CytoSim: A Simulation Platform for Active Cytoskeletal Matter

The cytoskeleton drives many essential processes in vivo. It is a system of filaments with associated activities such as molecular motors, capping proteins, nucleators, etc. Cytosim is an Open Source simulation platform that can simulate systems composed of tens of thousand filaments with bending flexibility in 2D or 3D. The filaments can represent Microtubules in detailed models of the mitotic spindle, or actin filaments in models of actin networks found in vivo or in vitro. Cytosim will calculate the bending mechanics of every filament in the systems using a custom Brownian Dynamics engine, and it will model chemical reactions individually stochastically. It uses an implicit integration method with algebraic constraints to maintain the length of the filaments. In addition, filament dynamics and the movements of molecular motors can also be simulated, pushing the system out of equilibrium. Overall, Cytosim can simulate relatively large systems rapidly enough to enable their biophysical analysis, while maintaining a high level of realism. Cytosim was validated on various processes ranging from nuclear positioning, spindle assembly and actin network contraction and has a growing user community resulting in more than 100 articles published.