Team:Valencia UPV/Modeling/sexyplants.nlogo

From 2014.igem.org

(Difference between revisions)

Latest revision as of 03:57, 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. https://2014.igem.org/Team:Valencia_UPV

1. HOW IT WORKS

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1. HOW TO USE IT

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1. THINGS TO TRY

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1. THINGS TO NOTICE

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1. EXTENDING THE MODEL

This model simulates a classic partial differential equation problem (that of heat diffusion with advection).

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:

Valencia_UPV iGEM, Alejandra González Boscá (2014) Pheromone diffusion and moths response with Sexyplants

1. COPYRIGHT AND LICENSE

Valencia_UPV iGEM 2014

Alejandra González Boscá

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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

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 This model simulates pheromone diffusion processes and its influence in moths response.
+https://2014.igem.org/Team:Valencia_UPV
-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.
-### Thermal diffusivity of selected materials
-<table border>
-<tr><th>Material<th>Thermal diffusivity<br>(alpha cm*cm/s)
-<tr><td>Wood (Maple)<td>0.00128
-<tr><td>Stone (Marble)<td>0.0120
-<tr><td>Iron<td>0.2034
-<tr><td>Aluminum<td>0.8418
-<tr><td>Silver<td>1.7004
-</table>
 ## HOW IT WORKS
+Visit our wiki!
-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.
 ## HOW TO USE IT
+Visit our wiki!
-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.
 ## THINGS TO TRY
+Visit our wiki!
-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.
 ## THINGS TO NOTICE
+Visit our wiki!
-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:
-<table border>
-<tr><th>Variables<th>Units
-<tr><td>time<td>0.1 second
-<tr><td>temperature<td>degrees Celsius
-<tr><td>length<td>centimeters
-<tr><td>diffusivity<td>square centimeters per second
-</table>
-## 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
 ## 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).
+This model simulates a classic partial differential equation problem (that of heat diffusion with advection).
-Add a slider to alter this thickness.
-Try modeling derivative or combined boundary conditions.
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 If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:
-*
+* Valencia_UPV iGEM, Alejandra González Boscá (2014) Pheromone diffusion and moths response with Sexyplants
-* 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.
 ## COPYRIGHT AND LICENSE
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-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.
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