Cytosim is a cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It has been used to study actin and microtubule systems alike. It is built around a cross-platform core engine running in 2D or 3D. Cytosim offers command-line tools with simulation and display capabilities. With its modular code base, it can easily be customized to meet particular tasks.

The simulation is specified in a configuration file, defining objects with their parameters and operations, such as advancing time, saving frames or generating reports. Below is a basic example, with parameters specified in units of seconds, micrometers and picoNewtons.

	set simul system
	{
	    time_step = 0.005
	    viscosity = 0.02
	}
	
	set space cell
	{
	    shape = sphere
	}
	
	set fiber microtubule
	{
	    rigidity = 20
	    segmentation = 0.5
	    confine = inside, 200, cell
	}
	    
	new cell
	{
	    radius = 5
	}
	
	new 5 microtubule
	{
	    length = 11
	}
	
	run 5000 system
	{
	    nb_frames = 10
	}

The Brownian dynamics approach was described in:
Collective Langevin Dynamics of Flexible Cytoskeletal Fibers

Recent Docs

Cytosim’s Configuration File The virtual system and the sequence of actions to be performed is specified in a configuration file. This config file must be a plain (ASCII) text file, as produced by many text editor (but not word processors). By default, it is called config.cym. Cytosim understand a small set of commands and predefined objects with their associated parameters. One needs to call at least: set to define a new object category, and set its parameter values, new to create objects, run to perform simulation steps.
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Getting numbers out of Cytosim using report You can extract formatted data from Cytosim in two different ways: by using the report command in the configuration file. by running the report executable on the trajectory file. Both methods produce nearly identical formatted text output with selected data, such as the coordinates of the filaments, their state or length, etc. The report command The command report can be called from the config file.
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Physical units in Cytosim Cytosim is not aware of units, and it is the user’s responsability to provide coherent values. The parameters could in principle be specified in any system of units, but the same system must be used consistently for all values! However, for convenience, Cytosim provides default values for some parameters, for example: Parameter Default value viscosity 1 pN.s/um^2 kT 0.
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