# Maths

## Reaction-Diffusion

The system of PDEs that we simulate in each compartment is the three-dimensional reaction-diffusion equation:

$\frac{\partial c_s}{\partial t} = D_s \left( \frac{\partial^2}{\partial x^2} + \frac{\partial^2}{\partial y^2} + \frac{\partial^2}{\partial z^2} \right) c_s + R_s$

where

• $$c_s$$ is the concentration of species $$s$$ at position $$(x, y, z)$$ and time $$t$$

• $$D_s$$ is the diffusion constant for species $$s$$

• $$R_s$$ is the reaction term for species $$s$$

and we assume that

• the diffusion constant $$D_s$$ is a scalar that does not vary with position or time

• the reaction term $$R_s$$ is a function that can depend on the concentrations of other species in the model, but only locally, i.e. the concentrations at the same spatial coordinate.

## Compartment Reactions

Compartment reaction terms correspond to the $$R_s$$ term in the reaction-diffusion equation, and describe the rate of change of species concentration with time. They are evaluated at every point inside the compartment

## Membrane reactions

Membrane reactions are reactions that occur on the membrane between two compartments, and describe the species amount that crosses the membrane per unit membrane area per unit time.

## Boundary Conditions

All boundaries have “zero-flux” Neumann boundary conditions, whether they are boundaries between two compartments or boundaries between a compartment and the outside (except for the flux caused by any membrane reactions).