Cytosim PI Cytoskeleton Simulator

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Variables
Parameters of ClassicFiber
All object parameters

## Variables
real | growing_speed [2]
| see ClassicFiber More...
real | growing_force
| Characteristic force of assembly state. More...
real | shrinking_speed
| speed of disassembly state
real | catastrophe_rate [2]
| Rate of stochastic switch from assembly to disassembly. More...
real | rescue_rate
| Rate of stochastic switch from disassembly to assembly.
real | min_length
| Minimum authorized length. More...
Fate | fate
| Action that is taken when the fiber shrinks below `min_length`

## Detailed Description

Inherits Parameters of Fiber.

## Variable Documentation

real catastrophe_rate[2]

The catastrophe rate depends on the growth rate of the corresponding tip, which is itself reduced by antagonistic force.
The correspondance is :

1/catastrophe_rate = a + b * growth_speed

where growth_speed is calculated as explained in growing_speed, and parameters a and b are derived from:

- catastrophe_rate[0] = the catastrophe rate in the absence of force.
- catastrophe_rate[1] = the catastrophe rate of a stalled tip.

real growing_force

Antagonistic force decrease assembly rate exponentially.

real growing_speed[2]

Speed of assembly state

growth_speed = monomer_fraction * growing_speed[0] * exp(force/growing_force) + growing_speed[1];

monomer_fraction in [0,1] reflect the amount of free monomers. Antagonistic force is negative ( force < 0 ). Force directed in the same direction as assembly has no effect.

The parameters are:

- growing_speed[0] = force-dependent assembly rate.
- growing_speed[1] = constant term, which can be negative to represent spontaneous disassembly.
- growing_force = characteristic force

real min_length

When the fiber becomes shorter than `min_length`, the action specified by `fate` is applied.