HIV dynamics: cellular automata approach

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Ricardo_cruz Ricardo Cruz (Author)

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Model correction

Hi Ricardo, thank you for making this model - that was exactly what I was looking for. However, when comparing the simulation to the published results of Santos et al I found that the regeneration of dead cells is treated incorrectly. This results in a kind of wave like behaviour of healthy and infected cell fractions in later stages of the simulation where they should be asymptotic. In your model implementation it is possible that a healty cell can become infected at any time with probability pinfec where in Santos publication that is only possible upon transition from a dead cell to a new healthy cell. I admit that the original paper from Santos can be easily misinterpreted at this point. It is better described in later publications [1]. I modified your model, where results are looking more like in literature. Regards Andreas Hillmann MSc Bioinformatics [1] Figueirêdo, P. H., Coutinho, S. & Zorzenon dos Santos, R. M. Robustness of a cellular automata model for the HIV infection. Phys. A Stat. Mech. its Appl. 387, 6545–6552 (2008).

Posted over 9 years ago

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; states
; T  healthy
; A1 infected stage 1
; A2 infected stage 2
; D  dead

globals [
  T T. A1 A2 D  ; status colors
]

patches-own [ nA1 nA2 time ]

to setup
  clear-all

  set T green
  set T. 63
  set A1 orange
  set A2 red
  set D black

  ask patches [
    set pcolor T
    set time 0
  ]
  ask n-of (Phiv * max-pxcor * max-pycor) patches [
    set pcolor A1
  ]

  reset-ticks
end 

to-report rule1  ; T
  if nA1 >= 1 or nA2 >= R [
    report A1
  ]
  report T
end 

to-report rule1.  ; T.
  if nA1 >= 1 or nA2 >= R [
    report A1
  ]
  if random-float 1 < Pinf [
    report A1
  ]
  report T.
end 

to-report rule2  ; A1
  if time >= tao [
    report A2
  ]
  report A1
end 

to-report rule3  ; A2
  report D
end 

to-report rule4  ; D
  if random-float 1 < Prepl [
    report T.
  ]
  report D
end 

to update
  ask patches [
    let N neighbors
    set nA1 count N with [ pcolor = A1 ]
    set nA2 count N with [ pcolor = A2 ]
  ]

  ask patches [
    let ncolor pcolor
    ifelse pcolor = T  [set ncolor rule1][
    ifelse pcolor = T. [set ncolor rule1.][
    ifelse pcolor = A1 [set ncolor rule2][
    ifelse pcolor = A2 [set ncolor rule3][
    ifelse pcolor = D  [set ncolor rule4][
    ]]]]]

    ifelse ncolor != pcolor [
      set pcolor ncolor
      set time 0
    ][
    set time time + 1
    ]
  ]
  tick
end 

There is only one version of this model, created over 9 years ago by Ricardo Cruz.

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