Ranges for Host-specific PRCC
Parameter	Unit*	Baseline Value	Min	Max
Bacterial carrying capacity of each grid compartment	Bacteria	115
Intracellular bacterial growth rate	h−1	0.027
Extracellular bacterial growth rate	h−1	0.015
Rate of death of bacteria trapped in caseated compartments	h−1	5.1
Number of host cell deaths causing caseation		9	7	11
Time to heal caseation	Days	10	8	12
TNF threshold for causing apoptosis	Molecules	1150	920	1380
Rate of TNF induced apoptosis	s−1	1.7×10-6	1.3×10-6	2.04×10-6
Minimum chemokine concentration allowing chemotaxis	Molecules	0.47	0.4	0.6
Maximum chemokine concentration allowing chemotaxis	Molecules	480	380	570
Initial macrophage density	Fraction of grid comp.	0.04	0.03	0.05
Time steps before a resting macrophage can move	Timesteps	3	2.4	3.6
Time steps before an activated macrophage can move	Timesteps	19	15	23
Time steps before an infected macrophage can move	Timesteps	170	135	200
TNF threshold for activating NFkB	Molecules	75	60	90
Rate of TNF induced NFkB activation	s−1	1.06×10-5	8.5×10-6	1.3×10-5
Number of bacteria resting macrophage can phagocytose	Bacteria	1
Probability of resting macrophage killing bacteria		0.12	0.1	0.15
Adjustment for killing probability of resting macrophages with NFkB activated		0.2	0.15	0.25
Number of extracellular bacteria that can activate NFkB	Bacteria	250	200	300
Threshold for intracellular bacteria causing chronically infected macrophages	Bacteria	12	10	15
Threshold for intracellular bacteria causing macrophage to burst	Bacteria	23	18	30
Number of bacteria activated macrophage can phagocytose	Bacteria	5	4	6
Probability of an activated macrophage healing a caseated compartment in its Moore neighborhood		0.0055	0.0044	0.0066
Probability of a T-cell moving to the same compartment as a macrophage		0.046	0.035	0.055
IFN γ-producing T-cell probability of inducing Fas/FasL mediated apoptosis		0.035	0.03	0.04
IFN γ-producing T-cell probability of producing TNF		0.045	0.04	0.05
IFN γ-producing T-cell probability of producing IFN		0.35	0.3	0.45
Cytotoxic T-cell probability of killing a macrophage		0.009	0.007	0.010
Cytotoxic T-cell probability of killing a macrophage and all of its intracellular bacteria		0.7	0.6	0.9
Cytotoxic T-cell probability of producing TNF		0.05	0.04	0.06
Regulatory T-cell probability of deactivating activated macrophage		0.008	0.006	0.01
Time before maximum recruitment rates are reached	Timesteps	980	790	1180
Macrophage maximal recruitment probability		0.32	0.25	0.4
Macrophage chemokine recruitment threshold	Molecules	0.86	0.7	1
Macrophage TNF recruitment threshold	Molecules	0.011	0.009	0.015
Macrophage half sat for TNF recruitment	Molecules	1.6	1.3	2
Macrophage half sat for chemokine recruitment	Molecules	2.2	1.8	2.6
IFN γ-producing T-cell maximal recruitment probability		0.15	0.12	0.18
IFN γ-producing T-cell chemokine recruitment threshold	Molecules	0.07	0.06	0.09
IFN γ-producing T-cell TNF recruitment threshold	Molecules	1.3	1	1.6
IFN γ-producing T-cell half sat for TNF recruitment	Molecules	1.3	1	1.6
IFN γ-producing T-cell half sat for chemokine recruitment	Molecules	2	1.5	2.5
Cytotoxic T-cell maximal recruitment probability		0.12	0.1	0.15
Cytotoxic T-cell chemokine recruitment threshold	Molecules	4.5	3.6	5.4
Cytotoxic T-cell TNF recruitment threshold	Molecules	1.3	1	1.5
Cytotoxic T-cell half sat for TNF recruitment	Molecules	1.2	1	1.5
Cytotoxic T-cell half sat for chemokine recruitment	Molecules	9	7	10
Regulatory T-cell maximal recruitment probability		0.03	0.02	0.04
Regulatory T-cell chemokine recruitment threshold	Molecules	2	1.5	2.5
Regulatory T-cell TNF recruitment threshold	Molecules	1.7	1.3	2
Regulatory T-cell half sat for TNF recruitment	Molecules	2.2	1.8	2.7
Regulatory T-cell half sat for chemokine recruitment	Molecules	1.5	1.2	1.8

^*Conversion factor: 10 min/timestep.