The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Fig 2
DNA damage from Beacon Calculus simulations.
(a) Cells undergo DNA damage (red) and may carry it forward for generations before an Ada molecule (blue) is generated to repair it. Ada is methylated (gold) as it repairs DNA damage creating a positive feedback loop whereby methylated Ada upregulates transcription of the ada gene. Ada levels are reduced through successive cell divisions. (b) DNA damage model written in the Beacon Calculus. (c-d) Average total Ada and meAda per cell over time. Each trace corresponds to a simulation of a growing population of cells for (c) low DNA damage (kdmg = 0.0001) and (d) high DNA damage (kdmg = 0.01). In each of panels (c-d), 25 simulations are shown. Values for k_basal and k_division are from [26] while k_me is from [30]. Values for k_dmg and kMax were approximated based on the results in [31].