Cytosim PI Cytoskeleton Simulator

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Variables
Parameters of Fiber
All object parameters

## Variables
real | length
| length or initial-length for dynamic fibers
real | viscosity
| effective viscosity (if not specified, simul:viscosity is used)
unsigned int | binding_key
| can be set to control which Hands may bind More...
real | rigidity
| modulus for bending elasticity More...
real | segmentation
| desired distance between model points More...
real | total_polymer
| amount of polymer available for this type of fiber
real | hydrodynamic_radius [2]
| radius used to calculate mobility More...
bool | surface_effect
| if true, the mobility of a cylinder moving near a plane will be used More...
real | cylinder_height
| distance of fluid between slide and cylinder surface (set as `surface_effect`[1])
Confinement | confine
| set forces between fiber and Space [none, inside, outside, surface]
real | confine_stiff
| stiffness of confinement (set as `confine`[1])
std::string | confine_space
| name of space for confinement (set as `confine`[2])
int | steric
| if true, include steric interaction for this object
real | steric_radius
| radius of repulsive steric interaction (also known as `steric`[1])
real | steric_range
| extra radius of attractive steric interaction (also known as `steric`[2])
int | glue
| type of glue (interaction between fiber tip and Space)
std::string | glue_single
| name of Single used for glue (set a `glue`[1])
std::string | activity
| specialization More...
std::string | display
| display string (see Display parameters: Fibers)

## Detailed Description

These are the parameters for Fiber

## Variable Documentation

std::string activity

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.

unsigned int binding_key

To decide if a Hand may bind to a Fiber, the two keys are compared: attachement is forbiden if the BITWISE-AND is 0:

if ( fiber:binding_key & hand:binding_key )
allowed = true;
else
allowed = false;

It is thus recommended to use powers of 2: 1, 2, 4, etc.

real hydrodynamic_radius[2]

hydrodynamic_radius[0] corresponds to the radius of the fiber hydrodynamic_radius[1] is a cut-off for the length of the fiber

real rigidity

This has units of pN.um^2, and it is related to the persitence length:

L_p = rigidity / kT

Many measurments have been made and they agree somewhat.
According to Gittes et al. (1993):

Filament | L_p | rigidity
--- | --- | ---
Microtubule | ~ 5200 um | ~22 pN.um^2
Actin | ~ 18 um | ~0.075 pN.um^2

Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. JCB vol. 120 no. 4 923-934 http://dx.doi.org/10.1083/jcb.120.4.923
http://jcb.rupress.org/content/120/4/923

real segmentation

This is a distance. As a rule of thumb, segmentation should scale with rigidity, depending on the expected external forces:

segmentation = sqrt(rigidity/force)
force ~ rigidity / segmentation^2

Furthermore, if any filament contains kinks (the angle between consecutive segments is above 45 deg), the simulation should not be trusted and instead should be recalculated with a reduced segmentation.

bool surface_effect

You can select between two possible formulas to calculate viscous drag coefficient:

if ( fiber:surface_effect )
setDragCoefficientSurface();
else
setDragCoefficientVolume();