3D Lymph Node Model Supplemental Movies

an on-line supplement for

Predicting lymph node output efficiency through systems biology

[ Time-Lapse Simulations Homepage | Kirschner Lab Homepage ]



Chang Gong, Joshua T. Mattila, Mark Miller, JoAnne L. Flynn, Jennifer J. Linderman, D. Kirschner, Predicting lymph node output efficiency through systems biology, Journal of Theoretical Biology, Volume 335, October 21 2013, Pages 169-184, ePUB: June 29, 2013, DOI: 10.1016/j.jtbi.2013.06.016, PMID: 23816876, PMCID: 3783027





Supplement 1: Appendix: Table of parameter values or ranges 44k

Supplement 2: Agent rules 100k




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Supplement Movie 1
T cell Track in the LN


LN is at a baseline steady state, with CD4+ (red), CD8+ (blue) T cells and DCs (green) on grid. No Ab-DC is recruited. One of the T cells is tracked with a yellow line from its entry of the grid from HEV (orange) to its exit from EL (yellow).

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

To extract the AVI 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



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Supplement Movie 2
The process of T cell priming


This is a illustration of how T cells are primed by DCs in our model. For clarity, one single Ab-DC (green) is placed at the center of the grid scanning its Moore neighborhood for cognate T cells. CD4+(red) and CD8+ (blue) T cells recruited from HEVs (orange) moves in the grid following the rules and bind to the DC if conditions are met. After priming, T cells unbind and begin to proliferate (pink), and eventually differentiate into effector cells (purple). Effector cells exit the grid via ELs (yellow).

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

To extract the AVI 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



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To preview the movie, click on the graphic image above


Supplement Movie 3
Acute infection


Time-lapse movie of simulated acute infection in the LN. Simulation lasts for 20 days. Antigen-bearing dendritic cells are recruited from day 5 to day 10. CD4+ T cells: red: naive; pink: proliferating; purple: effector. CD8+ T cells: blue: naive; sky blue: proliferating; cyan: effector. DC: green: Immature; light green: antigen-bearing; white: licensed.

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

To extract the AVI 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



[ Time-Lapse Simulations Homepage | Kirschner Lab Homepage ]