Comparison of 'deathrate' and 'removeM'

[zhssakura]

Dear authors,

I have some questions about the parameter 'deathrate' and function removeM.

I noticed that currently there are only two main factors that would affect the biomass accumulation process in BacArena: spaces and nutrient availability. The parameter 'deathrate' would affect the biomass curve only if there's no FBA solution to remain a growth. This is, however, a bit confusing me when I use the parameter of 'deathrate' since I assume that microbes would also die when there are sufficient nutrients if factors such as inhibitory substances, acidity, drying, temperature are not suitable for their living (ref: What Factors Are Required for Microbes to Grow, Survive, and Die? https://onlinelibrary.wiley.com/doi/full/10.1002/jcp.25428). So I would assume that the 'deathrate' described the reduction speed of biomass due to the limits of nutrients and space? Is this parameter a percentage when applied to exponential growth but a weight (unit pg) when for the linear growth? Please correct me if I'm wrong :)

---

@title Function for letting organisms grow linearly
growth <- fbasol$fluxes[object@rbiomass]
if(growth > 0){
grow_accum <- growth + biomass
} else grow_accum <- biomass - object@deathrate*tstep
#cat("\t", growth, biomass, grow_accum, "\n")
return(grow_accum)
})

#' @title Function for letting organisms grow exponentially
growth <- fbasol$fluxes[object@rbiomass]
if(growth > 0){
grow_accum <- (growth * biomass + biomass)
} else grow_accum <- biomass - object@deathratebiomasststep
#cat("\t", growth, biomass, grow_accum, "\n")
return(grow_accum)
})

Then I've found the function of removeM, which can remove individuals from a community randomly. This is a good representative function for cells being killed not because of the limitation of food or space. I wonder if this function can be further improved to achieve:
a) to set values to remove individuals of particular species (currently it is applied to the whole community);
b) to provide an option like lyse, so that when individuals were removed, their biomass composition can be available to their neighbouring cells.

Thank you very much.
P.S.My research is inclined to simulate a multi-species community.

Sincerely,

Shan