Growth Related
|
Maximum growth rate (μ m a x) |
1.25 |
h-1 |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Steepness of the growth rate function (K) |
0.0035 |
g.L-1 |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Per capita consumption of abiotic nutrient (q A) |
{1x10-5, if 0 < A ≤ 0.1, and 5x10-5, if 0.1 < A ≤ T } |
[A]/[m] |
Assumed |
Per capita consumption of goods (q G) |
{1x10-4, if 0 < G ≤ 0.2, and 5x10-4, if 0.2 < G } |
[G]/[m] |
Assumed |
Mass’ threshold for division (m d i v) |
500 |
fg |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Rate of mass loss due to starvation (λ) |
0.05 |
h-1 |
Assumed |
Cell mass (m) |
Varies |
fg |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Cell density (ρ) |
50 |
fg/µm3 |
Assumed |
Cell length (L) |
4 |
µm |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Substrate Related
|
Fraction of diffused abiotic nutrient (d A) |
0.9 |
unitless |
Assumed |
Concentration of abiotic nutrients (A) |
0 – T |
g.L-1 |
Emerged from simulation |
Concentration of goods (G) |
Varies |
g.L-1 |
Emerged from simulation |
Parameters
|
Cost of good production (c) |
0 – 1 |
unitless |
Assumed |
Fraction of secreted good (s) |
0 – 1 |
unitless |
Assumed |
Fraction of good diffused (d G) |
0 – 1 |
unitless |
Assumed |
Conversion factor of mass consumed given a concentration of abiotic nutrients (β 1) |
1 |
1/[A] |
Assumed |
Conversion factor of mass to goods (β 2) |
1 |
[G]/[A][m] |
Assumed |
Threshold for cell death (m d e a t h) |
0.05m d i v |
[m] |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Limiting concentration of molecules promoting growth (T) |
1 |
g.L-1 |
Assumed |
Length of a grid element (square) |
4 |
µm |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |
Time step (τ) |
1 |
min |
(Carvalho et al. 2018CARVALHO G, BALESTRINO D, FORESTIER C & MATHIAS JD. 2018. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4: 1-8. DOI: 10.1038/s41522-018-0049-2.) |