This code is a dedicated Kinetic Monte Carlo (KMC) algorithm
which simulates a model of the post-translational Kai circadian clock.
The code allows you to simulate the Kai system at the level of individual
KaiC hexamers and monomers and explicitly tracks the turnover of every ATP
nucleotide. This way, all the reaction rates in the simulation strictly obay
The application of the code is described in our article titled "A Thermodynamically consistent model of the post-translational Kai circadian clock", which is freely available at the open access journal PLOS Computational Biology:
The code is free for scientific use. Please contact us if you plan to use this software for commercial purposes. Do not further distribute without prior permission of the authors. Please forward links to related publications so we can learn about your research.
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