Cytosim  PI
Cytoskeleton Simulator
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();