Supplementary Material for An In Silico Model of Cytotoxic T-Lymphocyte Activation in the Lymph Node Following Short Peptide Vaccination, Journal of the Royal Society Interface Liam V Brown 1 , Eamonn A Gaffney 1 , Jonathan Wagg 2 , and Mark C Coles 3 1 Wolfson Centre For Mathematical Biology, Mathematical Institute, University of Oxford 2 Clinical Pharmacology, Roche Innovation Center Basel 3 Kennedy Institute of Rheumatology, University of Oxford A Comparison to previous work Parameter Our model Celli et al ’s model T cell motion Run-and-tumble Diffusion Velocity distribution Gamma Gaussian Mean 3D speed 10μm/min 22.6μm/min Variance of 3D speed 44.3μm/min 2 90.4μm/min 2 Mean free path 25μm 0 or vΔt Antigen off-rate k off N/A (0) DC contact radius 20μm 12μm LN radius 500μm 400μm Modelled animal Human Mouse Modelled cells CD8 + CD4 + Table A1. A summary of the changes that must be made to the model in order to reproduce the results of Celli et al. A component of our model is related to the in-silico mouse model reported by Celli et al : namely, that dendritic cells (DCs) and T cells interact in an off-lattice sphere. It is possible to reproduce their results for a consistency check by changing suitable elements of our model, as summarised in Tab. A1. In particular, the T cell velocity is made to imitate diffusion instead of drawing velocities and free paths from defined distributions, the antigen off-rate is set to zero and the initial cognate to total antigen ratio to unity, so that interactions are always successful. Celli et al model CD4 + T lymphocytes, whereas we model CD8 + cells. We could not find a reason to suggest that the na¨ ıve dynamics of Corresponding author, liam.brown@maths.ox.ac.uk 1