Time-lapse Simulations of T-zone
Lymph Node Agent Based Models

an on-line supplement for

Characterizing the Dynamics of CD4+ T Cell Priming within a Lymph Node
[ Time-Lapse Simulations Homepage | Kirschner Lab Homepage ]





Jennifer J. Linderman, Thomas Riggs, Manjusha Pande, Mark Miller, Simeone Marino, and Denise E. Kirschner, Characterizing the Dynamics of CD4+ T Cell Priming within a Lymph Node. Journal of Immunology, 2010, 184: pp 2873-2885, DOI: 10.4049/jimmunol.0903117, PMID: 20154206, PMCID: 3153313




Supplement 1: Agent-Based Model Rules Supplement 69k


Supplement 2: Uncertainty and Sensitivity Analysis Tables 44k


Supplement 3: Model Validation with Data: T cell motility 44k


Supplement 4: Figure for History vs. no History 44k



Figure: A - Zoom Level 2

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Time lapse simulation of T cell and dendritic cell (DC) movement in the lymph node (LN). Full LN T-zone is represented by a 200 X 25 unit grid; basic unit of the grid is a 5 micron X 5 micron square. Each grid unit can hold up to 4 T cells or one DC. T cells are represented by smaller spheres, larger spheres represent DCs; colors represent different cell types as described in the key. Time is shown at the top of the grid, in hours since the beginning of the simulation. DCs enter via afferent lymphatics (AL) represented by white cylinders at the top of the grid. T cells enter via HEV (not shown) and leave via efferent lymphatics (EL) represented by gray cylinders at the bottom of the grid. DCs usually spend their remaining lifespan in the lymph node. Some views show the entire grid while others show a close-up. A, B, C: Simulations of acute infection with cognate T cell to total T cells ratio of 1:300 - (A) Zoom Level 2 view, (B) Zoom Level 1 view, and (C) normal view of the grid. Simulations of acute infection with cognate T cell to total T cells ratio of 1:3000 - (D) Zoom Level 2 view, (E) Zoom Level 1 view, and (F) normal view of the grid.

Right click or CTRL-click on MOV icon, select "Save Link As" or "Save Target As" to download the archived MOV movie file version of time-lapse simulations

To extract the MOV movie from the archive, download the archive to your Mac or Windows desktop, double-click on them, and follow the on-screen instructions.

To extract on Linux, Unix, BSD, etc... use the command in a shell 'unzip (filename.zip)' or a desktop extraction utility

Flash time-lapse simulations are best played using Flash version 8 or greater




Simulations of acute infection with cognate T cell to total T cells ratio of 1:300

Figure A. - Zoom Level 2

Figure B. - Zoom Level 1

Figure C. - Normal view of the grid



Simulations of acute infection with cognate T cell to total T cells ratio of 1:3000

Figure D. - Zoom Level 2

Figure E. - Zoom Level 1

Figure F. - Normal view of the grid





[ Time-Lapse Simulations Homepage | Kirschner Lab Homepage ]