examples.rst

Examples

Here we discuss some example systems and how to code them up using cayenne.

Zero order system

$$\begin{aligned} \phi &\xrightarrow[]{k_1} A\\\ \\\ k_1 &= 1.1\\\ A(t=0) &= 100\\\ \end{aligned}$$

This can be coded up with:

>>> from cayenne import Simulation
>>> model_str = """
        const compartment comp1;
        comp1 = 1.0; # volume of compartment

        r1:  => A; k1;

        k1 = 1.1;
        chem_flag = false;

        A = 100;
    """
>>> sim = Simulation.load_model(model_str, "ModelString")
>>> sim.simulate()
>>> sim.plot()

First order system

$$\begin{aligned} A &\xrightarrow[]{k_1} B\\\ \\\ k_1 &= 1.1\\\ A(t=0) &= 100\\\ B(t=0) &= 20\\\ \end{aligned}$$

This can be coded up with:

>>> from cayenne import Simulation
>>> model_str = """
        const compartment comp1;
        comp1 = 1.0; # volume of compartment

        r1: A => B; k1;

        k1 = 1.1;
        chem_flag = false;

        A = 100;
        B = 20;
    """
>>> sim = Simulation.load_model(model_str, "ModelString")
>>> sim.simulate()
>>> sim.plot()

Suppose you want to use the tau_leaping algorithm, run 20 repetitions and plot only species B. Then do:

>>> sim.simulate(algorithm="tau_leaping", n_rep=20)
>>> sim.plot(species_names=["B"], new_names=["Species B"])

Enzyme kinetics (second order system with multiple reactions)

$$\begin{aligned} \text{Binding}: S + E &\xrightarrow{k1} SE \\\ \text{Dissociation}:SE &\xrightarrow{k2} S + E \\\ \text{Conversion}: SE &\xrightarrow{k3} P + E \\\ \\\ k1 &= 0.006 \\\ k2 &= 0.005 \\\ k3 &= 0.1 \\\ S(t=0) &= 200\\\ E(t=0) &= 50\\\ SE(t=0) &= 0\\\ P(t=0) &= 0\\\ \end{aligned}$$

This can be coded up with:

>>> from cayenne import Simulation
>>> model_str = """
        const compartment comp1;
        comp1 = 1.0; # volume of compartment

        binding: S + E => SE; k1;
        dissociation: SE => S + E; k2;
        conversion: SE => P + E; k3;

        k1 = 0.006;
        k2 = 0.005;
        k3 = 0.1;
        chem_flag = false;

        S = 200;
        E = 50;
        SE = 0;
        P = 0;
    """
>>> sim = Simulation.load_model(model_str, "ModelString")
>>> sim.simulate(max_t=50, n_rep=10)
>>> sim.plot()

Since this is a second order system, the size of the system affects the reaction rates. What happens in a larger system? :

>>> from cayenne import Simulation
>>> model_str = """
        const compartment comp1;
        comp1 = 5.0; # volume of compartment

        binding: S + E => SE; k1;
        dissociation: SE => S + E; k2;
        conversion: SE => P + E; k3;

        k1 = 0.006;
        k2 = 0.005;
        k3 = 0.1;
        chem_flag = false;

        S = 200;
        E = 50;
        SE = 0;
        P = 0;
    """
>>> sim = Simulation.load_model(model_str, "ModelString")
>>> sim.simulate(max_t=50, n_rep=10)
>>> sim.plot()

Here we see that the reaction proceeds slower. Less of the product is formed by t=50 compared to the previous case.