breeds [glutamate1 glutamate2 calcium magnesium sodium]
globals [exit sodium-through mag-back]
magnesium-own [counts]

to setup
    ca
    magnesium-setup                         ;; creates Mg++ in channel
    sodium-setup
    cct-calcium calcium-ions [              ;;creates variable number of calcium ions
        setxy ((random screen-edge-x) - 10) 
                    (random screen-edge-y)
        set color blue
        if ycor <= 1 
            [set heading 0 fd 2]
    ]
    cct-glutamate1 NMDA-glutamate [             ;;creates variable number of glutamate molecules
        setxy ((random screen-edge-x) - 10)     ;;with affinity towards NMDA receptor
                   (random screen-edge-y)                           
        set color red
        if ycor <= 1 
            [set heading 0 fd 2]
    ]
    cct-glutamate2 AMPA-glutamate [             ;;creates variable number of glutamtate molecules
        setxy ((random screen-edge-x) - 10)     ;;with affinity towards AMPA receptor
                   (random screen-edge-y)                           
        set color (red + 0.1)
        if ycor <= 1 
            [set heading 0 fd 2]
    ]
    ask patches [
        if pycor >= -2 and pycor <= 0 
            [set pcolor brown]              ;; creates lipid bilayer
        if pxcor >= 0 and pxcor <= 1  
            [set pcolor black]              ;;creates channel
        if pxcor = -8
            [set pcolor black]              ;;creates AMPA channel
        set pcolor-of patch -1 1 pink       ;;creates glutamate receptor
        set pcolor-of patch -7 1 pink
   ]
   ask magnesium [set counts 0]
   set mag-back 0
end


to go
    no-pass
    activate-AMPA
    sodium-flow
    glutamate1-flow
    glutamate2-flow
    calcium-flow
    pass-channel
    ask magnesium [
        set counts (counts + 1)
        if (ycor != 0) and (counts >= 17)
            [set heading 225 fd 8 
             set mag-back (mag-back + 1)]
    ]
    if mag-back > 0
        [stop]
        
end

        
to calcium-flow    
    ask calcium [
        stop-wrap1                               ;;keeps calcium from wrapping to other side of membrane
        set heading (random 360) fd 2            ;;gives random movement of Ca++
        set heading towardsxy-nowrap 0 0 fd 1    ;;gives direction towards channel
        if pcolor = brown 
            [set heading 0 fd 3]                  ;;doesn't allow to pass membrane-not working now, used to...
        if ycor <= -2                             ;;once through channel, keep on intracellular side- not quite
            [set heading 180 fd 1 set heading (random 360) fd 1]   
     ]    
end


to glutamate1-flow
    ask glutamate1 [
        stop-wrap2                        ;keeps Glu from wrapping
        set heading (random 360) fd 1     ;;random movement
        set heading towardsxy -1 1 fd 1   ;;gives direction towards receptor site
        if pcolor = brown                 ;;doesn't allow to pass membrane
            [set heading (180 - heading) fd 1]
  ]
end


to glutamate2-flow
    ask glutamate2 [
        stop-wrap3                        ;keeps Glu from wrapping
        set heading (random 360) fd 1     ;;random movement
        set heading towardsxy -7 1 fd 1   ;;gives direction towards receptor site
        if pcolor = brown                 ;;doesn't allow to pass membrane
            [set heading (180 - heading) fd 1]
  ]
end


to magnesium-setup
    cct-magnesium 2 [
        set color yellow                  ;;creates Mg++ ions in channel
        set heading 0                     ;;although there are 2 inos, they act as one
        ask turtle 1 [
            setxy 1 0 
        ]
    ]
end


to sodium-setup
    cct-sodium sodium-ions [
        setxy ((random screen-edge-x) - 10)    ;;creates varible number of sodium ions
                   (random screen-edge-y)      ;;disperses randomly in synapse
        set color (green + 1)
        if ycor <= 1 
            [set heading 0 fd 2]
    ]
end


to sodium-flow
    ask sodium [
        set heading (random 360) fd 1            ;;gives sodium ions an affinity towards the AMPA receptor
        set heading towardsxy-nowrap -8 1 fd 1
    if pcolor = brown 
            [set heading 0 fd 3]
        set sodium-through 0
        if ycor <= -2
        [set sodium-through (sodium-through + 1)]
    ]
    if sodium-through >= 10                    ;;if enough sodium is through the receptor (i.e. depolarized)
        [activate-NMDA]                        ;;activate the NMDA receptor
end

    


to stop-wrap1
    locals [new-py new-px]
    ask calcium [
        set new-py round (ycor + dy)            ;;keeps Ca++ from wrapping to other side of membrane
        if (abs new-py = screen-edge-y)        
            [set heading (180 - heading) fd 1]  ;;if calcium is at the screen-edge, should bounce off at  
        set new-px round (xcor + dx)            ;;angle it contacted it at
        if (abs new-px = screen-edge-x)
            [set heading (0 - heading) fd 1] 
    ]
end


to stop-wrap2
    locals [new-py new-px]
    ask glutamate1 [
        set new-py round (ycor + dy)            ;;keeps Glu from wrapping to other side of membrane
        if (abs new-py = screen-edge-y)
            [set heading (180 - heading) fd 1]  ;;if glu is at screen-edge, should bounce off at 
        set new-px round (xcor + dx)            ;;angle it contacted it at
        if (abs new-px = screen-edge-x)
            [set heading (0 - heading) fd 1] 
    ]
end


 to stop-wrap3
    locals [new-py new-px]
    ask glutamate2 [
        set new-py round (ycor + dy)            ;;keeps Glu from wrapping to other side of membrane
        if (abs new-py = screen-edge-y)
            [set heading (180 - heading) fd 1]  ;;if glu is at screen-edge, should bounce off at 
        set new-px round (xcor + dx)            ;;angle it contacted it at
        if (abs new-px = screen-edge-x)
            [set heading (0 - heading) fd 1] 
    ]
end 


to pass-channel
    ask calcium [
        if sum values-from neighbors 
            [count turtles-here with [color = yellow]] >= 1        ;;if Mg++ in channel, prohibits Ca++ from passing
                [set heading 0 fd 7]
        if sum values-from neighbors 
            [count turtles-here with [color = yellow]] = 0         ;;if Mg++ gone from channel, allows Ca++ to pass
                [set heading towardsxy-nowrap 0 -7 fd 2]           ;;through channel
   ]
end


to activate-NMDA
    ask patch -1 1 [                                         ;;if glutamate is bound to receptor site, 
        if count turtles-here with [color = red] > 0         ;;goes to depolarization procedure
            [depolarize-NMDA]
    ]
end 

 
to depolarize-NMDA 
    ask magnesium [                                    ;;responds to AMPA receptor activity
        ifelse xcor = 0 or xcor = 1
            [set heading 45 fd 8 set counts 0]         ;;if Na+ depolarizes and glu bound, channel opens
            []
                
    ]
    
end
 

to no-pass
    ask calcium [
        if pcolor = brown                        ;;should prohibit Ca++ from passing membrane all the time
            [set heading (180 - heading) fd 3]   ;;and prohibit passing through the channel unless Mg++ is expelled
        if sum values-from neighbors [count turtles-here with [color = yellow]] >= 1
            [set heading (180 - heading) fd 3]
    ]
end

to activate-AMPA
    ask patch -7 1 [                                            
        if count turtles-here with [color = (red + 0.1)] > 0   ;;if glutamate bound at receptor site
            [depolarize-AMPA]                                  ;;goes to depolarize-AMPA procedure
    ]
end

to depolarize-AMPA
    ask sodium [
        set heading towardsxy-nowrap -8 -7 fd 1 fd 1           ;;tells sodium ions to pass through channel
    ]                                                          ;;because it is active
end
@#$#@#$#@
GRAPHICS-WINDOW
321
10
646
356
17
17
9.0
1
10
0
0

CC-WINDOW
321
357
646
476
Command Center

BUTTON
37
32
104
65
setup
setup
NIL
1
T
OBSERVER

BUTTON
130
33
241
66
go
go
T
1
T
OBSERVER

SLIDER
37
84
233
117
NMDA-glutamate
NMDA-glutamate
0
20
8
1
1
NIL

SLIDER
38
205
210
238
calcium-ions
calcium-ions
0
75
50
1
1
NIL

SLIDER
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158
AMPA-glutamate
AMPA-glutamate
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1
1
NIL

TEXTBOX
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255
284
543
calcium                                     -blue\nglutamate                                 -red\nsodium                                     -green\nmagnesium                             -yellow\nglutamate receptors               -pink\nlipid bilayer                               -brown\nsynapse                                    -top\npostsynaptic space                -bottom

SLIDER
38
166
210
199
sodium-ions
sodium-ions
0
25
25
1
1
NIL

@#$#@#$#@
WHAT IS IT?
-----------
This section could give a general understanding of what the model is trying to show or explain.


HOW IT WORKS
------------
This section could explain what rules the agents use to create the overall behavior of the model.


HOW TO USE IT
-------------
This section could explain how to use the model, including a description of each of the items in the interface tab.


THINGS TO NOTICE
----------------
This section could give some ideas of things for the user to notice while running the model.


THINGS TO TRY
-------------
This section could give some ideas of things for the user to try to do (move sliders, switches, etc.) with the model.


EXTENDING THE MODEL
-------------------
This section could give some ideas of things to add or change in the procedures tab to make the model more complicated, detailed, accurate, etc.


NETLOGO FEATURES
----------------
This section could point out any especially interesting or unusual features of NetLogo that the model makes use of, particularly in the Procedures tab.  It might also point out places where workarounds were needed because of missing features.


RELATED MODELS
--------------
This section could give the names of models in the NetLogo Models Library or elsewhere which are of related interest.


CREDITS AND REFERENCES
----------------------
This section could contain a reference to the model's URL on the web if it has one, as well as any other necessary credits or references.
@#$#@#$#@
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@#$#@#$#@
NetLogo 1.3.1
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@