Adding oxygen after some time

delayed-o2.R

library(BacArena)
data("Ec_core")

bac  <- Bac(Ec_core)
arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac,amount=30)
arena <- addSubs(arena, smax=0.05, mediac="EX_glc(e)", unit="mM")
arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_nh4(e)"), unit="mM") 

 # Aenaerobic simulation for 6h
sim   <- simEnv(arena, time=6, with_shadow = T)

# Add oxygen and continue simulation for another 6 hours
sim <- addSubs(sim, smax=0.05, mediac="EX_o2(e)", unit="mM")
sim   <- simEnv(sim, time=6)

plotGrowthCurve(sim)

# anaerobic growth with production of fermentation products (acetate,formate),
# which stops after oxygen is added but continous with declining oxygen levels again.
plotSubCurve(sim, c("EX_glc(e)", "EX_o2(e)", "EX_for(e)", "EX_ac(e)"))[[2]]

growth.png

substances.png