This page was automatically generated by NetLogo 5.0.4.

The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.



Fluorescence Recovery After Photobleaching

powered by NetLogo

view/download model file: frap.nlogo

WHAT IS IT?

This model is demontrating fluorescence recovery after photobleaching (FRAP). Green dots represent molecules that are fluorescing, and black dots represent molecules that are permanently not fluorescing.

HOW IT WORKS

Mobile molecules have random movement. When the user hits "zap", molecules in the red square no longer fluoresce. The graph graphs the percentage of molecules in the red square that fluoresce.

HOW TO USE IT

Change the initial number of molecules and the amount of mobile molecules.

THINGS TO NOTICE

Notice how the graph changes when the initial variables change.

CODE

turtles-own[immobile?]
patches-own[in-box?]


to setup
  ca
  set-default-shape turtles "circle"
  setup-patches
  create-turtles initial-molecules [
    set color lime 
    setxy random-xcor random-ycor
    ifelse random 100 < immobile [set immobile? true][set immobile? false]
  ] 
  reset-ticks 
end

to zap
  ask turtles[
    let to-be-zapped? false
    ask patch-here[
      if in-box? [set to-be-zapped? true]
    ]
    if to-be-zapped? [set color black]
  
  ]
end

to setup-patches
  ask patches [
    ifelse (pxcor = 20 and pycor < 18 and pycor > -20) or 
       (pxcor = -20 and pycor < 18 and pycor > -20) or
       (pycor = 18 and pxcor <= 20 and pxcor >= -20) or
       (pycor = -20 and pxcor <= 20 and pxcor >= -20)
       [set pcolor red]
       [set pcolor white]
    ifelse (pxcor > -20 and pxcor < 20 and pycor > -20 and pycor < 18) 
      [set in-box? true]
      [set in-box? false]
  ]
end

to move
  ask turtles with [immobile? = false][set heading random 360 fd 1]
  tick
end
   
 
  • Click setup, and then click move. Notice that not all molecules are moving--some remain motionless.

  • Now, click zap and notice that the molecules inside of the red square are now all black. See how the molecules diffuse out of the red square and eventually are evenly distributed in the environment. What limit does the graph appear to be approaching? Why does it not return to 100?

  • Click zap again in the same experement. Does the percent fluorescing in the red box return to the same level? How do you explain this result?
  • Now raise the percent immobile to 75% and predict how you think the results might change. Repeat the procedure described above, and notice how it differs from the initial experement. Where these the results that you predicted?