ChemicalOscillators.rst

Chemical Oscillators

Chemical Oscillators, also known as chemical clocks, are chemical systems in which the concentrations of one or more reactants undergoes periodic changes.

These Oscillatory reactions can be modelled using moose. The examples below demonstrate different types of chemical oscillators, as well as how they can be simulated using moose. Each example has a short description, the code used in the simulation, and the default (gsl solver) output of the code.

Each example can be found as a python file within the main moose folder under

(...)/moose/moose-examples/tutorials/ChemicalOscillators

In order to run the example, run the script

python filename.py

in command line, where filename.py is the name of the python file you would like to run. The filenames of each example are written in bold at the beginning of their respective sections, and the files themselves can be found in the aformentioned directory.

In chemical models that use solvers, there are optional arguments that allow you to specify which solver you would like to use.

python filename.py [gsl | gssa | ee]

Where gsl is a deterministic solver, gssa stands for Gillespie stochastic simulation algorithm, and ee stands for exponential euler.

All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the gsl solver. These gsl outputs are the ones shown below.

Slow Feedback Oscillator

File name: slowFbOsc.py

This example illustrates loading, and running a kinetic model for a delayed -ve feedback oscillator, defined in kkit format. The model is one by Boris N. Kholodenko from Eur J Biochem. (2000) 267(6):1583-8

This model has a high-gain MAPK stage, whose effects are visible whem one looks at the traces from successive stages in the plots. The upstream pools have small early peaks, and the downstream pools have large delayed ones. The negative feedback step is mediated by a simple binding reaction of the end-product of oscillation with an upstream activator.

We use the gsl solver here. The model already defines some plots and sets the runtime to 4000 seconds. The model does not really play nicely with the GSSA solver, since it involves some really tiny amounts of the MAPKKK.