Table 3.
Summary of the Python modules developed for the multiscale simulator.
| Python rules | Rule | Objective |
|---|---|---|
| Simulator | simulator.py | Establish grid and neighborhood stencils; perform integrity checks |
| Particles | particle.py | Create new particles; initialize particles on grid |
| Macrophages: | resting.py | Phacytose bacteria or become infected; remove dead particles from grid (natural death or TNF-induced apoptosis) |
| activated.py | Emit chemokine and cytokine; phagocytose bacteria; remove dead cells from grid (natural death or TNF-induced apoptosis) | |
| infected.py | Emit chemokine and cytokine; intracellular bacteria replication; remove dead particles for grid; may be activated by T cells | |
| chronic.py | Emit chemokine and cytokine; intracellular bacteria replication; bursts if max bacterial load reached; remove dead cells | |
| biasmove.py | Create particle with probability p in vascular source site if chemokine value is above threshold | |
| recruit.py | Remove dead T cells from grid | |
| T cells: | Treg.py | regulates T-γ cell's ability to activate macrophages |
| Tgamma.py | Probability of apoptosis on infected or chronically infected macrophage | |
| Tcytotoxic.py | Chance of perforin/granulysin-mediated killing of infected and chronically infected macrophages | |
| biasmove.py | If within threshold for at least one chemokine, make biased move in the direction of the highest concentration of chemo agent | |
| recruit.py | Create particle with probability p in vascular source site if chemokine value is above threshold | |
| death.py | Remove dead T cells from grid | |
| Fields: | growth.py | Grow extracellular bacteria according to the Monod equation |
| solve.py | Calculate the steady-state solution (Av = f) for the oxygen field via Octave routines | |
| gene expression.py | Calculate gene expression for the component genes and run BioXyce | |
| source.py | Add chemokine and cytokine (TNF/CCL2/CCL5/CXCL9) to chemotactic fields | |
| update.py | Run finite-difference diffusion routine | |
| apoptotic phagocytosis | Dictate macrophage behavior under hypoxia | |
| Stats | stats.py | Time series report on key infection variables |
| Image | dump.py | Create images for animations |