Team:Valencia UPV/Modeling/sexyplants.nlogo

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(Difference between revisions)
(Created page with "breed [ moths moth ] breed [ females female ] breed [ standers stander ] ;breed [ sexyplants sexyplant] moths-own [ number-meeting count-down ocupado ;1 mating _ 0 f...")
Line 2: Line 2:
breed [ females female ]
breed [ females female ]
breed [ standers stander ]  
breed [ standers stander ]  
-
;breed [ sexyplants sexyplant]
 
moths-own
moths-own
[
[
-
   number-meeting
+
   number-encounter
   count-down
   count-down
   ocupado    ;1 mating _ 0 free
   ocupado    ;1 mating _ 0 free
Line 24: Line 23:
patches-own
patches-own
[
[
-
   old-pheromonelevel  ;; the pheromonelevel of the patch the last time thru go
+
   old-pheromonelevel  ; the pheromonelevel of the patch the last time thru go
-
   pheromonelevel      ;; the current pheromonelevel of the patch
+
   pheromonelevel      ; the current pheromonelevel of the patch
]
]
globals
globals
[
[
-
   plate-size          ;; the size of the plate on which heat is diffusing
+
   plate-size          ; the size of the plate on which pheromone is diffusing                  
-
                      ;; Used for scaling the color of the patches
+
   min-pherolevel      ; the minimum pheromonelevel  
-
   min-pherolevel      ;; the minimum pheromonelevel at setup time
+
   max-pherolevel      ; the maximum pheromonelevel                       
-
   max-pherolevel      ;; the maximum pheromonelevel at setup time
+
   old-number-encounter
-
                        
+
-
   old-number-meeting
+
  ]
  ]
Line 45: Line 42:
to setup
to setup
   clear-all
   clear-all
-
  ;; initialize variables
+
   set plate-size max-pxcor  
-
   set plate-size max-pxcor ;; use 0.6 to make a nice sized plate
+
    
    
    
    
Line 66: Line 62:
   set min-pherolevel min [old-pheromonelevel] of patches
   set min-pherolevel min [old-pheromonelevel] of patches
   set max-pherolevel max [old-pheromonelevel] of patches
   set max-pherolevel max [old-pheromonelevel] of patches
-
  draw-legend
 
   ask patches [ draw-plate ]
   ask patches [ draw-plate ]
    
    
Line 76: Line 71:
   make-females number-females
   make-females number-females
    
    
-
   ;set-default-shape sexyplants "flower"
+
    
   
   
  ;SEXYPLANTS
  ;SEXYPLANTS
Line 86: Line 81:
    
    
  ;CROP   
  ;CROP   
-
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 20 set color 44]
+
  crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 20 set color 44]
-
; crt 1 [set shape "plant" set size 2 set xcor 20 set ycor 0 set color 44]
+
  crt 1 [set shape "plant" set size 2 set xcor 20 set ycor 0 set color 44]
-
; crt 1 [set shape "plant" set size 2 set xcor -20 set ycor 0 set color 44]
+
  crt 1 [set shape "plant" set size 2 set xcor -20 set ycor 0 set color 44]
-
  ; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -20 set color 44]
+
  crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 0 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 0 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -10 set ycor -20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 10 set ycor -20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 0 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 0 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor 30 set ycor -20 set color 44]
 +
  crt 1 [set shape "plant" set size 2 set xcor -30 set ycor -20 set color 44]
 +
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 10 set color 44]
 +
  ; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -10 set color 44]
  ; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 0 set color 44]
  ; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 0 set color 44]
  ; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 40 set color 44]
  ; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 40 set color 44]
Line 113: Line 122:
     jump random-float max-pxcor
     jump random-float max-pxcor
     set size 2
     set size 2
-
     set number-meeting 0
+
     set number-encounter 0
     set count-down 40
     set count-down 40
     set ocupado 0
     set ocupado 0
Line 130: Line 139:
end
end
-
;; Sets the pheromonelevel for inside of the plate
+
; Sets the pheromonelevel for inside of the plate
to set-initial-pheromonelevels  ;; Patch Procedure
to set-initial-pheromonelevels  ;; Patch Procedure
   if ((abs pycor) < plate-size) and ((abs pxcor) < plate-size)
   if ((abs pycor) < plate-size) and ((abs pxcor) < plate-size)
Line 149: Line 158:
end
end
-
;; Draws the Color Scale Legend
 
-
to draw-legend  ;; Patch Procedure
 
-
  let x (1 + min-pxcor)
 
-
  repeat 3
 
-
  [
 
-
    let y 0
 
-
    repeat 10
 
-
    [
 
-
      ask patch (x + 4) (y * 2 - 11) [ set pheromonelevel (y * 10) ]
 
-
      ask patch (x + 4) (y * 2 - 10) [ set pheromonelevel (y * 10) ]
 
-
      set y y + 1
 
-
    ]
 
-
    set x x + 1
 
-
  ]
 
-
  set x (1 + min-pxcor)
 
-
  repeat 3
 
-
  [
 
-
    let y 0
 
-
    repeat 10
 
-
    [
 
-
      ask patch (x + 4) (y * 2 - 11) [color-patch ]
 
-
      ask patch (x + 4) (y * 2 - 10) [color-patch ]
 
-
      set y y + 1
 
-
    ]
 
-
    set x x + 1
 
-
  ]
 
-
 
-
 
-
  set x (1 + min-pxcor)
 
-
  repeat 3
 
-
  [
 
-
    let y 0
 
-
    repeat 11
 
-
    [
 
-
      if (x = (3 + min-pxcor)) [ ask patch  x (y * 2 - 12) [ set plabel (y * 10) ] ]
 
-
    set y y + 1
 
-
    ]
 
-
    set x x + 1
 
-
  ]
 
-
 
-
end
 
;; Sets the pheromonelevels of the plate edges and corners
;; Sets the pheromonelevels of the plate edges and corners
;In this simulation this command is not activated, since the we consider an opened volume.
;In this simulation this command is not activated, since the we consider an opened volume.
to set-edge-pheromonelevels  ;; patch procedure
to set-edge-pheromonelevels  ;; patch procedure
-
   ;; set the pheromonelevels of the edges
+
   ; set the pheromonelevels of the edges
   if (pxcor >= plate-size) and ((abs pycor) < plate-size)
   if (pxcor >= plate-size) and ((abs pycor) < plate-size)
   [set pheromonelevel 0]
   [set pheromonelevel 0]
Line 205: Line 173:
   [set pheromonelevel 0]
   [set pheromonelevel 0]
-
   ;; set the pheromonelevels of the corners
+
   ; set the pheromonelevels of the corners
   if (pxcor >= plate-size) and (pycor >= plate-size)
   if (pxcor >= plate-size) and (pycor >= plate-size)
   [set pheromonelevel 0]
   [set pheromonelevel 0]
Line 225: Line 193:
;; Runs the simulation through a loop
;; Runs the simulation through a loop
to go
to go
 +
 
 +
  set max-pherolevel max [old-pheromonelevel] of patches
 +
  set min-pherolevel min [old-pheromonelevel] of patches
    
    
   ask females [set color 125]
   ask females [set color 125]
Line 235: Line 206:
   ask patches [
   ask patches [
     ;Diffusion process with advection (wind)
     ;Diffusion process with advection (wind)
-
     set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4) - wind-forcey * ([old-pheromonelevel] of patch-at-heading-and-distance 0 1) - wind-forcex * ([old-pheromonelevel] of patch-at-heading-and-distance 90 1)) + ((1 - ( 4 * heat-diffusivity - 1 * wind-forcey - 1 * wind-forcex )) * old-pheromonelevel)
+
     set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4) - wind-forcey * ([old-pheromonelevel] of patch-at-heading-and-distance 0 1) - wind-forcex * ([old-pheromonelevel] of patch-at-heading-and-distance 90 1)) + ((1 - ( 4 * pheromone-diffusivity - 1 * wind-forcey - 1 * wind-forcex )) * old-pheromonelevel)
     ;set-edge-pheromonelevels
     ;set-edge-pheromonelevels
     set old-pheromonelevel pheromonelevel
     set old-pheromonelevel pheromonelevel
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   ask patches
   ask patches
   [
   [
-
     ;; diffuse the heat of a patch with its neighbors
+
     ;; diffuse the pheromone of a patch with its neighbors
     if ( (pycor)= 0 ) and ( (pxcor) = 0)
     if ( (pycor)= 0 ) and ( (pxcor) = 0)
-
     [set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
+
     [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
     if ( (pycor)= 20 ) and ( (pxcor) = 20)
     if ( (pycor)= 20 ) and ( (pxcor) = 20)
-
     [set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
+
     [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
     if ( (pycor)= 20 ) and ( (pxcor) = -20)
     if ( (pycor)= 20 ) and ( (pxcor) = -20)
-
     [set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
+
     [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
     if ( (pycor)= -20 ) and ( (pxcor) = 20)
     if ( (pycor)= -20 ) and ( (pxcor) = 20)
-
     [set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
+
     [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
     if ( (pycor)= -20 ) and ( (pxcor) = -20)
     if ( (pycor)= -20 ) and ( (pxcor) = -20)
-
     [set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
+
     [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
-
     ;; set the edges back to their constant heat
+
     ; set the edges back to their constant pheromone
     ;set-edge-pheromonelevels
     ;set-edge-pheromonelevels
     set old-pheromonelevel pheromonelevel
     set old-pheromonelevel pheromonelevel
Line 267: Line 238:
-
to move-thru-field    ;; turtle procedure for male moths behavior
+
to move-thru-field    ; turtle procedure for male moths behavior
                                                                                      
                                                                                      
   ask moths
   ask moths
   [
   [
   ;MATING PROCEDURE
   ;MATING PROCEDURE
-
   ifelse (ocupado = 1) ;;Si yo estoy ocupado
+
   ifelse (ocupado = 1) ;If i am mating
       [
       [
           stay
           stay
Line 286: Line 257:
             reset-count-down
             reset-count-down
             stay
             stay
-
             ]  ;Si ella esta libre y puede,
+
             ]  ;If she is free and can
             [
             [
             continue
             continue
Line 301: Line 272:
   ifelse count-down = 0  
   ifelse count-down = 0  
     [   
     [   
-
       set number-meeting number-meeting + 1
+
       set number-encounter number-encounter + 1
-
       set label number-meeting          
+
       set label number-encounter          
       reset-count-down
       reset-count-down
       set ocupado 0
       set ocupado 0
Line 325: Line 296:
   [                                                           
   [                                                           
     ifelse (random 25 = 0)                                     
     ifelse (random 25 = 0)                                     
-
     ;; add some additional randomness to the moth's movement, this allows some small
+
     ; add some additional randomness to the moth's movement, this allows some small
-
     ;; probability that the moth might "escape"
+
     ; probability that the moth might "escape"
     [
     [
       rt flutter-amount 60
       rt flutter-amount 60
Line 335: Line 306:
       [       
       [       
       maximize  
       maximize  
-
       if (xcor = 0) and (ycor = 0)      ;por si están revoloteando alrededor de las sexyplants??????????
+
       if (xcor = 0) and (ycor = 0)      ;flying around our sexy plants
       [jump 2
       [jump 2
         rt flutter-amount 70
         rt flutter-amount 70
Line 369: Line 340:
end
end
-
to move-thru-field-females    ;; turtle procedure for female moths behavior
+
to move-thru-field-females    ; turtle procedure for female moths behavior
    
    
   ask females  
   ask females  
Line 379: Line 350:
       stayfemale
       stayfemale
     ]
     ]
-
     [ ;;Si estoy libre
+
     [ ;If i am free
-
       ifelse (any? moths-on neighbors) ;;Hay vecinos
+
       ifelse (any? moths-on neighbors) ;There are neighbors
       [   
       [   
           let flockmates-fem moths-on neighbors
           let flockmates-fem moths-on neighbors
           let nearest-neighbor-fem min-one-of flockmates-fem [distance myself]
           let nearest-neighbor-fem min-one-of flockmates-fem [distance myself]
           ifelse (([nearest-neighbor] of nearest-neighbor-fem) != 0) [
           ifelse (([nearest-neighbor] of nearest-neighbor-fem) != 0) [
-
           ifelse ( ([who] of self)  = ( [who] of ([nearest-neighbor] of nearest-neighbor-fem) ) and (wait-time = 0) ) ;;preguntar si el vecino de mi vecino soy yo:  who-of myself
+
           ifelse ( ([who] of self)  = ( [who] of ([nearest-neighbor] of nearest-neighbor-fem) ) and (wait-time = 0) ) ;ask if the neighbor of my neighbor is me:  who-of myself
           [                     
           [                     
           set ocupado 1
           set ocupado 1
-
              ;change its colour in order to differentiate it by the observer
+
          set color 85    ;change its colour in order to differentiate it by the observer
           stayfemale
           stayfemale
           ] [          continuefemale      ]][continuefemale]
           ] [          continuefemale      ]][continuefemale]
Line 408: Line 379:
     ]
     ]
     [ set count-down count-down - 1  ;decrement-timer
     [ set count-down count-down - 1  ;decrement-timer
-
   set label count-down
+
   set label count-down  
-
  set color 85 
+
     ]
     ]
Line 428: Line 398:
   ask patches in-radius 1[   
   ask patches in-radius 1[   
   set pheromonelevel releaserate
   set pheromonelevel releaserate
-
   set pheromonelevel (heat-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * heat-diffusivity )) * old-pheromonelevel + releaserate)
+
   set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate)
   set old-pheromonelevel pheromonelevel   
   set old-pheromonelevel pheromonelevel   
   draw-plate ]  
   draw-plate ]  
Line 442: Line 412:
;CHEMOATTRACTION
;CHEMOATTRACTION
to maximize  ;; turtle procedure male moth
to maximize  ;; turtle procedure male moth
-
   move-to patch-here  ;; go to patch center
+
   move-to patch-here   
-
   let p max-one-of neighbors [pheromonelevel]  ; 8 surrounding patches (or neighbors4 for the 4 surrounding)
+
   let p max-one-of neighbors [pheromonelevel]   
   let gradient_p [pheromonelevel] of p - pheromonelevel
   let gradient_p [pheromonelevel] of p - pheromonelevel
   ifelse (gradient_p > delta) [
   ifelse (gradient_p > delta) [
   face p  
   face p  
-
   rt random-normal 0 (0.2 * (5 / gradient_p))
+
   rt random-normal 0 (0.2 * (5 / gradient_p))    ;; RANDOM TURNING ANGLE INVERSELY RELATED TO THE GRADIENT OF PHEROMONE CONCENTRATION (model project approximation)
   fd 1
   fd 1
   ]
   ]
Line 462: Line 432:
;; color the patch based on its pheromonelevel
;; color the patch based on its pheromonelevel
to color-patch  ;; Patch Procedure
to color-patch  ;; Patch Procedure
-
   set pcolor scale-color 123 pheromonelevel 30 0
+
   set pcolor scale-color 123 pheromonelevel 50 0
end
end
to-report releaserate
to-report releaserate
-
   report 3 * release-rate ;multiplied by 3 because of the color-patch (if not, the color yellow  48 is not as visible )
+
   report 3 * release-rate  
end  
end  
to-report releaserate-sexyplant
to-report releaserate-sexyplant
-
   report 3 * release-rate-sexyplant ;multiplied by 3 because of the color-patch (if not, the color yellow  48 is not as visible )
+
   report 3 * release-rate-sexyplant         ;Primary sex pheromone components are approximately defined as those emitted by the calling insect that are obligatory
-
end
+
end                                         ;for trap catch in the field at component emission rates similar to that used by the insect.
 +
                                            ;(W. L. Roelofs and R. T. Carde. Responses of Lepidoptera to Synthetic Sex Pheromone Chemicals and their Analogues, Page 386.
-
;; report the heat diffusivity constant that we use for the calculations
+
;; report the pheromone diffusivity constant that we use for the calculations of pheromone diffusion
-
to-report heat-diffusivity
+
to-report pheromone-diffusivity
-
  ;; a few notes on the constants used here:
+
   report number-diffusivity  
-
  ;; --we use .25 as a time step that causes the heat to diffuse at a reasonable pace
+
end  
-
  ;; --we use alpha + .3 instead of just alpha here since alpha would be too
+
-
  ;; small to view any changes between some of the preset materials
+
-
  ;; --these constants are necessary since this model uses an Euler approximation to
+
-
  ;; calculate the pheromonelevel.  the approximation is only valid within a certain range
+
-
  ;; of time-steps and this range changes depending upon the value of alpha.
+
-
  report number-diffusivity ;;.25 * e ^ (-1 / (0.19 + .3))
+
-
   ;;report number-diffusivity
+
-
end ;;0.19 es alpha para el aire
+
to-report wind-forcex
to-report wind-forcex
Line 497: Line 460:
to-report delta
to-report delta
   report 5 - moth-sensitivity
   report 5 - moth-sensitivity
-
  ;report 5 * pheromonelevel / (pheromonelevel + 5) 
+
 
-
end                                                      ;para modificar desde fuera la forma
+
end                                                       
          
          
-
                                                         ;de la funcion de saturación
+
                                                          
to-report saturationlevel
to-report saturationlevel
   report saturation-level-threshold  
   report saturation-level-threshold  
Line 517: Line 480:
-
; Copyright 1998 Uri Wilensky.
+
; Copyright 2014 Valencia_UPV iGEM team
; See Info tab for full copyright and license.
; See Info tab for full copyright and license.
@#$#@#$#@
@#$#@#$#@
GRAPHICS-WINDOW
GRAPHICS-WINDOW
-
956
+
976
-
15
+
12
-
1561
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-
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+
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 +
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5.9
5.9
1
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-50
-50
50
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-50
+
-49
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+
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1
1
1
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SLIDER
SLIDER
-
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+
978
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76
+
637
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826
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1178
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+
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initial-plate-pherolevel
initial-plate-pherolevel
initial-plate-pherolevel
initial-plate-pherolevel
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BUTTON
BUTTON
-
230
+
1480
-
10
+
640
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295
+
1545
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43
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Go
Go
go
go
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BUTTON
BUTTON
-
5
+
1273
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10
+
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+
1389
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672
Setup
Setup
setup
setup
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BUTTON
BUTTON
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137
+
1398
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10
+
640
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1471
-
43
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673
Go Once
Go Once
go
go
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SWITCH
SWITCH
-
1236
+
1216
-
10
+
12
-
1339
+
1317
-
43
+
45
switch
switch
switch
switch
-
0
+
1
1
1
-1000
-1000
SLIDER
SLIDER
-
258
+
32
-
76
+
33
-
430
+
204
-
109
+
66
number-moths
number-moths
number-moths
number-moths
0
0
100
100
-
15
+
5
1
1
1
1
Line 640: Line 603:
SLIDER
SLIDER
-
439
+
33
-
76
+
78
-
611
+
205
-
109
+
111
number-females
number-females
number-females
number-females
0
0
50
50
-
6
+
5
1
1
1
1
Line 655: Line 618:
SLIDER
SLIDER
-
658
+
32
-
10
+
443
-
871
+
245
-
43
+
476
number-diffusivity
number-diffusivity
number-diffusivity
number-diffusivity
0.01
0.01
0.2
0.2
-
0.142
+
0.177
0.001
0.001
1
1
Line 670: Line 633:
PLOT
PLOT
-
20
+
273
-
451
+
337
-
932
+
957
-
645
+
640
Meetings in time
Meetings in time
Time
Time
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SLIDER
SLIDER
-
17
+
27
-
266
+
304
-
189
+
199
-
299
+
337
moth-sensitivity
moth-sensitivity
moth-sensitivity
moth-sensitivity
Line 697: Line 660:
5
5
4.6
4.6
-
0.1
+
0.001
1
1
NIL
NIL
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SLIDER
SLIDER
-
16
+
26
-
222
+
262
-
204
+
214
-
255
+
295
saturation-level-threshold
saturation-level-threshold
saturation-level-threshold
saturation-level-threshold
-
5
+
1
100
100
8
8
Line 718: Line 681:
MONITOR
MONITOR
-
53
+
306
-
478
+
369
-
322
+
575
-
531
+
422
-
number of meetings at this instant
+
number of encounters at this instant
sum [ocupado] of moths
sum [ocupado] of moths
17
17
Line 729: Line 692:
PLOT
PLOT
-
259
+
275
-
118
+
12
-
939
+
955
-
435
+
329
-
Total number of meetings in time
+
Total number of encounters in time
Time
Time
-
Number of meetings
+
Number of encounters
0.0
0.0
1000.0
1000.0
Line 744: Line 707:
"" ""
"" ""
PENS
PENS
-
"total number of matings up to now" 1.0 0 -14070903 true "" "plot sum [number-meeting] of moths"
+
"total number of encounters up to now" 1.0 0 -14070903 true "" "plot sum [number-encounter] of moths"
"males mating at this moment" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"
"males mating at this moment" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"
MONITOR
MONITOR
-
297
+
314
-
147
+
39
-
468
+
507
-
200
+
93
-
total number of matings
+
total number of encounters
-
sum [number-meeting] of moths
+
sum [number-encounter] of moths
17
17
1
1
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SLIDER
SLIDER
-
15
+
27
-
176
+
217
-
186
+
198
-
209
+
250
detection-threshold
detection-threshold
detection-threshold
detection-threshold
0.5
0.5
5
5
-
1
+
1.2
0.1
0.1
1
1
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SLIDER
SLIDER
-
354
+
32
-
10
+
488
-
498
+
176
-
43
+
521
wind-force-x
wind-force-x
wind-force-x
wind-force-x
-0.1
-0.1
0.1
0.1
-
0.03
+
0
0.01
0.01
1
1
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SLIDER
SLIDER
-
507
+
33
-
10
+
534
-
646
+
172
-
43
+
567
wind-force-y
wind-force-y
wind-force-y
wind-force-y
-0.1
-0.1
0.1
0.1
-
0.03
+
0
0.01
0.01
1
1
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SLIDER
SLIDER
-
13
+
27
-
128
+
178
-
184
+
198
-
161
+
211
release-rate
release-rate
release-rate
release-rate
0
0
1
1
-
0.968
+
0.999
0.001
0.001
1
1
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SLIDER
SLIDER
-
14
+
27
-
79
+
346
-
233
+
246
-
112
+
379
release-rate-sexyplant
release-rate-sexyplant
release-rate-sexyplant
release-rate-sexyplant
0
0
-
2
+
1
-
2
+
0.998
0.001
0.001
1
1
Line 836: Line 799:
## WHAT IS IT?
## WHAT IS IT?
-
This model simulates transient and steady-state temperature distribution of a thin plate.
+
This model simulates pheromone diffusion processes and its influence in moths response.
 +
 
 +
 
 +
 
The View shows a square thin plate as viewed from above.  The plate is thermally isolated on the two faces parallel to the view such that heat can flow only in and out from the perimeter of the plate and not into or out of the world.  Heat is kept constant at the edges.  As the simulation runs, heat is transmitted from warmer parts of the plate to cooler parts of the plate as shown by the varying color of the plate.  Therefore, the temperature of the plate begins to change immediately and possibly differently at different locations, gradually converging to a stable state.  Overall, the temperature distribution over the plate is a function of time and location.  In addition to this simple use of the model, you are encouraged to control various paramaters, such as the temperature of each edge edge of the plate and of the center of the plate before--and even while--the model is running.
The View shows a square thin plate as viewed from above.  The plate is thermally isolated on the two faces parallel to the view such that heat can flow only in and out from the perimeter of the plate and not into or out of the world.  Heat is kept constant at the edges.  As the simulation runs, heat is transmitted from warmer parts of the plate to cooler parts of the plate as shown by the varying color of the plate.  Therefore, the temperature of the plate begins to change immediately and possibly differently at different locations, gradually converging to a stable state.  Overall, the temperature distribution over the plate is a function of time and location.  In addition to this simple use of the model, you are encouraged to control various paramaters, such as the temperature of each edge edge of the plate and of the center of the plate before--and even while--the model is running.
Line 920: Line 886:
If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:
If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:
 +
 +
*
* Wilensky, U. (1998).  NetLogo Heat Diffusion model.  http://ccl.northwestern.edu/netlogo/models/HeatDiffusion.  Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
* Wilensky, U. (1998).  NetLogo Heat Diffusion model.  http://ccl.northwestern.edu/netlogo/models/HeatDiffusion.  Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
Line 925: Line 893:
## COPYRIGHT AND LICENSE
## COPYRIGHT AND LICENSE
 +
 +
Valencia_UPV
 +
iGEM 2014
 +
 +
Alejandra González Boscá
 +
Copyright 1998 Uri Wilensky.
Copyright 1998 Uri Wilensky.
Line 1,221: Line 1,195:
@#$#@#$#@
@#$#@#$#@
-
NetLogo 5.0.5
+
NetLogo 5.1.0
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@

Revision as of 03:50, 18 October 2014

breed [ moths moth ] breed [ females female ] breed [ standers stander ]


moths-own [

 number-encounter
 count-down
 ocupado     ;1 mating _ 0 free
 flockmates
 nearest-neighbor

]

females-own [

 count-down
 ocupado    ;1 mating _ 0 free
 wait-time  ;after mating, females don't emit pheromone and shouldn't mate a male

]


patches-own [

 old-pheromonelevel   ; the pheromonelevel of the patch the last time thru go
 pheromonelevel       ; the current pheromonelevel of the patch

]

globals [

 plate-size           ; the size of the plate on which pheromone is diffusing                    
 min-pherolevel       ; the minimum pheromonelevel 
 max-pherolevel       ; the maximum pheromonelevel                       
 old-number-encounter
]


Setup Procedures ;;;

to setup

 clear-all
 set plate-size max-pxcor 
  
 
;TO SEE STANDARS JUST REMOVE ; FROM THE FIVE LINES BELOW 
 ;create-standers 20000
 ;[
  ; setxy random-xcor random-ycor
  ; set color gray
   ;set size 0.5
; ]
 
 ask patches
 [
   set pcolor white
   set-initial-pheromonelevels
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
 ]
 set min-pherolevel min [old-pheromonelevel] of patches
 set max-pherolevel max [old-pheromonelevel] of patches
 ask patches [ draw-plate ]
 
 
 set-default-shape moths "butterfly"
 make-moths number-moths
 
 set-default-shape females "butterfly"
 make-females number-females
 
 

;SEXYPLANTS
 crt 1 [set shape "flower" set size 5 set xcor 0 set ycor 0 set color 86 ]
 crt 1 [set shape "flower" set size 5 set xcor 20 set ycor 20 set color 86 ]
 crt 1 [set shape "flower" set size 5 set xcor -20 set ycor 20 set color 86]
 crt 1 [set shape "flower" set size 5 set xcor 20 set ycor -20 set color 86]
 crt 1 [set shape "flower" set size 5 set xcor -20 set ycor -20 set color 86]
 
;CROP   
 crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 20 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -20 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 10 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -10 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 40 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -40 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 60 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -60 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 60 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -60 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 20 set color 44]  
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 40 set color 44]
 
 reset-ticks

end

to make-moths [ number ]

 create-moths number [
   set color brown
   jump random-float max-pxcor
   set size 2
   set number-encounter 0
   set count-down 40
   set ocupado 0
 ]

end

to make-females [ number ]

 create-females number [
   set color 125
   jump random-float max-pxcor
   set size 2
   set count-down 40
   set ocupado 0
   set wait-time 0
 ]

end

Sets the pheromonelevel for inside of the plate

to set-initial-pheromonelevels  ;; Patch Procedure

 if ((abs pycor) < plate-size) and ((abs pxcor) < plate-size)
 [set pheromonelevel initial-plate-pherolevel]                     ;we consider no pheromone concentration in the field for t=0
 
 ;Sexyplants
 if ( (pycor)= 0 ) and ( (pxcor) = 0)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= 20 ) and ( (pxcor) = 20)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= 20 ) and ( (pxcor) = -20)
 [set pheromonelevel releaserate-sexyplant]
     if ( (pycor)= -20 ) and ( (pxcor) = 20)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= -20 ) and ( (pxcor) = -20)
 [set pheromonelevel releaserate-sexyplant]
 

end


Sets the pheromonelevels of the plate edges and corners
In this simulation this command is not activated, since the we consider an opened volume.

to set-edge-pheromonelevels  ;; patch procedure

 ; set the pheromonelevels of the edges
 if (pxcor >= plate-size) and ((abs pycor) < plate-size)
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and ((abs pycor) < plate-size)
 [set pheromonelevel 0]
 if (pycor >= plate-size) and ((abs pxcor) < plate-size)
 [set pheromonelevel 0]
 if (pycor <= (- plate-size)) and ((abs pxcor) < plate-size )
 [set pheromonelevel 0]
 ; set the pheromonelevels of the corners
 if (pxcor >= plate-size) and (pycor >= plate-size)
 [set pheromonelevel 0]
 if (pxcor >= plate-size) and (pycor <= (- plate-size))
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and (pycor >= plate-size)
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and (pycor <= (- plate-size))
 [set pheromonelevel 0]


end


Runtime Procedures ;;;
Runs the simulation through a loop

to go

 set max-pherolevel max [old-pheromonelevel] of patches
 set min-pherolevel min [old-pheromonelevel] of patches
 
 ask females [set color 125]
 ask standers [set color gray]
 
 move-thru-field ;males
     
 move-thru-field-females
 
 ask patches [
   ;Diffusion process with advection (wind)
   set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4) - wind-forcey * ([old-pheromonelevel] of patch-at-heading-and-distance 0 1) - wind-forcex * ([old-pheromonelevel] of patch-at-heading-and-distance 90 1)) + ((1 - ( 4 * pheromone-diffusivity - 1 * wind-forcey - 1 * wind-forcex )) * old-pheromonelevel)
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
   draw-plate
   ]

   
 if switch = TRUE [
 ask patches
 [
   ;; diffuse the pheromone of a patch with its neighbors
   if ( (pycor)= 0 ) and ( (pxcor) = 0)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
   if ( (pycor)= 20 ) and ( (pxcor) = 20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= 20 ) and ( (pxcor) = -20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= -20 ) and ( (pxcor) = 20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= -20 ) and ( (pxcor) = -20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
   ; set the edges back to their constant pheromone
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
   draw-plate
  ]
  
   ] 
 tick

end


to move-thru-field  ; turtle procedure for male moths behavior

  ask moths
  [
  ;MATING PROCEDURE
  ifelse (ocupado = 1) ;If i am mating
     [
         stay
     ]
     [
         ifelse any? (females-on neighbors) 
         [       
         set flockmates other females-on neighbors
         set nearest-neighbor min-one-of flockmates [distance myself]
         ifelse (([ocupado] of nearest-neighbor) = 0 and ([wait-time] of nearest-neighbor) = 0 )
            [
            set ocupado 1
            reset-count-down
            stay
            ]   ;If she is free and can
            [
            continue
            ]
         ][continue]   
     ]
  ] 

end

to stay

 ifelse count-down = 0 
   [  
     set number-encounter number-encounter + 1
     set label number-encounter         
     reset-count-down
     set ocupado 0
   ] 
   [
     set count-down count-down - 1   ;decrement-timer
     set label count-down   
   ]   

end

to continue  ;MALE MOTH RESPONSE


 ifelse ( pheromonelevel <= detectionthreshold)         
 [                                                            
   ; if there is no detectable pheromone move randomly
   ; flight by non-responding male moths involves short, fast movements in random directions  (J.N. Perry and C.Wall, 1984)
   rt flutter-amount 45    ;RANDOM FLIGHT                                   
 fd 1
 ]                                                            
 [                                                           
   ifelse (random 25 = 0)                                     
   ; add some additional randomness to the moth's movement, this allows some small
   ; probability that the moth might "escape"
   [
     rt flutter-amount 60
   fd 1
   ]
   [
     ifelse (pheromonelevel <= saturationlevel) 
     [       
      maximize 
      if (xcor = 0) and (ycor = 0)       ;flying around our sexy plants
      [jump 2
        rt flutter-amount 70
        fd 1
        ]
      if (xcor = 20) and (ycor = 20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = -20) and (ycor = -20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = 20) and (ycor = -20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = -20) and (ycor = 20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
     ]
    
     [
       rt flutter-amount 60
       fd 1
       ]                                                     
   ]
 ]                                                              
 if not can-move? 1
   [ maximize ]

end

to move-thru-field-females  ; turtle procedure for female moths behavior

  ask females 
  [
    
   ;MATING PROCEDURE 
   ifelse (ocupado = 1)
   [
     stayfemale
   ]
   [  ;If i am free
      ifelse (any? moths-on neighbors) ;There are neighbors
      [  
          let flockmates-fem moths-on neighbors
          let nearest-neighbor-fem min-one-of flockmates-fem [distance myself]
          ifelse (([nearest-neighbor] of nearest-neighbor-fem) != 0) [
          ifelse ( ([who] of self)  = ( [who] of ([nearest-neighbor] of nearest-neighbor-fem) ) and (wait-time = 0) ) ;ask if the neighbor of my neighbor is me:  who-of myself
          [                    
          set ocupado 1
          set color 85    ;change its colour in order to differentiate it by the observer
          stayfemale
          ] [          continuefemale       ]][continuefemale]
      ]
      [
         continuefemale
      ] 
    ]
   ]

end

to stayfemale

 ifelse (count-down = 0)
   [      
     reset-count-down
     set ocupado 0
     set wait-time 100
     continuefemale
    ]
   [ set count-down count-down - 1   ;decrement-timer
 set label count-down    
   ]

end

to continuefemale

      ifelse wait-time > 0 
       [set wait-time wait-time - 1]  ;decrement timer for females after mating
       [pheromone-emission]                                          
      rt flutter-amount 45      ;RANDOM FLIGHT                                            
      if not can-move? 1
      [rt flutter-amount 60]
      fd 1  

end

to pheromone-emission

  ask patches in-radius 1[  
  set pheromonelevel releaserate
  set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate)
  set old-pheromonelevel pheromonelevel  
  draw-plate ] 

end

to-report flutter-amount [limit]

 ;; This routine takes a number as an input and returns a random value between
 ;; (+1 * input value) and (-1 * input value).
 ;; It is used to add a random flutter to the moth's movements
 report random-float (2 * limit) - limit

end

CHEMOATTRACTION

to maximize  ;; turtle procedure male moth

 move-to patch-here  
 let p max-one-of neighbors [pheromonelevel]  
 let gradient_p [pheromonelevel] of p - pheromonelevel
 ifelse (gradient_p > delta) [
 face p 
 rt random-normal 0 (0.2 * (5 / gradient_p))    ;; RANDOM TURNING ANGLE INVERSELY RELATED TO THE GRADIENT OF PHEROMONE CONCENTRATION (model project approximation)
 fd 1
 ]
   [rt flutter-amount 60
     fd 1] 

end

Draws the patches that are within the plate

to draw-plate  ;; Patch Procedure

 if ((abs pycor) <= plate-size) and ((abs pxcor) <= plate-size)
 [color-patch]

end

color the patch based on its pheromonelevel

to color-patch  ;; Patch Procedure

 set pcolor scale-color 123 pheromonelevel 50 0

end

to-report releaserate

 report 3 * release-rate 

end


to-report releaserate-sexyplant

 report 3 * release-rate-sexyplant         ;Primary sex pheromone components are approximately defined as those emitted by the calling insect that are obligatory

end  ;for trap catch in the field at component emission rates similar to that used by the insect.

                                           ;(W. L. Roelofs and R. T. Carde. Responses of Lepidoptera to Synthetic Sex Pheromone Chemicals and their Analogues, Page 386.
report the pheromone diffusivity constant that we use for the calculations of pheromone diffusion

to-report pheromone-diffusivity

 report number-diffusivity 

end

to-report wind-forcex

 report wind-force-x

end

to-report wind-forcey

 report wind-force-y

end

to-report delta

 report 5 - moth-sensitivity
  

end


to-report saturationlevel

 report saturation-level-threshold 

end

to-report detectionthreshold

 report detection-threshold

end


to reset-count-down

 set count-down 40 

end



Copyright 2014 Valencia_UPV iGEM team
See Info tab for full copyright and license.

@#$#@#$#@ GRAPHICS-WINDOW 976 12 1581 627 50 49 5.9 1 2 1 1 1 0 1 1 1 -50 50 -49 49 1 1 1 ticks 20.0

SLIDER 978 637 1178 670 initial-plate-pherolevel initial-plate-pherolevel 0 25 0 1 1 NIL HORIZONTAL

BUTTON 1480 640 1545 673 Go go T 1 T OBSERVER NIL NIL NIL NIL 1

BUTTON 1273 639 1389 672 Setup setup NIL 1 T OBSERVER NIL NIL NIL NIL 1

BUTTON 1398 640 1471 673 Go Once go NIL 1 T OBSERVER NIL NIL NIL NIL 1

SWITCH 1216 12 1317 45 switch switch 1 1 -1000

SLIDER 32 33 204 66 number-moths number-moths 0 100 5 1 1 u HORIZONTAL

SLIDER 33 78 205 111 number-females number-females 0 50 5 1 1 u HORIZONTAL

SLIDER 32 443 245 476 number-diffusivity number-diffusivity 0.01 0.2 0.177 0.001 1 cm^2/s HORIZONTAL

PLOT 273 337 957 640 Meetings in time Time Number of meeting 0.0 1000.0 0.0 10.0 true false "" "" PENS "males mating" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"

SLIDER 27 304 199 337 moth-sensitivity moth-sensitivity 0 5 4.6 0.001 1 NIL HORIZONTAL

SLIDER 26 262 214 295 saturation-level-threshold saturation-level-threshold 1 100 8 1 1 NIL HORIZONTAL

MONITOR 306 369 575 422 number of encounters at this instant sum [ocupado] of moths 17 1 13

PLOT 275 12 955 329 Total number of encounters in time Time Number of encounters 0.0 1000.0 0.0 100.0 true true "" "" PENS "total number of encounters up to now" 1.0 0 -14070903 true "" "plot sum [number-encounter] of moths" "males mating at this moment" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"

MONITOR 314 39 507 93 total number of encounters sum [number-encounter] of moths 17 1 13

SLIDER 27 217 198 250 detection-threshold detection-threshold 0.5 5 1.2 0.1 1 NIL HORIZONTAL

SLIDER 32 488 176 521 wind-force-x wind-force-x -0.1 0.1 0 0.01 1 NIL HORIZONTAL

SLIDER 33 534 172 567 wind-force-y wind-force-y -0.1 0.1 0 0.01 1 NIL HORIZONTAL

SLIDER 27 178 198 211 release-rate release-rate 0 1 0.999 0.001 1 µg/h HORIZONTAL

SLIDER 27 346 246 379 release-rate-sexyplant release-rate-sexyplant 0 1 0.998 0.001 1 µg/h HORIZONTAL

@#$#@#$#@

    1. WHAT IS IT?

This model simulates pheromone diffusion processes and its influence in moths response.



The View shows a square thin plate as viewed from above. The plate is thermally isolated on the two faces parallel to the view such that heat can flow only in and out from the perimeter of the plate and not into or out of the world. Heat is kept constant at the edges. As the simulation runs, heat is transmitted from warmer parts of the plate to cooler parts of the plate as shown by the varying color of the plate. Therefore, the temperature of the plate begins to change immediately and possibly differently at different locations, gradually converging to a stable state. Overall, the temperature distribution over the plate is a function of time and location. In addition to this simple use of the model, you are encouraged to control various paramaters, such as the temperature of each edge edge of the plate and of the center of the plate before--and even while--the model is running.

Heat diffuses ("spreads") at different rates through different media. These rates can be determined and are called the Thermal Diffusivity of the material. The Greek letter alpha is often associated with this value. The diffusivity of a material does not change based on how much of the material there is. It is always the same. Below is a table containing several different materials with different diffusivity rates. See that wood (bottom row) has a lower heat diffusivity than, say, iron. This means that it takes a longer for heat to spread through a wooden object than an iron one. That is one reason why the handles of iron saucepans are wooden, and not the other way round. Also, think of a marble table with iron legs that has just been put out in the sun in a street-side cafe. Which material part of the table do you expect will warm up faster? The model allows you to change thermal diffusivity of the plate in two ways. You can directly change the value of ALPHA to any value you like, or you can indirectly change ALPHA by selecting a material.

      1. Thermal diffusivity of selected materials
MaterialThermal diffusivity
(alpha cm*cm/s)
Wood (Maple)0.00128
Stone (Marble)0.0120
Iron0.2034
Aluminum0.8418
Silver1.7004
    1. HOW IT WORKS

Initialize the plate and edges to have temperatures that equal their respective slider values. Each time through the GO procedure, diffuse the heat on each patch in the following way. Have each patch set its current temperature to the sum of the 4 neighbors' old temperature times a constant based on alpha plus a weighted version of the patch's old temperature. (For those interested, the updated temperature is calculated by using a Forward Euler Method.) Then the edges are set back to the specified values and the old temperature is updated to the current temperature. Then the plate is redrawn.

    1. HOW TO USE IT

There are five temperature sliders which enable users to set four fixed edge temperatures and one initial plate temperature: -- TOP-TEMP - Top edge temperature -- BOTTOM-TEMP - Bottom edge temperature -- IN-PLATE-TEMP - Initial plate temperature -- LEFT-TEMP - Left edge temperature -- RIGHT-TEMP - Right edge temperature

There are two sliders that govern the thermal diffusivity of the plate: -- MATERIAL-TYPE - The value of the chooser is that of the above chart. You must press UPDATE ALPHA for this to change the value of ALPHA. -- ALPHA - The alpha constant of thermal diffusivity

There are four buttons with the following functions: -- SETUP - Initializes the model -- GO - Runs the simulation indefinitely -- GO ONCE - Runs the simulation for 1 time step -- UPDATE ALPHA - press this if you want to set ALPHA to a preset value based on a material selected by the MATERIAL-TYPE chooser

The TIME monitor shows how many time steps the model has gone through.

    1. THINGS TO TRY

Set the paramters on the temperature sliders. Pick a value for ALPHA (or pick MATERIAL-TYPE and press UPDATE ALPHA). After you have changed all the sliders to values you like, press Setup followed by GO or GO ONCE.

    1. THINGS TO NOTICE

How does the equilibrium temperature distribution vary for different edge temperature settings?

Notice how an equilibrium (the steady-state condition) is reached.

Keep track of the units:

VariablesUnits
time0.1 second
temperaturedegrees Celsius
lengthcentimeters
diffusivitysquare centimeters per second
    1. THINGS TO TRY

Try different materials to observe the heat transfer speed. How does this compare to physical experiments?

Try the following sample settings: - Top:100, Bottom:0, Left:0, Right:0 - Top:0, Bottom:100, Left:100, Right:100 - Top:0, Bottom:66, Left:99, Right:33 - Top:25, Bottom:25, Left:100, Right:0

    1. EXTENDING THE MODEL

This model simulates a classic partial differential equation problem (that of heat diffusion). The thin square plate is a typical example, and the simplest model of the behavior. Try changing the shape or thickness of the plate (e.g. a circular or elliptical plate), or adding a hole in the center (the plate would then be a slice of a torus, a doughnut-shaped geometric object).

Add a slider to alter this thickness.

Try modeling derivative or combined boundary conditions.


    1. HOW TO CITE

If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:

  • Wilensky, U. (1998). NetLogo Heat Diffusion model. http://ccl.northwestern.edu/netlogo/models/HeatDiffusion. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
  • Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
    1. COPYRIGHT AND LICENSE

Valencia_UPV iGEM 2014

Alejandra González Boscá


Copyright 1998 Uri Wilensky.

![CC BY-NC-SA 3.0](http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png)

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.

Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at uri@northwestern.edu.

This model was created as part of the project: CONNECTED MATHEMATICS: MAKING SENSE OF COMPLEX PHENOMENA THROUGH BUILDING OBJECT-BASED PARALLEL MODELS (OBPML). The project gratefully acknowledges the support of the National Science Foundation (Applications of Advanced Technologies Program) -- grant numbers RED #9552950 and REC #9632612.

This model was converted to NetLogo as part of the projects: PARTICIPATORY SIMULATIONS: NETWORK-BASED DESIGN FOR SYSTEMS LEARNING IN CLASSROOMS and/or INTEGRATED SIMULATION AND MODELING ENVIRONMENT. The project gratefully acknowledges the support of the National Science Foundation (REPP & ROLE programs) -- grant numbers REC #9814682 and REC-0126227. Converted from StarLogoT to NetLogo, 2001. @#$#@#$#@ default true 0 Polygon -7500403 true true 150 5 40 250 150 205 260 250

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arrow true 0 Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150

box false 0 Polygon -7500403 true true 150 285 285 225 285 75 150 135 Polygon -7500403 true true 150 135 15 75 150 15 285 75 Polygon -7500403 true true 15 75 15 225 150 285 150 135 Line -16777216 false 150 285 150 135 Line -16777216 false 150 135 15 75 Line -16777216 false 150 135 285 75

bug true 0 Circle -7500403 true true 96 182 108 Circle -7500403 true true 110 127 80 Circle -7500403 true true 110 75 80 Line -7500403 true 150 100 80 30 Line -7500403 true 150 100 220 30

butterfly true 0 Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240 Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240 Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163 Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165 Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225 Circle -16777216 true false 135 90 30 Line -16777216 false 150 105 195 60 Line -16777216 false 150 105 105 60

car false 0 Polygon -7500403 true true 300 180 279 164 261 144 240 135 226 132 213 106 203 84 185 63 159 50 135 50 75 60 0 150 0 165 0 225 300 225 300 180 Circle -16777216 true false 180 180 90 Circle -16777216 true false 30 180 90 Polygon -16777216 true false 162 80 132 78 134 135 209 135 194 105 189 96 180 89 Circle -7500403 true true 47 195 58 Circle -7500403 true true 195 195 58

circle false 0 Circle -7500403 true true 0 0 300

circle 2 false 0 Circle -7500403 true true 0 0 300 Circle -16777216 true false 30 30 240

cow false 0 Polygon -7500403 true true 200 193 197 249 179 249 177 196 166 187 140 189 93 191 78 179 72 211 49 209 48 181 37 149 25 120 25 89 45 72 103 84 179 75 198 76 252 64 272 81 293 103 285 121 255 121 242 118 224 167 Polygon -7500403 true true 73 210 86 251 62 249 48 208 Polygon -7500403 true true 25 114 16 195 9 204 23 213 25 200 39 123

cylinder false 0 Circle -7500403 true true 0 0 300

dot false 0 Circle -7500403 true true 90 90 120

face happy false 0 Circle -7500403 true true 8 8 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Polygon -16777216 true false 150 255 90 239 62 213 47 191 67 179 90 203 109 218 150 225 192 218 210 203 227 181 251 194 236 217 212 240

face neutral false 0 Circle -7500403 true true 8 7 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Rectangle -16777216 true false 60 195 240 225

face sad false 0 Circle -7500403 true true 8 8 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Polygon -16777216 true false 150 168 90 184 62 210 47 232 67 244 90 220 109 205 150 198 192 205 210 220 227 242 251 229 236 206 212 183

fish false 0 Polygon -1 true false 44 131 21 87 15 86 0 120 15 150 0 180 13 214 20 212 45 166 Polygon -1 true false 135 195 119 235 95 218 76 210 46 204 60 165 Polygon -1 true false 75 45 83 77 71 103 86 114 166 78 135 60 Polygon -7500403 true true 30 136 151 77 226 81 280 119 292 146 292 160 287 170 270 195 195 210 151 212 30 166 Circle -16777216 true false 215 106 30

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flower false 0 Polygon -10899396 true false 135 120 165 165 180 210 180 240 150 300 165 300 195 240 195 195 165 135 Circle -7500403 true true 85 132 38 Circle -7500403 true true 130 147 38 Circle -7500403 true true 192 85 38 Circle -7500403 true true 85 40 38 Circle -7500403 true true 177 40 38 Circle -7500403 true true 177 132 38 Circle -7500403 true true 70 85 38 Circle -7500403 true true 130 25 38 Circle -7500403 true true 96 51 108 Circle -16777216 true false 113 68 74 Polygon -10899396 true false 189 233 219 188 249 173 279 188 234 218 Polygon -10899396 true false 180 255 150 210 105 210 75 240 135 240

house false 0 Rectangle -7500403 true true 45 120 255 285 Rectangle -16777216 true false 120 210 180 285 Polygon -7500403 true true 15 120 150 15 285 120 Line -16777216 false 30 120 270 120

leaf false 0 Polygon -7500403 true true 150 210 135 195 120 210 60 210 30 195 60 180 60 165 15 135 30 120 15 105 40 104 45 90 60 90 90 105 105 120 120 120 105 60 120 60 135 30 150 15 165 30 180 60 195 60 180 120 195 120 210 105 240 90 255 90 263 104 285 105 270 120 285 135 240 165 240 180 270 195 240 210 180 210 165 195 Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195

line true 0 Line -7500403 true 150 0 150 300

line half true 0 Line -7500403 true 150 0 150 150

pentagon false 0 Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120

person false 0 Circle -7500403 true true 110 5 80 Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90 Rectangle -7500403 true true 127 79 172 94 Polygon -7500403 true true 195 90 240 150 225 180 165 105 Polygon -7500403 true true 105 90 60 150 75 180 135 105

plant false 0 Rectangle -7500403 true true 135 90 165 300 Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285 Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285 Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210 Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135 Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135 Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60 Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90

square false 0 Rectangle -7500403 true true 30 30 270 270

square 2 false 0 Rectangle -7500403 true true 30 30 270 270 Rectangle -16777216 true false 60 60 240 240

star false 0 Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108

target false 0 Circle -7500403 true true 0 0 300 Circle -16777216 true false 30 30 240 Circle -7500403 true true 60 60 180 Circle -16777216 true false 90 90 120 Circle -7500403 true true 120 120 60

tree false 0 Circle -7500403 true true 118 3 94 Rectangle -6459832 true false 120 195 180 300 Circle -7500403 true true 65 21 108 Circle -7500403 true true 116 41 127 Circle -7500403 true true 45 90 120 Circle -7500403 true true 104 74 152

triangle false 0 Polygon -7500403 true true 150 30 15 255 285 255

triangle 2 false 0 Polygon -7500403 true true 150 30 15 255 285 255 Polygon -16777216 true false 151 99 225 223 75 224

truck false 0 Rectangle -7500403 true true 4 45 195 187 Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194 Rectangle -1 true false 195 60 195 105 Polygon -16777216 true false 238 112 252 141 219 141 218 112 Circle -16777216 true false 234 174 42 Rectangle -7500403 true true 181 185 214 194 Circle -16777216 true false 144 174 42 Circle -16777216 true false 24 174 42 Circle -7500403 false true 24 174 42 Circle -7500403 false true 144 174 42 Circle -7500403 false true 234 174 42

turtle true 0 Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel false 0 Circle -7500403 true true 3 3 294 Circle -16777216 true false 30 30 240 Line -7500403 true 150 285 150 15 Line -7500403 true 15 150 285 150 Circle -7500403 true true 120 120 60 Line -7500403 true 216 40 79 269 Line -7500403 true 40 84 269 221 Line -7500403 true 40 216 269 79 Line -7500403 true 84 40 221 269

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@#$#@#$#@ NetLogo 5.1.0 @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ default 0.0 -0.2 0 0.0 1.0 0.0 1 1.0 0.0 0.2 0 0.0 1.0 link direction true 0 Line -7500403 true 150 150 90 180 Line -7500403 true 150 150 210 180

@#$#@#$#@ 0 @#$#@#$#@