Table 2. Parameters varied in this work.

For a full list of parameters and their values, please refer to Appendix 1 and to Aghaallaei et al., 2021.

Symbol	Values tested(reference in bold)	Description
N	2; 3; 4	Number of concentric subdivisions in algorithm to generate TEC positions. The higher the value, the larger the number of TECs, thus the larger the TEC density.
p TEC	3; 4; 5	Number of protrusions initialized for each TEC.
r TEC	2.0 μm; 2.5 μm; 3.0 μm	Radius of the main TEC body. Also scales the radius of the spheres in the TEC protrusions.
DEPL	True; False	Boolean flag that sets if the simulation has thymocytes that internalize IL-7 according to Equation 4 in Materials and methods (True) or if it defaults to Equation 3 in Materials and methods (False).
a IL-7	120 hr–1; 240 hr–1; 480 hr–1	IL7R signaling activation rate
d IL-7	25 hr–1; 50 hr–1; 100 hr–1	IL7R signaling deactivation rate
θ prol	1.3; 1.4; 1.5	Threshold level of IL-7 and Notch signaling activity required to progress through G1 phase and to commit to the cell cycle.
μ	5 hr; 7 hr; 9 hr	Mean cell cycle duration.
T diff	15 hr; 24 hr; 33 hr	Minimum duration of the proliferative phase before terminal differentiation.