HIV dynamics: cellular automata approach
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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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HIV dynamics: cellular automata approach.png | preview | Preview for 'HIV dynamics: cellular automata approach' | over 9 years ago, by Ricardo Cruz | Download |
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Andreas Hillmann
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