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. Apart from ATP hydrolysis, all reactions obey detailed balance.
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:
*UPDATE* We made a fully reversible version of our model, including the inverse reactions for ATP hydrolysis. This makes it possible to run the model at thermodynamic equilibrium. This version of the model can be downloaded under KMC_KaiC_Rev.zip.
If you like to use our model for your own research, please cite our PLoS Computational Biology paper.
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