Use of DMSolver for Chemical/Biochemical Kinetics
DMSolver is especially suited for analyzing chemical kinetic problems, for a number of reasons we can mention:
-- Since there is a general-purpose programming language, there is flexibility and convenience in setting up the calculations.
-- Also because there is a programming language, complex functionality is possible.
-- If you have a relatively simple system to model, there is a simplified input language (SOSI) which our software can use to generate the full-fledged source code.
-- Most kinetic models involve a set of simultaneous equations; this is what DMSolver is designed to solve.
-- Limits on number of simultaneous variables are way above what would constrain typical problems.
-- The modular features of DMSolver (definition of repeating blocks of equations and variables which are linked together) may sometimes be of use as in using many sequentially-connected blocks to represent a tubular reactor.
-- We provide add-ins for fitting the numerical solution to data to estimate parameters. A user can design his/her own add-in connected in the same way as ours, e.g. to call the Solver routine, fetch specific values from the solution, compare them with data, adjust parameters, run another solution, etc. Our dedication to computational speed (all native compiled code) makes complex searches possible. The user writing an add-in is dealing only with simple old-fashioned "command-line"-style programming.
In 2007 we published a paper describing DMSolver programs for simulating chemical reaction kinetics and estimating rate parameters. The examples presented are test problems presented by the EUROKIN Consortium. We hope that the discussion and appendix of this paper illustrate the points we are trying to make above. The test problems involve batch, continuous well-mixed, and tubular reactors.
In 2006 and again recently, we looked for interesting kinetics problems in the library and found biological kinetic models for circadian rhythms in living organisms. For example, in a 1999 paper LeLoup et al1 present a model for circadian rhythms in Drosophila (the fruit fly). Also, in a 2005 paper and supplementary materials on the internet, Locke et al2 present a model for circadian rhythms in Arabidopsis thaliana, a plant. For these two cases we programmed the authors' equations and parameters into DMSolver source code and were able to closely reproduce the authors' results. Our work is presented in a pdf file.
1. Leloup, J-C., Gonze, D., and Goldbeter, A., "Limit Cycle Models for Circadian Rhythms based on Transcriptional Regulation in Drosophila and Neurospora, Journal of Biological Rhythms, Vol. 14 No.6, 433-448 (1999)
2. Locke, J. CW., Southern, M. M., Kozma-Bognar, L., Hibberd, V., Brown, P. E., Turner, M. S., and Millar, A. J., "Extension of a genetic network model by iterative experimentation and mathematical analysis", Molecular Systems Biology (2005) doi:10.1038/msb4100018