Cytosim PI Cytoskeleton Simulator

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Variables
Parameters of Hand
All object parameters

## Variables
real | binding_rate
| binding rate when the Hand is within binding_range (also known as `binding`[0]) More...
real | binding_range
| maximum distance at which the Hand can bind (also known as `binding`[1])
unsigned int | binding_key
| can be set to restrict binding to certain type of Fiber More...
real | unbinding_rate
| detachment rate at force=0 (also known as `unbinding`[0]) More...
real | unbinding_force
| characteristic force of unbinding (also known as `unbinding`[1]) More...
bool | bind_also_end
| if true, the Hand can also bind directly to the tip of fibers More...
bool | hold_growing_end
| if false, the Hand will detach immediately upon reaching a growing or a static fiber end More...
bool | hold_shrinking_end
| if false, the Hand will detach immediately upon reaching a shrinking fiber end More...
std::string | activity
| specialization More...
std::string | display
| display parameters (see Display parameters: Points)

## Detailed Description

## Variable Documentation

std::string activity

A plain Hand can only bind and unbind from a Fiber. Derived classes are available that implement more complex functionalities, for example molecular motors or severing enzymes.

List of classes accessible by specifying `hand:activity`:

`activity` | Class | Parameters
--- | --- | ---
`bind` | Hand | Parameters of Hand (default)
`move` | Motor | Parameters of Motor
`nucleate` | Nucleator | Parameters of Nucleator
`slide` | Slider | Parameters of Slider
`track` | Tracker | Parameters of Tracker
`rescue` | Rescuer | Parameters of Rescuer
`cut` | Cutter | Parameters of Cutter
`mighty` | Mighty | Parameters of Mighty
`act` | Actor | Parameters of Actor

Example:

set hand motor
{
binding = 10, 0.05
unbinding = 0.2, 3
activity = move
max_speed = 1
stall_force = 5
}

bool bind_also_end

This determines the binding ability of a Hand that is located within the binding_range of a fiber, but at a position where the orthogonal projection is outside the Fiber, ie. below the MINUS_END, or above the PLUS_END. This corresponds to two hemi-spheres at the two ends of a Fiber.

default value = false

unsigned int binding_key

The binding to a fiber is allowed only if the keys of the Hand and Fiber match. The test is a BITWISE-AND of the two keys:

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

real binding_rate

According to Leduc et al. PNAS 2004 vol. 101 no. 49 17096-17101 the molecular binding_rate of kinesin is 4.7 +/- 2.4 /s. http://dx.doi.org/10.1073/pnas.0406598101
http://www.pnas.org/content/101/49/17096.abstract

bool hold_growing_end

A Hand may reach the tip of the fiber on which it is bound, either if it is moving, or if is dragged by some other force. When this happens, hold_growing_end will determine if the Hand will detach or not.

default = false

bool hold_shrinking_end

A Hand may reach the tip of the fiber on which it is bound, of the tip of the fiber may reach a immobile hand because it is disassembling. When this happens, hold_shrinking_end will determine if the Hand will detach or not. If hold_shrinking_end is true, the hand will be relocated to track the end.

default = false

real unbinding_force

Kramers theory specifies that the detachment rate depends on the force in the link:

off_rate = RATE * exp( force / FORCE )

RATE is specified as unbinding_rate, and FORCE as unbinding_force, but one can also directly specify `unbinding = RATE, FORCE`. (see Stochastic Events)

real unbinding_rate

Kramers theory specifies that the detachment rate depends on the force in the link:

off_rate = RATE * exp( force / FORCE )

RATE is specified as unbinding_rate, and FORCE as unbinding_force, but one can also directly specify `unbinding = RATE, FORCE`. (see Stochastic Events)