Fiber Class Reference

Detailed Description

A Fiber is a Mecable that can be simulated.

• FiberProp * prop points to the physical properties (ie. parameters) of the Fiber.
• frBinders keeps track of all attached FiberBinders.
• frRods provides pointers to the Segments of the Fiber.
• FiberDisp * disp points to display parameters.

Fibers are stored in a FiberSet.

Inheritance diagram for Fiber:

Public Member Functions
	Fiber (FiberProp const *)
	constructor More...
virtual	~Fiber ()
	destructor
virtual unsigned int	allocatePoints (unsigned int nbp)
	allocate memory for 'nbp' points
void	setDragCoefficient ()
	calculate viscous drag coefficient More...
void	prepareMecable ()
	prepare for Meca
void	setInteractions (Meca &) const
	add interactions to a Meca
void	sever (real abs)
	cut fiber at abscissa abs from the ORIGIN, in the next time step
void	cutAlongPlane (FiberSet *, Vector const &n, real a)
	Cut all segments intersecting the plane defined by n.x + a = 0
virtual void	join (Fiber *fib)
	call FiberNaked::join(), and transfer Hands (caller should delete fib).
virtual void	step ()
	simulation step
FiberLocus &	segment (unsigned int p) const
	FiberLocus representing the segment [p, p+1].
real	projectPoint (Vector const &w, real &dist) const
	return the abscissa of the closest position to w on this Fiber, and set dist to the square of the distance
virtual int	dynamicState (FiberEnd which) const
	return assembly/disassembly state of the FiberEnd
virtual void	setDynamicState (FiberEnd which, int new_state)
	change state of FiberEnd which to new_state
virtual real	freshAssembly (FiberEnd which) const
	the amount of freshly assembled polymer during the last time step (this has units of length)
bool	isGrowing (FiberEnd which) const
	true if the tip which has grown in the last time step ( freshAssembly(which) > 0 )
bool	isShrinking (FiberEnd which) const
	true if the tip which has shrunk in the last time step ( freshAssembly(which) < 0 )
void	addBinder (FiberBinder *)
	register a new Binder
void	removeBinder (FiberBinder *)
	unregister bound Binder
FiberBinder *	firstBinder () const
	a FiberBinder bound to this fiber (use ->next() to access all other binders)
void	updateBinders ()
	update all binders
void	detachBinders ()
	detach all binders
int	nbBinders () const
	number of attached FiberBinders
int	nbBindersInRange (real aMin, real aMax, FiberEnd from) const
	number of attached FiberBinders in a range of abscissa More...
int	nbBindersNearEnd (real len, FiberEnd which) const
	number of attached FiberBinders at the specified FiberEnd
int	nbBinders (unsigned int(*count)(FiberBinder const &)) const
	a function to count binders using custom criteria
void	setGlue1 (Single *glue, FiberEnd which, const Space *space)
	set the box glue for pure pushing More...
void	setGlue2 (Single *glue, FiberEnd which, const Space *space)
	set the box glue for pure pulling More...
void	setGlue3 (Single *glue, FiberEnd which, const Space *space)
	set the box glue for pushing and pulling More...
void	setGlue (Single *&glue, FiberEnd which, const Space *space, int glue_type)
	a setGlue to rule them all
Fiber *	next () const
	a static_cast<> of Node::next()
Fiber *	prev () const
	a static_cast<> of Node::prev()
Tag	tag () const
	return unique character identifying the class
const Property *	property () const
	return Object Property
void	write (OutputWrapper &) const
	write to file
void	read (InputWrapper &, Simul &)
	read from file
Public Member Functions inherited from RigidFiber
	RigidFiber ()
	Constructor.
	RigidFiber (RigidFiber const &)
	copy constructor
RigidFiber &	operator= (RigidFiber const &)
	copy assignment
virtual	~RigidFiber ()
	Destructor.
virtual unsigned	allocatePoints (unsigned nbp)
	sets the number of points in the Fiber
real	lagrange (unsigned p) const
	Lagrange multiplier for segment p.
real	tension (unsigned p) const
	longitudinal force along segment p (positive=extension, negative=compression)
real	dragCoefficient () const
	total drag-coefficient of object (force = drag * speed)
real	pointMobility () const
	mobility of one point
void	makeProjection ()
	prepare for projection
void	projectForces (const real *X, real *Y, real s, real *work) const
	apply the projection: Y <- s * P * X More...
void	makeProjectionDiff (const real *)
	prepare the correction to the projection
void	addProjectionDiff (const real *, real *) const
	add the contribution from the projection correction
real	addBrownianForces (real *rhs, real sc) const
	add displacements due to the Brownian motion to rhs[] More...
void	setSpeedsFromForces (const real *X, real *Y, real, bool) const
	calculate the speeds from the forces, including projection More...
void	addRigidity (const real *X, real *Y) const
	add the rigidity force corresponding to configuration X into vector Y More...
void	addRigidityMatUp (Matrix &, int offset) const
	add rigidity terms into the matrix
Public Member Functions inherited from FiberNaked
	FiberNaked ()
	Constructor.
	~FiberNaked ()
	Destructor.
void	setStraight (Vector const &pos, Vector const &dir)
	set position of MINUS_END and direction (length and Nb of points are not modified) More...
void	setStraight (Vector const &pos, Vector const &dir, FiberEnd ref)
	set position of 'ref' and direction of Fiber
void	setStraight (Vector const &pos, Vector const &dir, real len, FiberEnd ref)
	set position of 'ref', direction and length of Fiber
void	setShape (const real pts[], unsigned n_pts, unsigned np)
	import shape from the given array of size DIM*n_pts, and create a shape with np points More...
PointExact	exactEnd (FiberEnd) const
	exact representation of given end
PointInterpolated	interpolateEnd (FiberEnd) const
	interpolation representing a given end (CENTER is also a valid argument)
PointInterpolated	interpolateCenter () const
	interpolation representing a given end
PointInterpolated	interpolateMinusEnd () const
	interpolation representing the MINUS_END
PointInterpolated	interpolatePlusEnd () const
	interpolation representing the PLUS_END
PointInterpolated	interpolate (real ab) const
	interpolation of the site specified by its distance from the ORIGIN More...
PointInterpolated	interpolateM (real ab) const
	interpolation of the site specified from the MINUS_END More...
PointInterpolated	interpolate (real ab, FiberEnd from) const
	interpolation of a site specified by its distance from a FiberEnd
real	abscissaM () const
	signed distance from ORIGIN to MINUS_END (abscissa of MINUS_END)
real	abscissaP () const
	signed distance from ORIGIN to PLUS_END (abscissa of PLUS_END)
real	abscissaP (const real n) const
	signed distance from ORIGIN to given point or intermediate position
real	abscissa (FiberEnd end) const
	signed distance from the ORIGIN to the specified FiberEnd More...
real	abscissa (real ab, FiberEnd from) const
	converts abscissa from the specified FiberEnd, to abscissa from the ORIGIN More...
real	length () const
	the total length of the Fiber
bool	within (const real ab) const
	true if ( abscissaM() < ab < abscissaP() )
bool	withinP (const real ab) const
	true if abscissa is below abscissaP
bool	withinM (const real ab) const
	true if abscissa is above abscissaM
unsigned int	signature () const
	a random number which is used in speckle display
void	signature (unsigned int s)
	set signature
FiberEnd	whichEndDomain (real ab, real lambda) const
	calculate the domain in which ab is located (near a FiberEnd, or central) More...
Vector	pos (real ab) const
	position of a point specified by abscissa from the origin
Vector	posM (real ab) const
	position of a point specified by abscissa from the MINUS_END
Vector	pos (real ab, FiberEnd from) const
	position of a point specified by abscissa on the Fiber
Vector	posEnd (FiberEnd which) const
	position of a FiberEnd (CENTER is also a valid argument)
Vector	dirP (unsigned p) const
	normalized tangent vector to the fiber at given model point More...
Vector	dir (real ab) const
	normalized tangent vector to the fiber at given abscissa from the origin
Vector	dir (real ab, FiberEnd from) const
	normalized tangent vector to the fiber at given abscissa from given reference
Vector	dirEnd (FiberEnd which) const
	normalized tangent vector to the fiber at given end
real	projectedForceOnEnd (FiberEnd which) const
	dot-product (force/km on the end of the Fiber).(direction of Fiber growth) More...
void	segmentation (real c)
	set desired segmentation (the actual segmentation might be different)
real	segmentation () const
	the current segment length (distance between successive model-points)
real	segmentationCub () const
	returns segmentation() ^ 3
void	resegment (unsigned int nb_points)
	recalculate fiber to have nb_points model points More...
void	adjustSegmentation ()
	set the number of points to minimize abs( fnCut - fnCutWished ) More...
void	reshape ()
	re-establish the distance between successive model-points
void	getPoints (const real *x)
	set position
void	minMaxSegments (real &, real &) const
	calculate the minimum and maximum segment length More...
void	infoSegments (real &, real &) const
	calculate average and variance of the segment length More...
real	minCosinus () const
	the cosine of the maximum segment angle: indicate the errors due to curvature
unsigned	nbKinks (real threshold=0) const
	number of joints at which ( cosine(angle) < threshold ) More...
void	join (FiberNaked const *fib)
	merge two fibers by joining the PLUS_END of fib with the MINUS_END of this More...
void	growM (real dlen)
	increase/decrease length of Fiber by dlen, at the MINUS_END More...
void	addSegmentM ()
	add a segment of length segmentation() at the MINUS_END More...
void	cutM (real dlen)
	remove a piece of length dlen >= 0 at the MINUS_END More...
void	growP (real dlen)
	increase/decrease length of Fiber by dlen, at the PLUS_END More...
void	addSegmentP ()
	add a segment of length segmentation() at the MINUS_END More...
void	cutP (real dlen)
	remove a piece of length dlen >= 0 at the PLUS_END More...
void	setLength (real len, FiberEnd ref)
	adjust length without changing the position of ref
void	truncateM (unsigned int p)
	Remove all model points in [ 0, P-1 ], keep [ P, nbPoints() ].
void	truncateP (unsigned int p)
	Keep model points [ 0, p ], remove other points.
void	write (OutputWrapper &) const
	write to OutputWrapper
void	read (InputWrapper &, Simul &)
	read from InputWrapper More...
Public Member Functions inherited from PointSet
	PointSet ()
	Constructor.
	PointSet (const PointSet &)
	Copy constructor.
PointSet &	operator= (const PointSet &)
	Assignement operator.
virtual	~PointSet ()
	Destructor.
virtual void	deallocatePoints ()
	free memory allocated by allocatePoints()
unsigned int	nbPoints () const
	Number of points.
unsigned int	lastPoint () const
	Index of the last point = nbPoints - 1.
unsigned int	nbSegments () const
	Number of segments = nbPoints - 1.
unsigned int	lastSegment () const
	Index of the last segment = nbPoints - 2.
Vector	posP (const unsigned p) const
	Position of point 'p' of the object.
real const *	addr () const
	Address of point p.
real const *	addrPoint (const unsigned p) const
	Address of point p.
void	setPoint (unsigned p, Vector const &w)
	Set position of point p to w.
void	nbPoints (const unsigned n)
	Set the number of points in the array.
unsigned int	addPoint (Vector const &w)
	Add a point, returning the array index that was used.
void	removePoint (unsigned int p)
	Remove a point from the array psPos, returns number of points remaining.
void	clearPoints ()
	Remove all points.
void	resetPoints ()
	Set all coordinates to zero (nicer for debug/testing)
void	addNoise (real amount)
	Add random noise uniformly to all coordinate (used for testing purposes)
virtual void	putPoints (real *) const
	copy current coordinates to argument
virtual void	getForces (const real *ptr)
	replace current forces by the ones provided
Vector	netForceP (const unsigned p) const
	Force on point p calculate by Brownian dynamics.
void	movePoint (const unsigned int p, Vector const &w)
	Shift point at index p by vector w.
Vector	diffPoints (const unsigned p) const
	Difference of two points = Q - P = vector PQ.
Vector	diffPoints (const unsigned int p, const unsigned int q) const
	Difference of two points = Q - P = vector PQ.
Vector	interpolatePoints (const unsigned int p, const unsigned int q, const real a) const
	Calculate intermediate position = P + a ( Q - P )
void	calculateMomentum (real[], bool divide=false)
	calculate first momentum of point coordinates More...
void	calculateMomentum (real[], real[], bool divide=false)
	calculate first and second momentum of point coordinates More...
virtual Vector	position () const
	Position of center of gravity. More...
virtual bool	translatable () const
	true if object accepts translations
virtual void	translate (Vector const &)
	Translate object (moves all the points by w)
virtual bool	rotatable () const
	true if object accepts translations
virtual void	rotate (Rotation const &)
	Rotate object by given rotation.
virtual void	foldPosition (const Modulo *)
	Modulo around the first point.
virtual void	foldPositionG (const Modulo *)
	Call modulo around the center of gravity.
void	write (OutputWrapper &) const
	Write to file.
void	read (InputWrapper &, Simul &)
	Read from file.
Public Member Functions inherited from Mecable
	Mecable ()
	The constructor resets the pointers.
virtual	~Mecable ()
	Destructor de-allocates memory.
virtual Vector	posP (unsigned int P) const =0
	return position of point P
virtual void	putPoints (real[]) const =0
	copy current coordinates to provided array
virtual void	getPoints (const real[])=0
	replace current coordinates of points by values from the provided array
virtual Vector	netForceP (unsigned int p) const =0
	return Force on point p calculated at previous step by Brownian dynamics
virtual void	getForces (const real[])=0
	replace current forces by the ones provided
void	matIndex (Matrix::index_type index)
	Store the index where coordinates are located in Meca.
Matrix::index_type	matIndex () const
	Index in mB of the first point. the index in the vectors is DIM*matIndex() More...
bool	useBlock () const
	Tell Meca to use preconditionning on this object or not.
void	useBlock (bool b)
	change preconditionning flag
real *	allocateBlock (unsigned)
	Allocate a block of the requested size.
real *	block () const
	return allocated block
Public Member Functions inherited from Object
	Object ()
	constructor
std::string	reference () const
	concatenation of [ tag(), property()->index(), number() ] in plain ascii More...
void	writeReference (OutputWrapper &) const
	write a reference that identifies the Object uniquely More...
void	writeReference (OutputWrapper &, Tag tag) const
	write a reference, but using the provided Tag More...
int	mark () const
	birth mark value
void	mark (int m)
	set birth mark
int	fleck () const
	fleck value (not stored in trajectory files)
void	fleck (int f) const
	set fleck (the value is not stored in trajectory files)
Object *	next () const
	extends Node::next(), with a cast to preserve type
Object *	prev () const
	extends Node::prev(), with a cast to preserve type
Public Member Functions inherited from Node
	Node ()
	constructor set as unlinked
virtual	~Node ()
	destructor More...
bool	linked () const
	true if Node is linked
Node *	next () const
	the next Node in the list, or zero if this is last
Node *	prev () const
	the previous Node in the list, or zero if this is first
NodeList *	list () const
	the list where the object is linked, or zero
ObjectSet *	objset () const
	return associated ObjectSet
Public Member Functions inherited from Inventoried
	Inventoried ()
	initialize (name=0)
	~Inventoried ()
	destructor
void	number (Number n)
	change the serial number
Number	number () const
	serial number : a integer identifier, unique within each class
Public Member Functions inherited from Movable
	Movable ()
	constructor
virtual	~Movable ()
	destructor
virtual void	setPosition (Vector const &)
	move object to specified position More...
virtual void	rotateP (Rotation const &)
	rotate the object around its current position More...
Public Member Functions inherited from Buddy
virtual	~Buddy ()
	upon destruction, goodbye is called for all buddies
void	hello (Buddy *b)
	will make this and b mutual buddies
virtual void	goodbye (Buddy *)
	this is called everytime a known buddy is destroyed
Buddy *	buddy (unsigned int ix) const
	return buddy at index ix
void	buddy (Buddy *b, unsigned int ix)
	replace the buddy that may have been at index ix

Public Attributes
FiberProp const *	prop
	the Property of this object
LineDisp mutable *	disp
	the display parameters

Static Public Attributes
static const Tag	TAG = 'f'
	a unique character identifying the class
Static Public Attributes inherited from Object
static const Tag	TAG = 'v'
	Object::TAG = 'v' represents the 'void' pointer.

Protected Member Functions
virtual Fiber *	severM (real abs)
	cut fiber at distance abs from the MINUS_END; returns section [ abs - PLUS_END ] More...
Fiber *	severNow (real abs)
	cut fiber at abscissa abs from the ORIGIN; returns section [ abs - PLUS_END ]
void	delayedSevering ()
	cut fiber at absicca given to sever() More...
virtual Fiber *	severPoint (unsigned int pti)
	cut Fiber at point pti, return section [ pti - PLUS_END ] More...
void	severKinkedFibers (FiberSet *set)
	cut fiber at points where consecutive segments make a kink More...
real	dragCoefficientSurface ()
	viscous drag coefficient for a cylinder moving close to a surface More...
real	dragCoefficientVolume ()
	viscous drag coefficient for a cylinder moving close to a surface More...
Protected Member Functions inherited from RigidFiber
void	storeDifferences ()
	calculate the average difference of successive model-point in rfDiff[] More...

Additional Inherited Members
Static Public Member Functions inherited from PointSet
static Vector	diffPoints (const real *src, const unsigned p)
	Difference of two points = P+1 - P.
Static Public Member Functions inherited from Object
static std::string	strReference (char, int, Number, int)
	build a string reference by concatenating (tag, property_index, number, mark) More...
static void	readReference (InputWrapper &, int &, Number &, int &, char pretag)
	read a reference (property_index, number, mark) from input More...
static void	writeNullReference (OutputWrapper &)
	write a reference that does not refer to any Object
Static Public Member Functions inherited from Movable
static Vector	readPrimitive (std::istream &, const Space *)
	read a position specified with primitives, such as 'circle 5', etc. More...
static Vector	readPosition (std::istream &, const Space *)
	read a position in space More...
static Vector	readDirection (std::istream &, const Vector &, const Space *)
	read an orientation, and return a normalized vector More...
static Rotation	readRotation (std::istream &, const Vector &, const Space *)
	read a rotation specified in is, at position pos More...
Protected Attributes inherited from RigidFiber
real	rfMobility
	mobility of the points More...
real	rfRigidity
	rigidity scaling factor used in addRigidity()
Protected Attributes inherited from PointSet
real *	psPos
	psPos[] of size DIM*psAllocated contains DIM*psSize point-coordinates
real const *	psFor
	psFor[] of size DIM*psAllocated contains DIM*psSize force-coordinates
Vector	psCenter
	Center of gravity calculed in calculatePosition()
Protected Attributes inherited from Node
Node *	nNext
	the next Node in the list
Node *	nPrev
	the previous Node in the list
Protected Attributes inherited from Inventoried
Number	nNumber
	object identifier, unique within the class defined by tag()

Constructor & Destructor Documentation

Fiber

(

FiberProp const *

p

)

The rest of the initialization is done in FiberProp::newFiber(), and other newFiber() functions where the initial length is known.

Member Function Documentation

void delayedSevering ( )

protected

Performs the delayed severing events. This is called at the end of the time-step. Multiple cuts can occur. Fiber parts are added to set.

real dragCoefficientSurface ( )

protected

Fiber::setDragCoefficientSurface() uses a formula calculated by F. Gittes in:
Hunt et al. Biophysical Journal (1994) v 67 pp 766-781
http://dx.doi.org/10.1016/S0006-3495(94)80537-5

It applies to a cylinder moving parallel to its axis and near an immobile surface:

drag-per-unit-length = 2 &pi &eta / acosh(h/r)

With:

• r = cylinder radius,
• h = distance between cylinder bottom and surface,
• &eta = viscosity of the fluid.

If the cylinder is exactly touching the surface, h=0 and the drag coefficient is infinite.

The drag coefficient for motion perpendicular to the cylinder axis would be twice higher, but for gliding assays, the parallel drag coefficient is the appropriate choice.

Note that this is usually equivalent to the approximate formula:

drag-per-unit-length = 2 &pi &eta / log(2*h/r)

because acosh(x) = ln[ x + sqrt(x^2-1)) ] ~ ln[2x] if x >> 1

Hunt et al. also credit this reference for the formula:
The slow motion of a cylinder next to a plane wall. Jeffrey, D.J. & Onishi, Y. (1981) Quant. J. Mech. Appl. Math. 34, 129-137.

real dragCoefficientVolume ( )

protected

Fiber::setDragCoefficientVolume() calculates the mobility for the entire fiber, considering that the cylinder is straight and moving in a infinite fluid. fiber:hydrodynamic_radius[1] is a hydrodynamic cutoff that makes the drag coefficient proportional to length for length longer than the cutoff.

The formula for a cylinder is taken from:
Tirado and de la Torre. J. Chem. Phys 71(6) 1979
http://link.aip.org/link/doi/10.1063/1.438613

We calculate the translational drag coefficient averaged over all possible configurations:

cylinder_drag = 3*PI*length*viscosity / ( log(length/diameter) + 0.312 )

If the length is shorter than the diameter, the formula above fails and may even give negative result. Hence we also calculate the drag of a sphere with the same radius as the cylinder:

sphere_drag = 6*PI*visc*R

We use the maximum of these two coefficients.

int nbBindersInRange	(	real	aMin,
		real	aMax,
		FiberEnd	from
	)		const

Todo:

: Convert aMin and aMax instead of converting each Binder abscissa

void setDragCoefficient ( )

virtual

Calculate drag coefficient from two possible formulas

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

Implements Mecable.

void setGlue1	(	Single *	glue,
		FiberEnd	which,
		const Space *	space
	)

setGlue1 creates a pushing force from the cortex

void setGlue2	(	Single *	glue,
		FiberEnd	which,
		const Space *	space
	)

setGlue2 creates a pulling force from the cortex

void setGlue3	(	Single *	glue,
		FiberEnd	which,
		const Space *	space
	)

setGlue3 creates pulling and pushing force from the cortex

void severKinkedFibers ( FiberSet *  set )

protected

This function tests the angle between consecutive segments on the Fiber. The Fiber is severed at points where the angle is such that ( cosine < 0 ), ie. if the angle 90 degrees or less. Multiple cuts can occur. Fiber parts are added to set.

Fiber * severM ( real  abs )

protectedvirtual

The Fiber is cut at distance abs from its MINUS_END:

• current Fiber is truncated to keep only the section [ MINUS_END - abs ]
• A new Fiber is created from the section [ abs - PLUS_END ],
• all FiberBinder attached to the section are transfered to the new Fiber,
• a pointer to the new Fiber is returned, and it should be added to the Simul

The return value is zero, if abs is not within the valid range of abscissa.

Reimplemented in DynamicFiber, ClassicFiber, Tubule, and TreadmillingFiber.

Fiber * severPoint ( unsigned int  pti )

protectedvirtual

The Fiber is cut at point P

• A new Fiber is created from the section [ P - PLUS_END ],
• all FiberBinder attached to this section are transferred to the new Fiber,
• a pointer to the new Fiber is returned, which should be added to the Simul

Returns

zero, if pti is not an internal point