CYTOSIM

Introduction

Cytosim is a simulation of the cytoskeleton. It can handle large systems of fibers with associated proteins such as molecular motors. The fibers are flexible, and our simulation engine was optimized for the inertia-less equations of motion. The Brownian dynamics approach was described in the New Journal of Physics: "Collective Langevin Dynamics of Flexible Cytoskeletal Fibers".

Current Status

The next version of Cytosim will be available soon. We have entirely revised the code, and the changes are almost complete. We still need to extensively test the new functionalities, and we would like to write a documentation.

Beta Version

Improvements

• parameters are grouped in logical units,
• these units correspond to entities in the simulation,
• an arbitrary number of definitions and objects can be created (within memory limitations),
• parameter names are more intuitive; some values can be specified literally (eg. "sphere"),
• definitions and commands can be mixed.

Example of Configuration File

set simul example
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( sphere 5 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 100
}

new 2 fiber microtubule
{
    length = 8
}

run simul * 5000

Gallery

Previous versions

• Cytosim 2.0 (2007)
  
• Cytosim 1.7 (2003)
  
• Cytosim 1.0 (2002)
  

Note: to use cytosim in conjunction with our published work, download the appropriate package from our publication page.