|
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
|
