Table I.

All parameters used in ABM simulations. For each parameter, the name, brief description, baseline value and range used for uncertainty and sensitivity analysis is given. Parameter values are based on experimental data or estimated based on related systems and the ability of the model to produce reasonable behavior (calibration) during a chronic infection scenario. For example, recruitment parameters prob_T4_recruitment and prob_T8_recruitment were fixed in order to achieve a ‘normal level’ steady state in the system before infection was introduced. T4 refers to CD4+ T cells, T8 refers to CD8+ T cells.

		Parameter	Baseline value	Range	Description
+*	1	pMHC half-life	60hrs (58)	30-60 hrs	Half-life of pMHCII on DC
+*	2	unbinding threshold	100	80 – 120	pMHC level at which T cell unbinds from DC
+*	3	binding threshold	150 (59, 60)	100–200	pMHCII level corresponding to 50% CD4+ T cell binding probability
+*	4	binding shape	15	10-30	Shape parameter for CD4+ T cell binding probability curve (Fig. 3)
+*	5	priming threshold	6 hrs (46)	4 - 8 hrs	Value of pMHC*binding duration at 50% CD4+ T cell priming probability
+*	6	priming shape	0.6	0.3-0.9	Shape parameter for CD4+ T cell priming probability curve (Fig. 3)
+*	7	binding threshold (CD8 cell)	200 (11)	100 - 200	pMHCI level corresponding to 50% CD8+ T cell binding probability
+*	8	binding shape (CD8 cell)	15	10-30	Shape parameter for CD8+ T cell binding probability curve (Fig. 3)
+*	9	priming threshold (CD8 cell)	6 hrs	4 - 8 hrs	Value of pMHC* binding duration at 50% CD8+ T cells priming probability
+*	10	priming shape (CD8 cell)	0.6	0.3 - 0.9	Shape parameter for CD8+ T cell priming probability curve (Fig. 3)
+*	11	LDC lifespan	36 hrs (56, 57)	24 – 48 hrs	Lifespan of an LDC
+*	12	Prob T4 licenses Ab-DC	50%	30 – 80 %	Probability of primed CD4+ T cell licensing Ab-DC
+	13	Cognate Frequency	0.25 (see text)	1:100 – 1:10000	Frequency of cognate naïve T cells
+	14	Ab-DC lifespan	60 hrs (61)	40 – 80 hrs	Lifespan of an Ab-DC
+	15a	Number of divisions primed CD4+ T cells	4 (7, 58)	2 – 8	Max # of divisions allowed for a primed T cell
	15b	Number of divisions CD8+ T cells	8 (7)	2-12	Max # of divisions allowed for a primed T cell
+	16	Division time	8 hrs	2 – 16 hrs	Time for primed CD4/CD8 division
	17	Prob_T4_recruitment	99%	50 – 100 %	Probability of naïve CD4+ T cell recruitment at every 20 time steps
	18	Prob_T8_recruitment	95%	50 – 100 %	Probability of naïve CD8 recruitment at every 20 time steps
	19	Initial_naiveT4_cells	6000		initial no. of naïve CD4+ T cells
	20	Initial_primedT4_cells	0		initial no. of primed CD4+ T cells
	21	Initial_naiveT8_cells	5000		initial no. of naïve CD8+ T cells
	22	Initial_primedT8_cells	0		initial no. of primed CD8+ T cells
	23	Initial_total DCs_cells	8		initial no. of total DCs (IDC+Ab-DC)
	24	%AB-DCs	60%		percent of total DCs that are antigen bearing
	25	Peak_DCs_level	100		Max no. of total DCs on the grid
	26	IDC_Ab-DC_threshold	50		pMHC level below which a DC is IDC
	27	n_tcells_bind_DC	32		Max no. of T cells that bind to a DC
	28	max_time_T4_primed	60 hrs (55)		Max time after which primed T4 cells die
	29	max_time_T8_primed	60 hrs (55)		Max time after which primed T8 cells die
	30	min_T4cell_age	165 days (54)		Minimum age of naïve T4 when it appears on the grid
	31	max_T4cell_age	365 days (54)		Maximum age of naïve T4 when it appears on the grid
	32	min_T8cell_age	165 days (54)		Minimum age of naïve T8 when it appears on the grid
	33	min_T8cell age	365 days (54)		Maximum age of naïve T8 when it appears on the grid
	34	min_DC_age	24 hrs (61)		Minimum age of DC when it appears on the grid
	35	max_DC_age	11 days (61)		Maximum age of DC when it appears on the grid
	36	Initial number of pMHC	taken from a distribution (59, 60)	range 125-200	Initial number of pMHC placed on surface of DC

⁺Parameters included in 16 parameter (full) lhs

^*Parameters included in 12 parameter lhs