Structure of the S4 class "growthSimulation"

Structure of the S4 class growthSimulation as framework for the growth environment and container for agent-based flux balance analysis.

Slots

n_rounds

integer for the number of simulation rounds that were already performed for this growthSimulation object.

deltaTime

double for length of each time step for the simulation in hours.

rMotion

double. Maximum x- and y distance a cell can travel by means of random movement per simulation round. Unit: \(\mu\)m per minute.

models

List for Organism objects to represent the different strains in the simulation.

history

list with recordings of simulation status information at each simulation round.

cellDT

Data table with individual cell information (e.g. size, position, velocity, type)

universePolygon

Matrix specifying the corners of the polygon that defines the growth environment boundaries. 2-dimensional: x and y.

environ

Object of S4-class growthEnvironment, that specifies the environment mesh layout, compounds, and their concentrations.

recordDir

Directory name, in which intermediate compound concentrations are recorded if turned on in run_simulation. Files in this directory are meant as internal resource and not for direct analysis outside of this package.

rcdt

data.table that stores the last reduced cost values of each cell's exchange reactions. This information could indicate growth limiting compounds.