Software for simulating active matter dynamics
MEDYAN software package


The cell cytoskeleton plays a key role in human biology and disease, contributing ubiquitously to such important processes as embryonic development, wound repair and cancer metastasis. Papoian laboratory is interested in gaining deeper understanding of the physical chemistry behind these complex, far-from-equilibrium mechanochemical processes. Their approach and model, named Mechanochemical Dynamics of Active Networks (MEDYAN), is based on combining stochastic reaction-diffusion treatment of cellular biochemical processes with polymer physics of cytoskeletal filament network growth, while explicitly coupling chemistry and mechanics.

Papoian laboratory has developed a third-generation software package based on the MEDYAN model, to simulate growth dynamics of actin based filamentous networks in vitro and in vivo. Recent papers where MEDYAN or its second-generation predecessor, StochTools, were used can be found on the publication section of the Papoian group's main web page or on the MEDYAN web page. The MEDYAN package can also be extended to simulate the dynamics of any active matter network.


Step 1: Prerequisites

The following libraries need to be installed first: See Installation guide (docs/InstallGuide.pdf) for more details.

  • Boost 1.49
  • GSL ...

Step 2: Installation of MEDYAN itself

Untar the MEDYAN source code into some directory, enter into the "MEDYAN" folder and execute "make" from the command line.

See Installation guide (docs/InstallGuide.pdf) for more information on setting command line compilation macros, compiler compatibility, etc.

Step 3: Running MEDYAN

See the Usage guide (docs/UsageGuide.pdf) for more information. The MEDYAN executable must be run with the following command line arguments:

-s : System input file to be used. Must be an absolute path -i : Input directory to be used, where all files specified in the system input file must be located. Must be an absolute path. -o : Output directory to be used (must be created beforehand), where all output files will be placed. Must be an absolute path.

Run -h for help.