---perforant.nlogo

NETLOGO

breeds [entorhinal dentategyrus ca3 ca1 neuron1 neuron2]
globals [lifespan fade]
patches-own [passover]
neuron1-own [age]
neuron2-own [age]


to  setup
    ca
    entorhinal-setup
    dentategyrus-setup
    ca3-setup
    ca1-setup
    axon
    setup-constants
    ask patches [set passover 0]
end
    
to entorhinal-setup ;placement of the entorhinal cortex neurons
    create-custom-entorhinal 17[
    set color green
    set shape "circle"
    ask turtle 0 [setxy 2 -20] set heading 180
    ask turtle 1 [setxy 2 -20] set heading 175
    ask turtle 2 [setxy 4 -18] set heading 170
    ask turtle 3 [setxy 6 -18] set heading 165
    ask turtle 4 [setxy 8 -16] set heading 160
    ask turtle 5 [setxy 10 -16] set heading 155
    ask turtle 6 [setxy -2 -20] set heading 185
    ask turtle 7 [setxy -4 -18] set heading 190
    ask turtle 8 [setxy -6 -18] set heading 195
    ask turtle 9 [setxy -8 -16] set heading 200
    ask turtle 10 [setxy -10 -16] set heading 205
    ask turtle 11 [setxy 13 -14] set heading 150
    ask turtle 12 [setxy 12 -15] set heading 145
    ask turtle 13 [setxy -16 -12] set heading 140
    ask turtle 14 [setxy -12 -14] set heading 210
    ask turtle 15 [setxy -14 -14] set heading 215
    ask turtle 16 [setxy -16 -12] set heading 180
    ]
end

to DentateGyrus-setup ;placement of the Dentate Gyrus neurons
create-custom-dentategyrus 13[
    set color orange
    set shape "circle"
    ask turtle 17 [setxy -4 10] 
    ask turtle 18 [setxy -4 8] 
    ask turtle 19 [setxy -6 6] 
    ask turtle 20 [setxy -6 4] 
    ask turtle 21 [setxy -8 2] 
    ask turtle 22 [setxy -10 0] 
    ask turtle 23 [setxy -12 0] 
    ask turtle 24 [setxy -12 0] 
    ask turtle 25 [setxy -16 2] 
    ask turtle 26 [setxy -18 4] 
    ask turtle 27 [setxy -18 6] 
    ask turtle 28 [setxy -20 8] 
    ask turtle 29 [setxy -20 10] 
    ]
end

to ca3-setup ;placement of the CA 3 field neurons
create-custom-ca3 15[
    set color blue
    set shape "circle"
    set heading 150
    ask turtle 30 [setxy 2 22] 
    ask turtle 31 [setxy -12 8] 
    ask turtle 32 [setxy -12 10]
    ask turtle 33 [setxy -12 10] 
    ask turtle 34 [setxy -12 12] 
    ask turtle 35 [setxy -12 12] 
    ask turtle 36 [setxy -12 16] 
    ask turtle 37 [setxy -12 18] 
    ask turtle 38 [setxy -12 18] 
    ask turtle 39 [setxy -10 20] 
    ask turtle 40 [setxy -8 21] 
    ask turtle 41 [setxy -6 22] 
    ask turtle 42 [setxy -4 22] 
    ask turtle 43 [setxy -2 22] 
    ask turtle 44 [setxy 0 22] 
        ]

end

to ca1-setup ;placement of the CA 1 Field neurons
create-custom-ca1 15[
    set color red
    set shape "circle"
    set heading 250
    ask turtle 45 [setxy 3 22] 
    ask turtle 46 [setxy 4 22] 
    ask turtle 47 [setxy 6 22] 
    ask turtle 48 [setxy 8 21] 
    ask turtle 49 [setxy 10 20] 
    ask turtle 50 [setxy 14 16] 
    ask turtle 51 [setxy 14 16] 
    ask turtle 52 [setxy 14 0] 
    ask turtle 53 [setxy 14 14] 
    ask turtle 54 [setxy 14 12] 
    ask turtle 55 [setxy 14 10] 
    ask turtle 56 [setxy 14 8] 
    ask turtle 57 [setxy 14 6] 
    ask turtle 58 [setxy 14 4] 
    ask turtle 59 [setxy 14 2] 
        ]

end

to axon ;mimics the axon sites in the hippocampus
ask (patch 0 -20) [ set pcolor green ]
ask (patch -14 0) [ set pcolor orange ]
ask (patch -12 14) [ set pcolor blue ]
ask (patch 12 18) [ set pcolor red ]
ask (patch 2 25) [ set pcolor yellow ] ;yellow patches represent regions where incoming signals come from outside the hippocampus
ask (patch -0 -25) [ set pcolor yellow ]
end

to setup-constants ; defines the  age of the signals.
    set lifespan 500
    set fade 0
end    

to incoming
    signal
end

to kill
    ask neuron1
        [die]
    ask neuron2
        [die]
end           


to go
    ;neuron-signal
    working-memory
    stop-wrap
    grow-older
    trails
    ifelse potentiation ;toggles on and off the axon "trails"
         [ask patches
             [if any neuron2-here
                 [set pcolor scale-color black passover 0 screen-size-x]]]
                 ;[set pcolor (pcolor + .5)]]]
          [ask patches [set pcolor 0 set passover 0]]             
    ifelse potentiation ;toggles on and off the axon "trails"
         [ask patches
             [if any neuron1-here
                 [set pcolor scale-color black passover 0 screen-size-x]]]
                 ;[set pcolor (pcolor + .5)]]]
          [ask patches [set pcolor 0 set passover 0] ]
    deteriorate
    axon
end

to trails ;this counts the number of times each signal moves over a patch and allows for the coloring of the patch
    ask patches
        [if any neuron2-here
            [set passover passover + 3]]
    ask patches
        [if any neuron1-here
            [set passover passover + 3]]
end
                    
to deteriorate ; the triggers the natural decay of any connection in the brain
     if potentiation
         [ask patches
             [set fade (fade + random 3)
             if fade > 800
                     [fader]
             if passover > 50
                     [passover-catchup]]]
                     ;[set passover (passover - .05)]]]
                        
end

to passover-catchup
    set passover (passover - .05)
end

to fader ;part of the timing mehanism of the deterioration within the connectivity of the brain
      if passover > 1
              [if pcolor > .4 [
                  set pcolor (pcolor - random .05)
                  set fade 0
                  set passover (passover - random (alcohol-consumption / 5) + .1)]]
end

to signal ;Sends incoming signal towards hippocampal formation
        ask (patch 2 25) [
        sprout 1 [
        set breed neuron1
        set color yellow 
        ]]
        
        ask neuron1 [
        set heading towards-nowrap patch 12 18 
        ;fd 2 rt random 360 bk 1 
        set age (1) ]
        
        ask (patch 0 -25) [
        sprout 1 [
        set breed neuron2 
        set color yellow]]
        
        ask neuron2 [
        set heading towards-nowrap patch 0 -20
        ;fd 2 rt random 360 bk 1
        set age (1)]
end

to neuron-signal ;orientates the signals towards the recepter site, the pathway taken represents creation of the axons
    ask neuron1 
        [set heading towards-nowrap patch 12 18 
         fd 2 rt random 360 bk 1 ]
         
    ask neuron2 
        [set heading towards-nowrap patch 0 -20 
         fd 1 rt random 360 bk 2 ]      
end

to stop-wrap ;Keeps the signals from wrapping around the screen edge
    locals [new-py]
    ask neuron2 [
        set new-py round (ycor + dy)
        if (abs new-py = screen-edge-y) [
        set heading (180 - heading) fd 1 rt random 360 bk 2 lt random 360]]
end

to working-memory ; An attempt to mimic some form of hippocampal function. i.e. short term working memory store and the cycling of signals
    ask turtles-at 0 -25
          [set color 44]
    ask turtles [
          if color = 44 [
          set heading towards-nowrap patch 0 -20
          fd 2 rt random 360 bk 1 lt random 360]]
    ask turtles-at 2 25      
          [set color 46]
    ask turtles [
          if color = 46 [
          set heading towards-nowrap patch 12 18
          fd 2 rt random 360 bk 1 lt random 360]]  
    ask turtles-at 12 18 
          [set color 17]
    ask turtles [
          if color = 17      
           [set heading towards-nowrap patch 0 -20
           fd 2 rt random 360 bk 1 lt random 360]]
     ask turtles-at 0 -20 
          [set color 54]
     ask turtles [
          if color = 54      
           [set heading towards-nowrap patch -14 0
           fd 2 rt random 360 bk 1 lt random 360]]
    ask turtles-at -14 0 
          [set color 24]
    ask turtles [
          if color = 24      
           [set heading towards-nowrap patch -12 14
           fd 2 rt random 360 bk 1 lt random 360]]
    ask turtles-at -12 14 
          [set color 104]
    ask turtles [
          if color = 104      
           [set heading towards-nowrap patch 12 18
           fd 2 rt random 360 bk 1 lt random 360]]
    ask turtles-at 12 18 
          [set color 17]
    ask turtles [
          if color = 17      
           [set heading towards-nowrap patch 0 -20
           fd 2 rt random 360 bk 1 lt random 360]]               
end

to grow-older ; this function ages the neurons and causes them to die out with time
     ask neuron1
     [set age (age + random 5)
     if age > lifespan
        [ die ]   ]
     ask neuron2
     [set age (age + random 5)
     if age > lifespan
        [ die ]   ]   
end
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