Program Flow - Revision history

Markdayel: moved How comet works to Program Flow

2009-04-27T00:56:22Z

Markdayel at 00:56, 27 April 2009

2009-04-27T00:56:12Z

Markdayel: Replaced content with '=Program flow= The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown: [[file:Overvie...'

2009-04-27T00:53:03Z

Replaced content with '=Program flow= The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown: [[file:Overvie...'

Markdayel: /* Program flow */

2009-04-27T00:52:24Z

‎Program flow

Markdayel at 00:51, 27 April 2009

2009-04-27T00:51:24Z

Markdayel at 00:03, 18 April 2009

2009-04-18T00:03:00Z

Markdayel at 23:38, 17 April 2009

2009-04-17T23:38:22Z

Markdayel at 22:44, 17 April 2009

2009-04-17T22:44:01Z

Markdayel: /* Simple Overview */

2009-04-17T22:02:10Z

‎Simple Overview

Markdayel: /* Simple Overview */

2009-04-17T21:42:53Z

‎Simple Overview

← Older revision		Revision as of 00:56, 27 April 2009
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−	~~=Program flow=~~

	The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown:		The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown:

	[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]		[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]

← Older revision		Revision as of 00:53, 27 April 2009
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	[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]		[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]
−
−	~~=Description of model=~~
−
−
−	~~[[file:mymodel.png\|right\|thumb\|200px\|Figure 1: Schematic of node and link arrangement]]~~
−
−	The <code>comet</code> program is a Monte-Carlo/Lagrangian model that calculates the 3 dimensional positions of a large number of `nodes' representing material in an actin network. For each time step <code>DELTA_T</code>, nodes move a displacement proportional to the force acting upon them. There is no inertia, since this is a low Reynolds number regime. The forces acting on each node are as follows: [[file:mymodel_forces.png\|right\|thumb\|400px\|Figure 1: Forces acting on bead]]
−
−	*Repulsive forces between nodes
−	*Link forces between nodes
−	*Link forces between node and nucleator
−
−	~~[[file:Links_crosssection_inset.jpg\|right\|thumb\|400px\|Figure 1: 3D Cross section of part of shell showing links around bead]]~~
−
−	The nucleator object is treated as incompressible i.e. if during an iteration a node enters the nucleator, then in the next iteration it is simply moved out of the nucleator along a normal to the nucleator surface.
−
−	Nodes are nucleated at a constant rate, proportional to <code>P_NUC</code> , at the nucleator surface. To allow it to find an equilibrium position before being crosslinked into the network, a new node has its <code>harbinger</code> flag set when created, it experiences only repulsive forces for <code>CROSSLINKDELAY</code> iterations. Crosslinks are then formed as follows: All nodes with within <code>XLINK_NODE_RANGE</code> are counted, and links are either formed in random order, or if <code>XLINK_NEAREST</code> nearest first, until the number of crosslinks reaches <code>MAX_LINKS_PER_NODE</code>. Once a link is formed, its original distance is stored and used to calculate link forces. If the link is stretched or compressed away from its original length it behaves as a Hooke's Law spring and excerts a force proportional to, and opposing, the displacement. The scale multiple for this force is <code>LINK_FORCE</code> . This is to simulate an actin filament acting as an entropic spring by flexing motions. If the link force exceeds <code>LINK_BREAKAGE_FORCE</code> then the link breaks.
−
−	The nucleator is allowed to move and rotate, subject to displacement and torque vectors from the summed node repulsion from the nucleator, and the nucleator-node link forces. A full treatment of nucleator inertia is beyond the scope of the current model, and drag is simply scaled by a supplied parameter <code>NUCLEATOR_INERTIA</code> multiplied by the node inertia, and similarly the nucleator moment of inertia is scaled by the supplied parameter <code>MofI</code> . As a first approximation of how this should change with nucleator size, we scale the inertia and moment of inertia by the radius (or radius and length for long axes of the ellipsoids and capsules) if the <code>VARY_INERT_W_RAD</code> parameter is set. Given that this is not drag through a Newtonian fluid, but largely a product of complex fluid and network drag forces, this may not be very accurate. On the other hand the behavior is not very sensitive to the <code>NUCLEATOR_INERTIA</code> parameter anyway.
−
−	Output files are saved as jpgs for the x,y and z projections (convolved with a Gaussian to make it look like a microscope image). Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen. Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code> program to add text to the images and save as jpgs and calls <code>bzip2</code> to compress the data files.

← Older revision		Revision as of 00:52, 27 April 2009
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	=Program flow=		=Program flow=
		+
		+	The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown:

	[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]		[[file:Overview_simple.png\|800px\|Figure 2: Comet program flow (simple)]]

@@ Line 1: / Line 1: @@
-=Simple Overview=
+=Program flow=
 [[file:mymodel.png|right|thumb|200px|Figure 1: Schematic of node and link arrangement]]
@@ Line 18: / Line 23: @@
 Output files are saved as jpgs for the x,y and z projections (convolved with a Gaussian to make it look like a microscope image).  Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen.  Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code>  program to add text to the images and save as jpgs and calls <code>bzip2</code>  to compress the data files.

@@ Line 3: / Line 3: @@
 [[file:mymodel.png|right|thumb|200px|Figure 1: Schematic of node and link arrangement]]
-The <code>comet</code> program is a Monte-Carlo/Lagrangian model that calculates the 3 dimensional positions of a large number of `nodes' representing material in an actin network.  For each timestep <code>DELTA_T</code> , nodes move a displacement proportional to the force acting upon them.  There is no inertia, since this is a low Reynolds number regime.  The forces acting on each node are as follows: [[file:mymodel_forces.png|right|thumb|400px|Figure 1: Forces acting on bead]]
+The <code>comet</code> program is a Monte-Carlo/Lagrangian model that calculates the 3 dimensional positions of a large number of `nodes' representing material in an actin network.  For each time step <code>DELTA_T</code>, nodes move a displacement proportional to the force acting upon them.  There is no inertia, since this is a low Reynolds number regime.  The forces acting on each node are as follows: [[file:mymodel_forces.png|right|thumb|400px|Figure 1: Forces acting on bead]]
 *Repulsive forces between nodes
@@ Line 11: / Line 11: @@
 [[file:Links_crosssection_inset.jpg|right|thumb|400px|Figure 1: 3D Cross section of part of shell showing links around bead]]
-The nucleator object is treated as incompressible i.e.~if during an iteration a node enters the nucleator, then in the next iteration it is simply moved out of the nucleator along a normal to the nucleator surface.
+The nucleator object is treated as incompressible i.e. if during an iteration a node enters the nucleator, then in the next iteration it is simply moved out of the nucleator along a normal to the nucleator surface.
-Nodes are nucleated at a constant rate, proportional to <code>P_NUC</code> , at the nucleator surface.  To allow it to find an equilibrium position before being crosslinked into the network, a new node has its <code>harbinger</code>  flag set when created, it experiences only repulsive forces for <code>CROSSLINKDELAY</code>  iterations.  Crosslinks are then formed as follows:  All nodes with within <code>XLINK_NODE_RANGE</code>  are counted, and links are either formed in random order, or if <code>XLINK_NEAREST</code>  nearest first, until the number of crosslinks reaches <code>MAX_LINKS_PER_NODE</code> .  Once a link is formed, its original distance is stored and used to calculate link forces.  If the link is stretched or compressed away from its original length it behaves as a Hooke's Law spring and excerts a force proportional to, and opposing, the displacment.  The scale multiple for this force is <code>LINK_FORCE</code> .  This is to simulate an actin filament acting as an entropic spring by flexing motions. If the link force exceeds <code>LINK_BREAKAGE_FORCE</code>  then the link breaks.
+Nodes are nucleated at a constant rate, proportional to <code>P_NUC</code> , at the nucleator surface.  To allow it to find an equilibrium position before being crosslinked into the network, a new node has its <code>harbinger</code>  flag set when created, it experiences only repulsive forces for <code>CROSSLINKDELAY</code>  iterations.  Crosslinks are then formed as follows:  All nodes with within <code>XLINK_NODE_RANGE</code>  are counted, and links are either formed in random order, or if <code>XLINK_NEAREST</code>  nearest first, until the number of crosslinks reaches <code>MAX_LINKS_PER_NODE</code>.  Once a link is formed, its original distance is stored and used to calculate link forces.  If the link is stretched or compressed away from its original length it behaves as a Hooke's Law spring and excerts a force proportional to, and opposing, the displacement.  The scale multiple for this force is <code>LINK_FORCE</code> .  This is to simulate an actin filament acting as an entropic spring by flexing motions. If the link force exceeds <code>LINK_BREAKAGE_FORCE</code>  then the link breaks.
 The nucleator is allowed to move and rotate, subject to displacement and torque vectors from the summed node repulsion from the nucleator, and the nucleator-node link forces.  A full treatment of nucleator inertia is beyond the scope of the current model, and drag is simply scaled by a supplied parameter <code>NUCLEATOR_INERTIA</code>  multiplied by the node inertia,  and similarly the nucleator moment of inertia is scaled by the supplied parameter <code>MofI</code> .  As a first approximation of how this should change with nucleator size, we scale the inertia and moment of inertia by the radius (or radius and length for long axes of the ellipsoids and capsules) if the <code>VARY_INERT_W_RAD</code>  parameter is set.  Given that this is not drag through a Newtonian fluid, but largely a product of complex fluid and network drag forces, this may not be very accurate.  On the other hand the behavior is not very sensitive to the <code>NUCLEATOR_INERTIA</code> parameter anyway.
-Output files are saved as jpgs for the x,y and z projections (convolved with a gaussian to make it look like a microscope image).  Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen.  Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code>  program to add text to the images and save as jpgs and calls <code>bzip2</code>  to compress the data files.
+Output files are saved as jpgs for the x,y and z projections (convolved with a Gaussian to make it look like a microscope image).  Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen.  Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code>  program to add text to the images and save as jpgs and calls <code>bzip2</code>  to compress the data files.
 [[file:Overview_simple.svg|frame|right|Figure 2: Comet program flow (simple)]]

← Older revision	Revision as of 00:56, 27 April 2009
(No difference)

← Older revision		Revision as of 23:38, 17 April 2009
Line 18:		Line 18:

	Output files are saved as jpgs for the x,y and z projections (convolved with a gaussian to make it look like a microscope image). Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen. Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code> program to add text to the images and save as jpgs and calls <code>bzip2</code> to compress the data files.		Output files are saved as jpgs for the x,y and z projections (convolved with a gaussian to make it look like a microscope image). Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen. Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code> program to add text to the images and save as jpgs and calls <code>bzip2</code> to compress the data files.
−
−

	[[file:Overview_simple.svg\|frame\|right\|Figure 2: Comet program flow (simple)]]		[[file:Overview_simple.svg\|frame\|right\|Figure 2: Comet program flow (simple)]]
−
−	~~=Detailed Overview=~~
−
−	~~[[file:Overview_complex.svg\|frame\|right\|Figure 2: Comet program flow (detailed)]]~~

← Older revision		Revision as of 22:02, 17 April 2009
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	=Simple Overview=		=Simple Overview=
		+
		+
		+	[[file:mymodel.png\|right\|thumb\|200px\|Figure 1: Schematic of node and link arrangement]]
		+
		+	[[file:mymodel_forces.png\|right\|thumb\|400px\|Figure 1: Forces acting on bead]]

	[[file:Links_crosssection_inset.jpg\|right\|thumb\|400px\|Figure 1: 3D Cross section of part of shell showing links around bead]]		[[file:Links_crosssection_inset.jpg\|right\|thumb\|400px\|Figure 1: 3D Cross section of part of shell showing links around bead]]