Mathematical & Computer Modeling Laboratory

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Modelling complex homogeneous reaction mechanisms

The present work is related to numerical simulation of any homogeneous kinetic reaction mechanisms and determination of their parameters by applying optimization methods. Obtained theoretical results can be used in photochemistry, organic chemistry and biochemical investigations. The main result of joint work is a software package "KinFitSim" which can be applied in scientific research and in educational process.

Figure shows concentrations of three species taking part in an oscillating chemical mechanism (Briggs-Rauscher reaction) simulated using "KinFitSim".

The two versions of "KinFitSim" software have been described in the following two articles (versions 1.12 and 2.1 respectively):

"A new software package, 'KinFitSim', for fitting and simulating kinetic data is presented. The main goals of the KinFitSim package are to obtain the best-fit parameters – rate constants, amplitudes and others – to a user specified chemical mechanism, plots of the calculated and experimental absorbance versus time, and a report to the user with the results. The KinFitSim package can be used in either chemical research or for educational purposes."
Computers and Chemistry, 26, 2002, p. 379-386. - doi:10.1016/S0097-8485(02)00014-1

"A new version of the software package KinFitSim (version 2.1) for kinetic simulation and experimental data fitting is presented. In addition to the possibilities offered by the previous version of KinFitSim, which was described before (Computers and Chemistry, V.26, 2002, p. 379-386), new features have been added to the program that include a robust automatic regime for kinetic simulation which simplifies the operation with KinFitSim for the user. KinFitSim 2.1 allows simultaneous fitting of several experimental curves corresponding to the same reaction mechanism that permits better quality of the results due to the better use of input information. The program can be used for both research and educational purposes."
Radioelectronika i informatika, 4, 2004, p. 22-25. - pdf file

"KinFitSim" users' comments:

"the area of my primary interest is the investigation of the kinetic mechanism of an ATP-dependent protease known as Lon, and 'KinFitSim' package is used for discriminating between reaction mechanisms and obtaining rate constants of chemical interactions by fitting experimental data. Using this computer package, I have been able to determine the timing of ATP hydrolysis and activation of protease activity in my enzyme system, and the results have been published in the journal Biochemistry V.44, 2005, p. 1671-1682..."
Professor Irene Lee
Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA


"...in my laboratories 'KinFitSim' has been used to study complex biocatalytical synergistic reactions including several reversible steps of the second order. The solution of such processes cannot be obtained in analytical way and therefore the use of 'KinFitSim' greatly facilitated this study. The results obtained with the aid of 'KinFitSim' have been published in several scientific articles. The 'KinFitSim' package is also used for the teaching enzyme kinetics to students.
The program may be successfully applied in various branches of chemistry and biology where homogeneous reactions are studied. Its advantages over existing analogues are conditioned by its efficiency, simplicity of operation and user-friendly interface..."
Professor Juozas Kulys, Member of the Lithuanian Academy of Sciences
Institute of Biochemistry, Vilnius, Lithuania

Main publications:

1. I.B. Svir, A.V. Klymenko, M.S. Platz "KinFitSim" - a software to fit kinetic data to a user selected mechanism / Computers and Chemistry. V.26/4, 2002, p. 379 - 386.
   
2. I. Svir, O.V. Klymenko, A.I. Oleinick, M.S. Platz KinFitSim (Version 2.1) - a powerful tool for kinetic simulation of any reaction mechanism and fitting of any number of pairs of theoretical and experimental data sets (in English) / Radioelektronika i informatika, No.4, 2004, p. 21 - 24.