Cytosim can handle systems of fibers with associated proteins such as molecular motors. The fibers can bend but are incompressible along their axis. Besides fiber that are linear objects, cytosim can also simulate beads, spheres and solids of custom shapes.

The objects can be connected by springs, without any restriction on the topology of the connections:

the attachment points on the fibers can be located anywhere along their length,
an object can be connected to any other object, or to itself.

The motion of the objects is calculated taking into account Brownian agitation, and neglecting inertia. These approximations are correct inside living cells, for cytoskeletal fibers, micro-meter sized beads and larger assemblies.

A physicist may say that each fiber is represented by a worm-like chain model, and that the system is characterized by a low Reynolds number. The equations of motion in this case are called overdamped Langevin equations, and the method is also called Brownian dynamics.

The simulation engine was optimized to handle large systems with thousands of interconnected fibers. Implicit integration allows large time steps to be used.

All molecular events are stochastic (see Stochastic Events).

For more information, please read:

Collective Langevin Dynamics of Flexible Cytoskeletal Fibers.
Nedelec F, Foethke D. New Journal of Physics 9 (11) 427, Nov 2007.
http://www.iop.org/EJ/abstract/1367-2630/9/11/427
doi:10.1088/1367-2630/9/11/427

In parallel to the mechanical calculation, cytosim has a stochastic engine to simulate the different chemical processes, for instance the diffusion, binding/unbinding of molecules. Other activities such as the stepping of molecular motors or nucleation events, etc. Molecular motors can be modelled using a continuous approximation or as discrete stochastic steppers. The fibers themselves can lengthen and shorten, which is the case with microtubules or actin filaments in cells. Different models of dynamic instability are available.

Cytosim has a modular architecture and can be customized. The entities (fiber, motor, nucleator, etc.) are specified in derived C++ classes with very few lines of code. These classes can be modified easily for custom application. They can be added to the main source tree, shared or exchanged.