The Neighbour-Sensing program operates in three spatial dimensions, so your simulations will produce some solid tissues. The slice command allows you to investigate the internal structure of these tissues. This is illustrated in these simple examples. Also illustrated is the fact that some surprises emerge from these experiments!
A spherical colony is formed under conditions when all growth regulation is turned off (so
that branching occurs at random times and new branches grow in random directions). The red colour
in the figure below indicates growing and branching tips. Making a slice of the
colony shows that the colony is much denser in the centre than at the boundary.
Slice:
A spherical colony is also formed when branching is set to be sensitive to the density of hyphal tips in the neighbourhood; this is a branching model that corresponds to the Boletus default parameter set. In the simulation shown below, growing and branching tips are colour-coded red, tips that are not branching in this iteration of the algorithm (because their local environment is too dense to permit branching) are colour-coded blue.
With branching set to be regulated by the hyphal density field a spherical colony is again formed. This tropic field is described using physical laws derived from the properties of electric fields, and produces the most regular colony shape, but the slice shows that it, too, contains a high density zone in the centre. In the illustration below, growing and branching tips are colour-coded red, tips that were not eligible to branch in this iteration because of a too dense environment are colour-coded blue.
Applying the rule that both negative autotropism and branching should be based on the hyphal density field, also produces a regular spherical colony (see below), but the internal structure (see slice below) is markedly radial.
Another interesting example is the spherical colony formed using negative autotropism but setting branching to be regulated by the number of neighbouring tips (not by the density field). Again, growing and branching tips are red, tips that are not eligible to branch are blue. This colony morphology is much more 'open' and the colony margin is ragged.
During the early stages of development of such a colony a curious and unexpected feature emerges. It seems that the hyphae differentiate into two morphological classes - those that grow from the centre directly to the border, and those that fill the rest of the space (as in the Figure below). It is important to stress that the parameter set used here does not specify that there will be the two types of hyphae! They emerge as a natural outcome of the operation of a parameter set applied initially to one hyphal type. It would be interesting to experiment further with this parameter set to establish why and how the two hyphal types differentiate. This branching model corresponds the Amanita rubsecens default parameter set. Growing and branching tips are red, tips that do not branch due a too dense environment are blue.
Finally, causing the tips to try to grow at a 45 degree angle in relation to the orientation (gravitropism) field produces a conical or cup-shaped structure (see below). Please remember that although we call this a gravitropism, in terms of the mathematics of the model it is simply an orientation field around the vertical axis. In physiological terms it could be gravity, but it could equally well be incident illumination, a temperature gradient or a chemical gradient. That's up to you to define. Apart from the gravitropism, the parameter set defining the hyphal avoidance reactions used in this simulation started off with the default parameters known as the Tricholoma type. The most unexpected outcome of this simulation is that the slice shows that voids or 'locules' are formed within the tissue of the cup-shaped structure (see slice at bottom).
Slice:
So there's another set of in silico experiments that need to be done - what is it about this combination of control parameters that leads to the formation of voids? How can the morphology, size, number and distribution of the voids be controlled? And what might all that tell you about the way that real live fungi structure their fruit bodies?
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