Examples


Case 1 - Single Substrate and Particulate Case

Download link: Case1.jl (right-click & Save Link As)

This case is the same the case shown on the Installation page. It simulates a single particulate ("Heterotroph") and a single substrate ("Nutrient"). The particulate has a growthrate of

\[\mu = \mu_\mathrm{max} \frac{S}{K_M + S}\]

Case 2 - Multiple Substrates

Download link: Case2.jl (right-click & Save Link As)

This is a simple example of how multiple substrates can be simulated. Substrate 1 is used by "Bug" while substrate 2 is completely indpendent (not very interesting).

Case 3 - Live/Dead Bugs

Download link: Case3.jl (right-click & Save Link As)

This example has living bugs that use the substrate to grow. The bugs die and the concentration of dead bugs is also computed. The source term, src, is used to transfer living bugs to dead bugs.

\[\mathrm{src}_{X_1} = \mathrm{src}_\mathrm{living} = -b X_1\\ \mathrm{src}_{X_2} = \mathrm{src}_\mathrm{dead} = b X_1\]

where b=0.1 is a constant. The first source term reduces living bugs and the second adds these to the dead bugs.

Case 4 - Multiple Particulate and Substrates

Download link: Case4.jl (right-click & Save Link As)

Case 5 - Phototroph

Download link: Case5_Photroph.jl (right-click & Save Link As)

This case shows how you can simulate a species that grows in light. The light turns off and on throughout each day and also only penetrates the top of the biofilm. Since the light has discontinuities, the case has an additional parameter

    discontinuityPeriod=0.25,

that tells the solver the discontinuities can occur every 0.25 days.