Table 2 Model parameters used in simulations of infection and immune response unless otherwise specified
Parameter | Value | Reference / justification |
|---|---|---|
Immune killing rate dei2 | 1.16 × 10−11 cell−1 s−1 | Selected for comparable killing rate by viral death |
Cytokine production rate pC | 1.16 × 10−4 cell−1 s−1 | Selected for maximum total cytokine on the order of 1 k in typical simulations |
Cytokine decay rate cC | 2.31 × 10−5 s−1 | Selected for a diffusion length of approximately eight cells |
Cytokine transport rate kC | 5.79 × 10−6 site s−1 | Selected for appreciable delay in inflammatory signaling |
Lymph node cytokine decay rate ccl | 5.79 × 10−6 s−1 | Selected for cytokine clearance by two weeks |
Immune cell transport rate ke | 1.16 × 10−5 s−1 | Selected for appreciable delay in immune cell recruitment |
Immune cell decay rate dE | 1.16 × 10−5 s−1 | Selected for immune cell clearance by two weeks |
Cytokine-induced immune cell production rate pel | 1.16 × 10−9 cell s−1 | Selected for marginal induction of immune cell production |
Cytokine-activated immune cell production rate rel | 5.79 × 10−8 s−1 | Selected for significant rate-limited production of immune cell production |
Immune cell production midpoint Kel | 500 cells | Selected for maximum total immune cells on the order of 3 k in typical simulations |
Number of local epithelial cells Ne | 1600 cells | Calculated from spatial model specification |
Total contact surface area AE | 25 site surfaces | Assumed based on epithelial sheet geometry |
Cytokine diffusion parameter DC | 0.16 μm2 s−1 | [17] |
Sampling fraction | 0.1% | Selected for mostly random immune cell seeding |
Chemotaxis multiplier λc | 10,000 | Typical CPM value for reasonable chemotaxis |
Immune cell-medium contact coefficient | 20 | Selected for preferential attachment of immune cells not with each other |
All other contact coefficients | 25 | Selected for preferential attachment of immune cells not with each other |