Drosophila Circadian Clock

This is a model of the oscillating Drosophila period protein(PER). This model is based on the model introduced in the following publication.

    1. Goldbeter, “A model for circadian oscillations in the Drosophila period protein(PER)”, Proc R Soc Lond B Biol Sci, Vol.261:319-324, Sep 1995.
[1]:

%matplotlib inline
import numpy
from ecell4 import *

[2]:

with reaction_rules():
    ~M > M | 0.76 / (1 + Pn ** 3)
    M > ~M | 0.65 * M / (0.5 + M)
    ~P0 > P0 | 0.38 * M
    P0 == P1 | (3.2 * P0 / (2 + P0), 1.58 * P1 / (2 + P1))
    P1 == P2 | (5 * P1 / (2 + P1), 2.5 * P2 / (2 + P2))
    P2 == Pn | (1.9, 1.3)
    P2 > ~P2 | 0.95 * P2 / (0.2 + P2)

[3]:

y0 = {"M": 3.61328202e-01, "Pn": 6.21367e-01, "P0": 3.01106835e-01, "P1": 3.01106835e-01, "P2": 3.61328202e-01}
obs = run_simulation(numpy.linspace(0, 100, 400), y0, return_type='observer')

[4]:

show(obs)
../_images/examples_example2_4_0.png 
[5]:

viz.plot_number_observer_with_nya(obs, x="Pn", y=("M", "P0", "P1", "P2"), to_png=True)