Cytosim PI Cytoskeleton Simulator

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Classes
Fiber and Derived Activities
List of objects | How to create objects

The default Fiber is of fixed length, but derived class can change length. More...

## Classes
class | ClassicFiber
| A Fiber with a standard two-state model of dynamic instability at the PLUS_END. More...
class | DynamicFiber
| A Fiber with discrete growth and dynamic instability at the PLUS_END. More...
class | TreadmillingFiber
| A Fiber with assembly at both ends. More...
class | Tubule
| Adds dynamic instability (growth/shrinkage of the ends) to a Fiber. More...

## Detailed Description

A fiber is a filament of constant length. Derived classes are available, where different models of how length may change have been implemented.

List of classes accessible by specifying `fiber:activity`.

`activity` | Class | Parameter
--- | --- | ---
`none` | Fiber | Parameters of Fiber (default)
`classic` | ClassicFiber | Parameters of ClassicFiber
`dynamic` | DynamicFiber | Parameters of DynamicFiber
`treadmill` | TreadmillingFiber | Parameters of TreadmillingFiber
`tubule` | Tubule (deprecated) | Parameters of Tubule

When creating a new Fiber, you may specify:

- the initial length,
- the initial state of the PLUS_END and MINUS_END,
- if the position refers to the center or to the tip of the fiber

Syntax:

new fiber ...
{
length = REAL, LENGTH_MODIFIER
end_state = PLUS_END_STATE, MINUS_END_STATE
reference = REFERENCE
}

The optional LENGTH_MODIFIER can be:

- `exponential`,
- REAL

This introduces variability, without changing the mean length. The second form generates a flat distribution of width 2*LENGTH_MODIFIER.

The initial states PLUS_END_STATE and MINUS_END_STATE can be:

- 0 = white
- 1 = green
- 4 = red

Optional reference specificiation:

- center [default]
- plus_end
- minus_end

Examples:

new fiber ...
{
length = 1
plus_end_state = 1
minus_end_state = 0
}

which is equivalent to:

new fiber ...
{
length = 1
end_state = green, white
}

You may add a Picket to immobilize a Fiber to the ground:

new fiber microtubule
{
single = NAME_OF_SINGLE, MODE
}

NAME should be the name of a defined single. Possible MODE:

- minus_end
- plus_end
- minus_dir, [distance]
- center

For MODE == minus_dir, 2 Singles are added, and their distance should be specified as the third argument:

new fiber actin
{
single = NAME_OF_SINGLE, MODE, DISTANCE
}

Add Couple pre-attached to the Fiber:

new fiber microtubule
{
couple = NAME_OF_SINGLE, NUMBER, LEN
}

Couples are attached via their first Hand, and they are distributed along Fiber, at distance LEN from the MINUS_END. If LEN is not specified, they are distributed all along the fiber.