From: Phage-induced diversification improves host evolvability
Symbol | Description | Value | Unit |
---|---|---|---|
R | Resource concentration | Variable | μg m l −1 |
N i | Density of host strain i | Variable | cells m l −1 |
V i | Density of virus strain i | Variable | virions m l −1 |
N init | Initial host density | 4.6×104 | cells m l −1 |
V init | Initial virus density | 8.1×105 | virions m l −1 |
ω | Chemostat dilution rate | 0.0033 | mi n −1 |
R 0 | Resource supply concentration | 2.2 | μg m l −1 |
ε | Resource conversion rate | 2.6×10−6 | μg cel l −1 |
γ | Maximum resource uptake rate | 0.0123 | μg mi n −1 |
K | Half-saturation constant | 4 | μg m l −1 |
δ i | Growth scaling for host h i | Range [δ min ,δ max ] | scalar |
δ min | Min. growth scaling factor | 0.8 | scalar |
δ max | Max. growth scaling factor | 1.2 | scalar |
ϕ | Maximum adsorption rate | 0.104×10−8 | ml(min cell)−1 |
θ ij | Ads. scaling for v j on h i | Range [0,ϕ] | scalar |
β | Burst size | 71 | virions |
h i | Genotype of bacteria i | Range [0,1] | scalar |
v j | Genotype of phage j | Range [0,1] | scalar |
| Resistance phenotype of bacteria i | Range [0,1] | scalar |
| Infection phenotype of phage j | Range [0,1] | scalar |
h init | Initial bacteria genotype | 0.2 | scalar |
v init | Initial phage genotype | 0.2 | scalar |
s | Specificity of phage | 100 | scalar |
M B | Host mutation rate | 10−6 | cel l −1 |
M V | Virus mutation rate | 10−6 | virio n −1 |
σ B | Std. dev. of host mut. range | 0.01 | scalar |
σ V | Std. dev. of virus mut. range | 0.01 | scalar |
μ B | Bacterial mutation size | Random variable | scalar |
μ V | Phage mutation size | Random variable | scalar |
Δt | Integration timestep | 10 | min |
T | Simulation duration | 20×106 | min |
ρ | Resolution of genotype diversity | 0.01 | scalar |
L | Chemostat volume | 1 | ml |