So far I worked with a simplified model with a single dendrite. But moving the signal to layer two with more inter-neuronal connections allowed, it led to obvious errors. Why is this important ? In my model distance matter, synapses further away from the neuronal body contribute less to the overall neuronal potential. The dendrites, with their growth, provide that variable distance. I could not find a model in literature to fit my requirements so I came up with two very different models, eventually I decided to start with the one that seems easier because it does not require any calculations (as in geometrical calculations). This model should lead to structures close enough to what is observed in literature, but regardless if it’s close or not, it should clearly link synapses based on distance. It will allow for branching, this is very important since branching allow for synapses with same distance to the neuronal body.
However there are still many questions unanswered. What happens when a synapse is removed from a dendrite ? Does it bind to a further away position ? It is removed forever ? It binds to a different dendrite ? Should I allow multiple synapses in between 2 neurons ? What happens with the vacancy left by the removed synapse ? remains empty ? is occupied by other synapses ? a further away synapse takes its place ? What should I do about far away synapse (away from the neuron), their contributions to the overall potential is insignificant even with a linear decrease in contribution with distance, I now have an exponential decrease so it’s even worse.. Sure in some cases the synaptic strength (AMPA receptors equivalent) increase and the contribution is a bit bigger, but still small. Whys so many direct connections with so small contributions ? The signal would still reach a target neuron through its neighbors, more like in a GNN network .. that would make more sense to me.
As far as I can tell, I now have a good model for :
- Glutamatergic synapse (kinetics of glutmate and of AMPA)
- GABA synapses (half baked.. is acting on the axon resulting in 100% percent inhibition, but is also affecting active synapses.. so it’s a half man half bear kind of a situation.. maybe half pig as well)