Parameters of Hand

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)