Input to Synaptic Channels

We want to set the neurotransmitter concentration that influences the synaptic channels for a short period of time, say just a single time step. The neurotransmitter concentration is stored in the activation field of the synaptic channels. However, if you try to find that field, hsolve gives an error message:

    genesis > echo {findsolvefield /main /main/main/basket activation}
    ** Error -  unknown or unavailable field activation for basket.

This means that we cannot set that field during simulation, so we have to use messages created before the SETUP call instead. A small trick is to set the coordinates of neutral elements, then have messages transport the coordinate values to the activation field of the synaptic channels.

    genesis > // point 1
    genesis > create neutral /messengers
    genesis > create neutral /messengers/n1
    genesis > setfield /messengers/n1 x 0.0 y 0.0 z 0.0
    genesis > addmsg /messengers/n1 /main/soma/basket ACTIVATION x
    genesis > addmsg /messengers/n1 /main/main[0-4]/basket ACTIVATION y
    genesis > addmsg /messengers/n1 /main/main[5-8]/basket ACTIVATION z

To activate the messages, we set the coordinate values for the neutral element for a single step of the simulation. Hsolve automatically fetches the new values and uses them to calculate the new conductance of the synaptic channel:

    genesis > // point 2
    genesis > step 0.2 -time
    genesis > setfield /messengers/n1 x 1.0 y 1.0 z 1.0
    genesis > step
    genesis > setfield /messengers/n1 x 0.0 y 0.0 z 0.0
    genesis > step 0.2 -time
    genesis > setfield /messengers/n1 x 1.0 y 1.0 z 1.0
    genesis > step
    genesis > setfield /messengers/n1 x 0.0 y 0.0 z 0.0
    genesis > step 0.2 -time

NOTE: Of course hsolve does store the activation field, but in an optimized and recalculated form. That is why it is not accessible with findsolvefield.

NOTE: The Purkinje cell tutorial that comes with the Genesis source code contains a Purkinje cell model with 4000 compartments that is simulated with hsolve[3]. Besides being a good example of graphical output using hsolve, various 'experiments' are implemented with the findsolvefield command and the script_out object. If you want to dig into the code of the tutorial, the gctrace and gftrace commands will prove useful.