Table I. Parameters varied for Latin hypercube sampling.

Parameter	Description1	Default	Range	Distribution	Varied in focused analysis?
αBi	Intracellular Mtb growth rate (per 10 minutes)	0.0015	[0.0002, 0.002]	Uniform	No
αBe	Extracellular Mtb growth rate (per 10 minutes)	0.0007	[0.00015, 0.015]	Log-Uniform	No
pk	Probability of Mr killing bacteria	0.0187	[0.01, 0.1]	Uniform	No
Tactm	Probability of Mi activation by Tγ	0.03	[0.0001, 0.1]	Log-Uniform	No
Mrecr	Probability of macrophage recruitment	0.04	[0.01, 0.1]	Uniform	No
Trecr	Probability of T cell recruitment	0.09	[0.01, 0.1]	Uniform	No
Tmove	Prob of a T cell moving onto an occupied micro-compartment	0.02	[0.00001, 0.1]	Log-Uniform	No
Trrecr	Proportion of Treg cells out of all T cells recruited	0.1	[0.01, 0.2]	Uniform	No
λc	Chemokine diffusion rate (cm2 per 0.1 minutes)	6.27×10−7	[1,7]×10−7	Uniform	No
δc	Chemokine degradation rate (per 0.1 minutes)	0.000916	[0.0005, 0.0015]	Uniform	No
rT	Combined TNF/chemokine threshold for T cell recruitment at a vascular source2	1,767	[0.1,10]×l04	Log-Uniform	No
rM	Combined TNF/chemokine threshold for Mr recruitment at a vascular source2	6,507	[0.1,10]×l04	Log-Uniform	No
sc5	CCL5 production rate (molecules per 10 minutes)	3.55×106	[1,10]×106	Uniform	No
s5m	Macrophage CCL5 saturation threshold (molecules)	5.79×106	[1,100]×l06	Log-Uniform	No
τ5m	Macrophage CCL5 threshold (molecules)	2×l04	[1,100]×104	Log-Uniform	No
λTNF	TNF diffusion rate (cm2 per 0.1 minutes)	6.56×10−7	[1,7]×10−7	Uniform	Yes
δTNF	TNF degradation rate (per 0.1 minutes)	0.0005	[0.0001, 0.001]	Uniform	Yes
sTNF	TNF production rate (molecules per 10 minutes)	1.80×105	[1,100]×l04	Log-Uniform	Yes
papopt	Probability of TNF-induced apopt per 10 minute interval	0.04	[0.001, 0.2]	Uniform	Yes
τTNF3	Macrophage TNF detection threshold (molecules)	10×105	[1,15]×105	Uniform	Yes
rMTNF	Effect of TNF on Mr recruitment2	676	[10,1000]	Log-Uniform	Yes

¹All probabilities are per 10 minute interval.

²Non-dimensional; c.f. II.3.iv-v. of the Agent-Based Model Rules (Supplement 1).

³τ_TNF was divided into separate thresholds for activation (τ_TNFact) and apoptosis (τ_TNFapopt) in the focused analysis.