Table 1.
Parameter values for individual based models (IBMs).
| Parameter | Definition | Value(s) |
|---|---|---|
| ENVIRONMENTAL | ||
| Width, height, length | Spatial extent of the three-dimensional environment | 43,200 μm |
| RESOURCE-RELATED | ||
| Resource supply rate | Probability of a resource particle entering per time step | 0.1–1.0 |
| Resource particle size | Simulated diameter based on the equation for the volume of a sphere and realistic resource particle sizes | 4000–8600 μm |
| Necromass value | Nutritional worth of necromass | 1–100 |
| Resource diversity | Number of resource types that are supplied | 1–10 |
| Resource-specific “lock-and-key” constraint | For “lock-and-key” models, the probability of breaking down a resource particle in a given time step | 0.01–1.0 |
| SPECIES TRAITS | ||
| Specific maintenance | Value deducted from an individual's cell quota for maintenance. Intended to be independent of cell size | 0.001–0.01 |
| Dispersal rate | Greatest distance individuals can disperse in one time step, a percent of 43,200 μm | 1–100% |
| Resuscitation rate | Probability that each individual has of randomly resuscitating; varies among species | 0.001–0.01 |
| Maintenance-reduction | Amount by which maintenance energy is decreased when transitioning to dormancy; varies among species | 10–100% |
| Immigration rate | Probability of an individual entering per time step | 0.01–0.1 |
| Growth rate | Species-specific probability of reproducing per time step | 0.1–1.0 |
| Log-series parameter (α) | Species form of the log-series distribution, often used to simulate ecological metacommunities, which generally takes values greater than 0.95 | 0.95–0.99 |
Values for input parameters were randomly chosen with ranges that fulfilled several requirements, including: (1) spanning an order of magnitude, (2) biologically reasonable values when available, (3) ranges that produced computationally feasible abundances of organisms and resource particles (up to ~104) within reasonable simulation times (up to several minutes for a single IBM). Each time step represented 20 min of real time, i.e., the amount of time a cell of E. coli can either reproduce once or disperse across 43,200 μm.