The following results were gotten with nothing being changed except for the initial conditions (primarily the location of initial fiber deposits and the initial location of the astrocytes). They were set up using all default parameter values in the batch simulation and letting the initial astrocyte count vary between 100 and 100 (the default for this parameter).
The final amyloid and neuron health pictures are presented in the same order as the following graphs:
The size of the dead neuron region varies greatly:
I believe this is due in large part to the location of the astrocytes. An interesting measure would be to compute the average astrocyte's distance from the center. This can be added as a button in the regular simulation and simply included in the label of the batch results.
What is still unclear and probably wrong is the correlation between fiber growth and neuron death. (What is a plaque? A region of neuronal death? A region of dense fibers? Both?) This is due to two factors. In order to confine neuron death, the TNF health effects need to eventually dominate the death effects due to IL-6. Thus, all neurons outside of the region of death will remain forever healthy and may be amyloid sources as can be seen in the final amyloid displays:
If the spread of neuronal death is smaller than the spread
of IL-1B, new amyloid sources can appear which will
lead to fiber growth outside the region of death. One
way that this may be adjusted is to change the health
effects of IL-1B from zero to some negative number that
will allow for death to occur again. However, this
needs to be done in such a way that not all neurons die
like in the first case.