CHEMical KINetics SimuLATOR (Chemkinlator): A friendly user interface for chemical kinetics simulations

Abstract

CHEMical KINetics SimuLATOR is a Graphical User Interface for the simulation of reaction mechanisms. The interface allows the user to see and change the parameters of a reaction network within a single window. Chemkinlator comes with built-in support for three types of kinetic simulations: Time Series, which computes the concentration of all species in an interval of time in a defined model; Bifurcation diagrams, which are the result of running several Time Series simulations over gradually different kinetic rate constants; and Flow/Temperature time series, which takes into account the effect of flow in the Continuous-flow well-Stirred Tank Reactor, and the effect of temperature on the rates constants according to the Arrhenius equation. In our research group, Chemkinlator has been the primary tool used to test the predictions made by algorithms that analyze homochirality phenomena. Chemkinlator is written in C++14 and Qt, and it uses the Fortran subroutine DLSODE to solve the differential equations associated with the reaction networks. Chemkinlator is open source software under the Apache 2.0 license and can be downloaded freely from https://gitlab.com/homochirality/chemkinlator.

Linear stability analysis of chemical mechanism, Listanalchem: A tool for the search of spontaneous mirror symmetry breaking

“…Additionally, those unstable states require that some rate constants turn to zero, which means that those reactions are not part of the model, then it is a new model. These results can be verified by numerical simulations using Chemkinlator [30] or similar software. In this case, the unlimited growth in the concentration of the enantiomers is evident.…”

“…The specific model generated in this way can be tested using Chemkinlator [30] or any other software capable of making chemical kinetics simulations.…”

“…Those samples can be optionally saved in text files with “.json” format using the line “ samples-folder”: 'samples/File-name-to-save-samples' . Those files also have a “.simu.” pre-extension and can be read by Chemkinlator [30] to obtain graphical time series and bifurcation diagrams.…”

“…The third algorithm determines whether the network can contain symmetry-breaking states and, if it has, computes a sample of those states, producing files with a set of rate constants that solve the set of equalities and inequalities proposed in reference [22] . Those files, as before, have *.json format and can be read by Chemkinlator [30] to make the respective simulations (time series and bifurcation diagrams). Notice that the *.json are open standard format files that the users can take for chemical kinetic simulations with their preferred software, probably making the required modifications (if necessary) to the *.json results files.…”

“…What is left to do is to sample a single point from the ranges above and test if it is indeed unstable, using the generated files with the *.simu.json format and Chemkinlator [30] (or any other similar software), as mentioned before.…”