idea parallels tabulation efforts in computationally intensive chemical kinetics simulations (Pope, 1997). In turn, the KMC technique computes system averages, which are usually of interest, as well as the probability density function (pdf) or higher moments, and spatiotemporal information in a spatially distributed simulation. 

Another way of generating reaction schemes consisting of global reactions is to fit the parameters of one or a few global reactions to some kind of kinetic data. The data may come from experiments or detailed chemical kinetic simulations. Fitting a small kinetic scheme requires the optimization of the parameters of a system of ordinary differential equations. If the reaction scheme consists of elementary reactions, and the parameters are optimized only within the physically feasible boundaries, the approach of the GRI mechanism (Section 4.3.7) is reproduced. The fitting of parameters in small schemes is described in the following sections. 

W.R. Leppard, A Detailed Chemical Kinetics Simulation of Engine Knock, Comb. Sci. Tech. 43 (1985) 1. 

Efficient and accurate numerical solution of chemical kinetic simulations, and... 

The challenge of documenting large chemical kinetic simulations... 

Fig. 4. The inputs needed to construct a chemical kinetic simulation. The Chemistry Knowledge underlying the model is embedded in the functional group database. This is the most important input to any large kinetic model, but also the most challenging to obtain and to document.

The methods described in Section II carry out the first step in Fig. 1, constructing a detailed chemical kinetic model from our current understanding of chemistry. However, this step is only useful if we can numerically solve the chemical kinetic simulation to obtain quantitative predictions. In many cases, solving the model is even more challenging than constructing it. 

Below we present 21st century numerical solution methods suitable for large chemical kinetic simulations. We present both a method that does not introduce any approximations, and an automated model-reduction method that allows rigorous error control in steady-state simulations. 

Frequently, the next step after numerically solving a chemical kinetic simulation is to compare the model predictions with some experimental data, to check whether it is consistent with reality at least in one case. This is called validating the model. In the 20th century, it was a common practice to plot chemical kinetic model predictions with some experimental data, without any attempt to indicate the uncertainties in either. The reader then had to make his or her own judgment about whether the model and the data were close enough to be considered consistent , or whether the data had disproved the model. 

Acetate Example Using cks At this point a mention of a different kind of program seems appropriate, cks (Chemical Kinetics Simulator) is a program distributed... 

W D Hinsberg, F A Houle. Chemical Kinetics Simulator 1.01. IBM Alma-den Research Center, San Jose, California, 1996. 

The Chemical Kinetics Simulator (CKS) program package is available for a no-cost license from IBM at http //www.almaden.ibm.com/st/msim/... 

Gepasi 3.30, (Bio(chemical Kinetics Simulation Software written by Pedro Mendes, University of Wales Aberystwyth., downloadable at http /www.gepasi.org. 

Anacker, L. W. Kopelman, R. Fractal chemical kinetics simulations and experiments., 1984,81(12), 6402-6403. 

In summary, the combination of experimental studies and detailed chemical kinetic simulations provides a more complete picture of surface kinetics and identifies new regions of parameter space that would offer higher efHdency. 

Barni, R. Esena, P. Riccardi, C. (2005). Chemical kinetics simulation for atmospheric pressure air plasmas in a streamer regime. Journal of Applied. Physics, Vol. 97, pp. 073301.1-7... 

In most uncertainty studies published so far (see e.g. Brown et al. (1999), Turanyi et al. (2002), Zsely et al. (2005), Zador et al. (2005a, b, 2006a) and Zsely et al. (2008)), where the uncertainties of the rate coefficients were utilised, the uncertainty of k was considered to be equal to the xmcertainty of the pre-exponential factor A. This implies that the uncertainty of parameters E and n is zero, which is an unrealistic assumption. In a global sensitivity analysis study of a turbulent reacting atmospheric plume, Ziehn et al. (2009a) demonstrated the importance of uncertainties in EIR for the reaction N0 + 03 = N02 + 02. In this case for the prediction of mean plume centre line O3 concentratiOTis, the sensitivity to the assumed value for EIR was almost a factor of 20 higher than that of the A-factor, based on input parameter uncertainty factors provided by the evaluation of Androulakis (2004, 2004). However, in this case the parameters of the Anhenius expression for the chemical reactions considered were allowed to vary independently. In fact, the characterisation of the joint uncertainty of the Arrhenius parameters is important for the reahstic calculatiOTi of the uncertainty of chemical kinetic simulation results as will be discussed in the next section. 

Application of the QSSA is successful if the solution of ODE (7.69) is almost identical to the solution of the coupled DAEs (7.70 and 7.71). What is considered as almost identical may depend on the actual problem and the accuracy required, but in reaction kinetic modelling, a 1 % error for all species at any time is usually considered acceptable. It was emphasised in Sect. 7.2 that the aim of chemical kinetic simulations is the accurate calculation of the concentrations of important species or those of important reaction features. Therefore, the statement above can be refined so that the application of the QSSA is successful if the solutions of Eqs. (7.69) and (7.70-7.71) are almost identical considering the concentrations of important species and the important features. 

Reaction kinetic models can be simulated not only by solving the kinetic system of differential equations but also via simulating the equivalent stochastic models. Computer codes are available that solve the stochastic kinetic equations. One of these is the Chemical Kinetics Simulator (CKS) program that was developed at IBM s Almaden Research Centre. It provides a rapid, interactive method for the accurate simulation of chemical reactions. CKS is a good tool for teaching the principles of stochastic reaction kinetics to students and trainees. 

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