Description Usage Arguments Details See Also Examples
The generic function chemotaxis
implements a bacterial movement in the Moore neighbourhood to the highest substrate concentration.
1 2 3 4 | chemotaxis(object, population, j, chemo, occupyM)
## S4 method for signature 'Bac'
chemotaxis(object, population, j, chemo, occupyM)
|
object |
An object of class Bac. |
population |
An object of class Arena. |
j |
The number of the iteration of interest. |
chemo |
The vector that contains the prefered substrate. |
occupyM |
A matrix indicating grid cells that are obstacles |
Bacteria move to a position in the Moore neighbourhood which has the highest concentration of the prefered substrate, which is not occupied by other individuals. The prefered substance is given by slot chem
in the Bac
object. If there is no free space the individuals stays in the same position. If the concentration in the Moore neighbourhood has the same concentration in every position, then random movement is implemented.
1 2 3 4 5 6 7 | data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05, chem = "EX_o2(e)",
minweight=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
arena <- addOrg(arena,bac,amount=10) #add 10 organisms
arena <- addSubs(arena,40) #add all possible substances
chemotaxis(bac,arena,1, "EX_glc(e)", arena@occupyM)
|
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
Tutorials: https://bacarena.github.io
Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
Development and help: https://github.com/euba/bacarena
[1] "Median lower bound for non-zero and non-Inf exchanges is:-106"
Loading required package: glpkAPI
using GLPK version 4.65
[1] 17 13
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