Table 3.

Parameters. When there is a range for a value, it is set randomly by the model.

Parameter	Description	Value	Source
N	Size of grid (N × N)	100	(Segovia-Juarez et al., 2004)
Nv	Number of blood vessels	49	(Cilfone et al., 2013)
${\varphi }_{O_b}$ (Micromoles/cell/hr)	Oxygen consumption rate of bacteria	$20.8\times {10}^{-6}$	(Sershen et al., 2016)
${\varphi }_{O_{mr}}$ (Micromoles/cell/hr)	Oxygen consumption rate of Mr	$1.15\times {10}^{-7}$	(Sershen et al., 2016)
${\varphi }_{O_{ma}}$ (Micromoles/cell/hr)	Oxygen consumption rate of Ma	$2.3\times {10}^{-7}$	(Sershen et al., 2016)
${\varphi }_{O_{mi}}$ (Micromoles/cell/hr)	Oxygen consumption rate of Mi	$3.45\times {10}^{-7}$	(Sershen et al., 2016)
${\varphi }_{O_{mci}}$ (Micromoles/cell/hr)	Oxygen consumption rate of Mci	$4.6\times {10}^{-7}$	(Sershen et al., 2016)
${\varphi }_{O_t}$ (Micromoles/cell/hr)	Oxygen consumption rate of T cells	$0.14375\times {10}^{-7}$	(Sershen et al., 2016)
${\varphi }_{{Drug}_b}$ (Micromoles/cell/hr)	Antibiotic consumption rate of extracellular bacteria	$2.1\times {10}^{-11}$	(Pienaar et al., 2015)
${\varphi }_{{Drug}_{mi}}$ (Micromoles/cell/hr)	Antibiotic consumption rate of infected macrophages	$1.9\times {10}^{-6}$	(Pienaar et al., 2015)
Repf (hours)	Replication rate of fast-growing bacteria	15–32	(Shorten et al., 2013)
Reps (hours)	Replication rate of slow-growing bacteria	48–96	(Hendon-Dunn et al., 2016)
Olow (%)	O2 threshold for fast → slow-growing bacteria	6	Estimated - see Section 4.1
Ohigh (%)	O2 threshold for slow → fast-growing bacteria	65	Estimated - see Section 4.1
Mrinit	Initial number of Mr in the domain	105	(Cilfone et al., 2013)
MrMa	Probability of Mr → Ma (multiplied by no. of T cells in neighbourhood)	9	(Cilfone et al., 2013)
Nici	Number of bacteria needed for Mi → Mci	10	(Cilfone et al., 2013)
Ncib	Number of bacteria needed for Mci to burst	20	(Cilfone et al., 2013)
Mlife (days)	Lifespan of Mr, Mi and Mci	0–100	(Van Furth et al., 1973)
Malife (days)	Lifespan of Ma	10	(Segovia-Juarez et al., 2004)
tmoveMr (mins)	Time interval for Mr movement	20	(Segovia-Juarez et al., 2004)
tmoveMa (hours)	Time interval for Ma movement	7.8	(Segovia-Juarez et al., 2004)
tmoveMi (hours)	Time interval for Mi/Mci movement	24	(Segovia-Juarez et al., 2004)
Mrrecr	Probability of Mr recruitment	0.07	(Cilfone et al., 2013)
Tenter	Bacteria needed for T cells to enter the system	50	(Cilfone et al., 2013)
Trecr	Probability of T cell recruitment	0.02	(Cilfone et al., 2013)
Tlife (days)	Lifespan of T cells	0–3	(Sprent, 1993)
Tkill	Probability of T cell killing Mi/Mci	0.75	(Cilfone et al., 2013)
tmoveT (mins)	Time interval for T cell movement	10	(Segovia-Juarez et al., 2004)
tdrug (hours)	Time at which drug is administered	168–2160	(Asefa, Teshome, 2014, Osei, Akweongo, Binka, 2015)
DrugKillf (%)	Drug needed to kill fast-growing bacteria	2	(Hammond et al., 2015)
DrugKills (%)	Drug needed to kill slow-growing bacteria	10	(Hammond et al., 2015)
DrugKillMi (%)	Drug needed to kill intracellular bacteria	20	(Aljayyoussi et al., 2017)