User guide

Layout of the parameter file for simulations

Parameters are set by specifying the (i) the BlockParameter tag, (ii) the ParameterTag and (iii) the numerical value(s). For example, Capping protein and Arp2/3 concentration (given in micromole/liter) are set by the following group of lines. 

  set ChemicalParameters
  {
	  Cap_C 0.025
	  Arp_C 0.06
  }

where ChemicalParameters is the BlockParameter, Cap_C and Arp_C are ParameterTags. Similarly, the simulation duration (in seconds) and the number of generated frames are given by :

  set TimeParameters
  {
	  t_end 100
	  dt_obs 100
  }

with TimeParameters as BlockParameter and t_end or dt_obs as ParameterTag.

Patterns and subpatterns are used to specify the domain(s) where filaments are nucleated, branched and elongated. A Pattern (up to 2 patterns in the present version) is a collection of subpatterns (up to 20 subpatterns) coming in two elementary shapes, either a rectangle or a disc. By composition of different rectangle(s) and/or disc(s), we can model a large variety of nucleation domains. Before specifying the number of subpatterns, their shape and position, one should give the total number of patterns and subpatterns in the simulation.

   set Patterns
  {
	  pat_num 2
	  total_subpat 4
  }

Here, these lines specify two patterns and a total of four subpatterns. Then, one can specify the parameters for each patterns by the following commands :

   set PatternElements
  {
	  subpat_num 2
	  patId 3 2 0 0 10
	  patId 3 2 5 5 10
	  patMech 50 20 5 1
  }

for the first pattern and 

   set PatternElements
  {
	 subpat_num 2
 	  patId 2 2 10 0 0 10
 	  patId 2 2 10 15 0 10
  	  patMech 20 20 3 2
  }

for the second pattern. Each block of commands starts with the number of subpattern in the pattern (subpat_num as ParameterTag). Then, there are as many lines starting with patId as there are subpatterns in the pattern. Numbers after patId specify the nature, the position and the number of “primer” filaments in the subpattern. Rectangular subpatterns are coded by

   [2][Xwidth][Ywidth][X left,bottom][Y left, Bottom][Number of primers]

whereas discs are specified by 

   [3][Radius][Xcenter][Ycenter][Number of primers]

The last line with patMech ParameterTag specifies the following parameters valid for all subpatterns of the pattern

   [SpringConstant][FrictionConstant][DragCoefficient][ NucleatorDensity]

SpringConstant (pN/micrometer) is the stiffness of the springs in the “coarse-grained” model;

 FrictionConstant (pN.seconds/micrometer) describes the friction between the mass-spring structure and the possible barriers (see following section).

DragCoefficient (pN.seconds/micrometers) is used to compute the viscous force exerted on the mass-spring system moving in a fluid.

NucleatorDensity (no dimensions) codes for the density of actin filaments nucleators

The presence of obstacles (e.g. the cover slip) is coded by specifying the number of barriers, their shapes and positions. First, specify the total number of barriers by

   set Barriers
  {
	  barrier_num 1
  }

then, use

  set BarrierElements
  {
	  barId 2 4.5 1
  }

to specify the nature of the barrier and its position. An infinite planar barrier is coded by

   [x=0,1,2] [Position][1/-1]

where x=0, 1 or 2 indicates that the barrier is along the X, Y or Z axis at a distance of Position (micrometers) from the origin. The last digit gives the direction growth towards the barrier : put 1 if the barrier is on top (or left) to the network; put -1 if the barrier is below or right to the network.  The syntax for walls, for example

   barId 3 5 7.5 6 1

has the following form

   [Id][X][Ylow][Yup][1/-1]

where Id=3 codes for a wall at position X (on the X axis). This wall extends from Ylow to Yup. The last digit gives the direction growth towards the barrier : put 1 if the barrier is on top (or left) to the network; put -1 if the barrier is below or right to the network. Note that the wall is infinite in the Z direction. For Id=5, the following line codes for a wall

   [5][Y][Xlow][Xup][1/-1]

on the Y axis (at position Y) extending from Xlow to Xup. Pillars can be assembled from walls as shown in the example

   set BarrierElements
  {
	  barId 2 5 1
	  barId 3 3.5 15 10 1
	  barId 5 3.5 10 6.5 1
	  barId 3 6.5 15 10 -1
  }

where one has a plane barrier at z=5, a wall at x=3.5, extending from Y=15 to 10 , a wall at x=6.5 extending from Y=15 to 10 and a wall at Y=3.5, extending from x=10 to 6.5.

Here are four examples of input files (Right-click and choose "Save as" to download a file) :

Layout of the output files

Simulation generates files, one per time frame. Each time frame file is made of two parts. First, parameters for the “microcoscopic model” structure, describing the filaments at the microscopic level with the following format

line 1: Number of initial primers used in simulations.
line 2: Total number of filaments.

Then, each filament is described by a line

Line x: PrimerIndex, BranchIndex, FilamentLength, Xpointed, Ypointed, Zpointed, Xbarbed, Ybarbed, Zbarbed, Ux, Uy Uz, PointedEndStatus, BarbedEndStatus, TimeToCap/UnCap PointedEnd, TimeToCap/UnCap Barbed end, FilamentAge, NumberOfChildren, MotherIndex,

In a second section, the output file provides information for the “coarse-grained” model.

Line 1: number of nodes (or masses) of the “coarse-grained model”.

Then, a series of lines (one per node) giving

line x: Xmass, Ymass, Zmass, FactinMass, PatternIndex, ElasticStress

where (Xmass, Ymass, Zmass) is the position of the node, FactinMass is the equivalent of Factin, PatternIndex is an internal tag assigning the node to one of the pattern in the model.

ElasticStress is the stress seen by the node during its displacement. Then, for each node, we indicate the list of nodes that are directly connected to it.

This is an example of the ouput file:

71
-3.71605 9.99651 0.400814 28919.7 1 5.36872e-06 -3.67855 9.99425 2.42288 9229.3 1 3.69536e-06
....
2 4 5 6 7 1 4 3 8
….

Using the Matlab script, one can generate tif images illustrating the time evolution of the model.