Table 1 The list of model parameters
Parameter symbol | Description | Values |
|---|---|---|
L | Protein binding site amino acid sequence length | 5, 10, 15, 20, 25, 30 |
μ hp | Host protein mutation rate per a set of receptors | 0.002, 0.01, 0.05 |
μ vp | Virus protein mutation rate | 0.1 |
N TF | The number of transcription factor genes | 5 |
N R | The number of receptor genes | 5 |
N ER | The minimum number of required expressed receptors | 1, 3 |
ϵ seqM | Amino acid matching threshold for receptor binding | 90 %, 75 % |
k I | Offspring survival probability from both infected parents | 0.5, 0.8 |
ξ | \( \frac{\#\ of\ infections}{\#\ of\ contacts} \) | Self-determined during simulations |
η | \( \frac{\#\ of\ survived\ of fspring}{\#\ of\ of fspring\ candidates} \) | Self-determined during simulations |
K | Carrying capacity | 1000 |
M init | Initial host population size | 150 |
b | Growth rate | 0.15 |
λ N | Natural death rate | 0.09 |
λ D | Disease-related death rate | 0.06 |
γ | Recovery rate | 0.2 |
r | Host-virus contact rate | 2 |
c | Network density | 0.4 |
μ | Mutation rate per gene regulatory network | 0.1 |
ρ | Conditional rate of interaction addition in gene regulatory network | 0.028 |
ϕ | Conditional rate of interaction deletion in gene regulatory network | 0. 042 |
δ | Conditional rate of interaction modification in gene regulatory network | 0. 958 |
σ | Selection pressure | 0.1 |
a | Gene expression mapping sigmoid function parameter | 100 |