Simulation for lipids and bacteria

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alvin lam (Author)

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globals [time speed R pHFactor TFactor Ea A pHs lipidConNow]
breed [bacteria bacterias]
breed [lipids lipid]
bacteria-own [age timing]

to setup
  clear-all
  set-default-shape bacteria "bacteria-2-membrane"
  create-bacteria 50 [
    set color green
    set size 1.5
    setxy random-xcor random-ycor
    set age 0
  ]

  set-default-shape lipids "circle"
  create-lipids lipid-concentration * 300 [
    set color white
    set size 1
    setxy random-xcor random-ycor
  ]

  set R 8.314
  set pHs pH
  set A 0
  set Ea 0

  check-Activation-energy T pH
  check-speed A Ea T
  set time 0
  reset-ticks
end 

to spawn
  create-bacteria 50 [
    set color green
    set size 1.5
    setxy random-xcor random-ycor
    set age 0
  ]
end 

to go
  ChangepH
  check-Activation-energy T pHs
  check-speed A Ea T

  ask bacteria [
    move
    reproduce
    aging
  ]

  ask lipids [
    move
  ]

  check-collisions
  tick
  set time time + 1
end 

to move
  rt random 360
  fd 1
end 

to reproduce
  set timing timing + speed
  if age > 10 and timing > 1 [
    hatch-bacteria 1 [
      set age 0
      set color green
      set timing 0
    ]
    set age 0
    set timing 0
  ]
end 

to aging
  set age age + 1
  if age > 20 [
    die
  ]
end 

to check-collisions
  ask bacteria [
    let collided-turtle one-of lipids with [distance myself < 1]
    if collided-turtle != nobody [
      ; Handle collision
        ask collided-turtle [ die ]
        die
    ]
  ]
end 

to check-speed[AV Energy TV]
  let Es Energy * -1
  let Arrhenius (A * exp ( Es / (R * TV)))
  if Arrhenius != 0 [
    set speed (ln 2 / Arrhenius)
  ]
end 

to check-Activation-energy[TV pHV]

  ifelse pHV < 5.5 [
    pHLow
  ] [
  ifelse pHV >= 5.5 and pH <= 8.5 [
    set pHFactor 1
  ] [

  if pHV > 8.5 [
    pHHigh
  ]
    ]
  ]

  ifelse TV < 30 [
    TLow
  ] [

  ifelse TV >= 30 and TV <= 45 [
    set TFactor 1
  ] [

  if TV > 45[
    THigh
  ]
      ]
  ]

  set Ea (50000 + random 50000) * pHFactor * TFactor
  set A (10 ^ 8 + random-float (10 ^ 12 - 10 ^ 8)) * pHFactor * TFactor
end 

to pHLow
  let Lower 5.5 - pHs
  set pHFactor (Lower / 10) + 1
end 

to pHHigh
  let High pHs - 8.5
  set pHFactor (High / 10) + 1
end 

to TLow
  let Lower 30 - T
  set TFactor (Lower / 10) + 1
end 

to THigh
  let High T - 45
  set TFactor (High / 10) + 1
end 

to ChangepH
  let lc100 lipid-concentration * 100
  let minusing pH - 7

  if pHs > 7
  [
    set pHs pH + ((count lipids / lc100) - minusing)
  ]


  set lipidConNow (count lipids / lc100 / 3) * lipid-concentration
  output-print (word "pH: " pHs word " lipidConcentration: "  lipidConNow)
end

There is only one version of this model, created 12 months ago by alvin lam.

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