This is a distribution of D3D, a software package for computing diffusion-reaction simulations in 3D using either finite-difference or Monte Carlo algorithms. This version of D3D has been specifically formatted to run simulations for the following eLife paper:
"Physical determinants of vesicle mobility and supply at a central synapse" Rothman JS, Kocsis L, Herzog E, Nusser Z, Silver RA eLife. 2016 Aug 19. pii: e15133. doi: 10.7554/eLife.15133.
Once the java code has been compiled and executed, a GUI will be created with an "eLife" menu at the top. Users can select which simulation to initialize via the following menu items:
- Init Finite-Difference Frap (figures 2C 3D; Torok iPSF).
- Init Monte Carlo FRAP (figures 3C,D 4A,B,D; Torok iPSF).
- Init Monte Carlo FRAP Movie (no figure; default demo; Gaussian iPSF).
- Init Monte Carlo MSD (figures 4C 5A).
- Init Monte Carlo AZ (figures 7 8).
Note, simulations with "Torok iPSF" may take a while to initialize.
D3D will run on most machines which run Java. Install Java J2SE 5 or higher. It's better to download the JDK (Java Development Kit) which includes command line tools for Java.
D3D was created by the The Silver Lab - R. Angus Silver - Department of Neuroscience, Physiology & Pharmacology - University College London - Gower Street - London WC1E 6BT - UK
Java code was written by Jason Rothman.
For more information contact j.rothman@ucl.ac.uk