💊 Reactions

The Reactions trait models intracellular reactions for invididual cellular agents. It uses a single method calculate_intracellular_increment to calculate the derivative for a given cellular configuration. In addition, the ReactionsExtra can be used to interact with the physical domain eg. to model uptake or secretion. The ReactionsContact trait describes reactions which can occur between cells which are in close proximity to each other and coupled eg. via cell walls.

Example: Autonomous ODEs

Autonomous Ordinary Differential Equations (ODEs) are typically represented by a state vector $x\in\mathbb{R}^n$ of type VectorN and a function $f(x,p)$ together with initial conditions $x_0\in\mathbb{R}^n$.

In our case, we can solve such a system by implementing the Reactions trait.

struct Cell {
    intracellular: VectorN,
}

impl Reactions<VectorN> for Cell {
    fn calculate_intracellular_increment(
        &sele,
        intracellular: &VectorN
    ) -> Result<VectorN, CalcError> {
        // Here we insert the functionality of f(x,p)
        Ok(...)
    }
}

Remarks on Contact Reactions

Similarly to the Reactions trait, we describe changes to the intracellular state of cellular agents. The calculate_contact_increment method is called for each neighboring cell as defined by the domain-decomposition.

More Examples

• cr_trichome
• Bacterial Branching