---electron_transport.nlogo

NETLOGO

; add model procedures here
globals [rat atp total_atp nad total_nad time]

to setup
ca
set total_atp [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
set total_nad [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
ask patches with [(pxcor = (-1 * screen-edge-x))] [set pcolor white] 
ask patches with [(pxcor = screen-edge-x)] [set pcolor white]
ask patches with [(pycor = (-1 * screen-edge-y))] [set pcolor white]
ask patches with [(pycor = screen-edge-y)] [set pcolor white]
ask patches with [pycor = 0] [set pcolor white]

ask patches with [(pycor = 0) and (pxcor = -16)] [set pcolor blue] ;FeS1
ask patches with [(pycor = 0) and (pxcor = -14)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -12)] [set pcolor blue] ;FeS2
ask patches with [(pycor = 0) and (pxcor = -10)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -8)] [set pcolor blue] ;CytA
ask patches with [(pycor = 0) and (pxcor = -6)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -4)] [set pcolor blue] ;CytA
ask patches with [(pycor = 0) and (pxcor = -2)] [set pcolor red] ;CytA

ask patches with [(pycor = 0) and (pxcor = 16)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 14)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 12)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 10)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 8)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 6)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 4)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 2)] [set pcolor red] ;ATP Synthase

cct 100 [set shape "circle" set size 1 set color yellow set heading random 360 fd random 10]

end

to go 
locals[nad_cnt atp_cnt]
set nad_cnt 0
set atp_cnt 0
set rat count turtles with [ycor > 0]
ask turtles [

  fd 1
  rt random 60 
  lt random 60 
  if (pcolor-of patch-at dx dy = white) and (NOT uncouplers) [set heading heading - 180]
  if (pcolor-of patch-at dx dy = blue) [if (heading >= 270 or heading < 90 ) [ifelse (NOT poison_et) and (random 90 > rat) and (50 - nad > 0) [fd 2 set nad nad + 1 set nad_cnt nad_cnt + 1] [set heading heading - 180] ] ]
  if (pcolor-of patch-at dx dy = blue) [if (heading  >= 90 and heading < 270 ) [set heading heading - 180]]
  if (pcolor-of patch-at dx dy = red)  [if (heading  >= 90 and heading < 270 )  [ifelse (NOT poison_as) and (rat > 60 ) and (50 - atp > 0)[ fd 2  if (atp < 50) [set atp atp + 1 set atp_cnt atp_cnt + 1]] [set heading heading - 180] ] ]
  if (pcolor-of patch-at dx dy = red)  [if (heading >= 270 or heading < 90) [set heading heading - 180]]
  ]
  if (random 200 < atp_consumption) and (atp > 1) [set atp atp - 1]
  if (random 200 < nad_consumption) and (nad > 1) [set nad nad - 1]
  no-display
  plot-levels
  plot-atp
  set total_nad replace-item time total_nad nad_cnt
  set total_atp replace-item time total_atp atp_cnt
    set time time + 1
  if(time >= 40) [set time 0]
  plot-rates 
  display
end

to plot-levels ;; this creates creates the bar graph 
    set-current-plot "Proton Gradient"
    clear-plot
    ppd
    set-current-plot-pen "matrix"
    plotxy 1 count turtles with [ycor < 0] 
    set-current-plot-pen "intermembrane"
  plotxy 2 rat 

end

to plot-atp ;; this creates creates the bar graph 
    set-current-plot "ADP-ATP NADH-NAD+"
    clear-plot
    ppd
    set-current-plot-pen "adp"
    plotxy 1 (50 - atp) 
    set-current-plot-pen "atp"
    plotxy 2 atp 
    set-current-plot-pen "nadh"
    plotxy 4 (50 - nad) 
    set-current-plot-pen "nad+"
    plotxy 5 nad

end

to plot-rates ;; this creates creates a line graph 
    set-current-plot "ATP and NAD Rates"
    ppd
    set-current-plot-pen "atp"
    plot ((sum total_atp) / 40) 
    set-current-plot-pen "nad"
    plot ((sum total_nad) / 40) 

end

; Copyright 2004 by Steven Brewer.  All rights reserved.
;
; Permission to use, modify or redistribute this model is hereby granted,
; provided that both of the following requirements are followed:
; a) this copyright notice is included.
; b) this model will not be redistributed for profit without permission
;    from the authors.
; Contact the authors for appropriate licenses for redistribution for
; profit.
;
; To refer to this model in academic publications, please use:
; Brewer, S.D. (2004).  Electron Transport: Simulating Proton Gradient,
; ADP-ATP, and NADH-NAD+ Interactions.  
; http://bcrc.bio.umass.edu/netlogo/models/ElectronTransport/
; Biology Computer Resource Center
;
; In other publications, please use:
; Copyright 2004 by Steven Brewer.  All rights reserved.  See
; http://bcrc.bio.umass.edu/netlogo/models/ElectronTransport/
@#$#@#$#@
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Command Center

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setup
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OBSERVER
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go
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OBSERVER
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Poison_ET
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Proton Gradient
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ADP-ATP NADH-NAD+
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atp_consumption
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ATP and NAD Rates
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mitochondrial matrix

TEXTBOX
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intermembrane region

BUTTON
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