work on cytosim process

vivarium_models/processes/cytosim.py

@@ -73,10 +73,20 @@ def load_report(output):
         for id, fiber_points, n_points, fiber_type in zip(all_ids, all_fibers, all_n_points, all_types)}
 
 
+def temperature_to_kT(temp):
+    return 1.3806e-5 * (temp + 273.15)
+
+
+# def random_actin_fiber(bounds):
+
+
 class CytosimProcess(Process):
     defaults = {
         'model_name': 'cytosim_model',
         'internal_timestep': 0.001,
+        'viscosity': 1,
+        'actin_segmentation': 0.1,
+        'temperature': 37, # in Celsius
         'cytosim_template': "cytosim-buckling.cym",
         'cell_radius': 5,
         'confine': None,
@@ -121,6 +131,9 @@ def next_update(self, timestep, state):
         cytosim_config = template.render(
             internal_timestep=self.parameters['internal_timestep'],
             # radius=self.parameters['cell_radius'],
+            kT=temperature_to_kT(self.parameters['temperature']),
+            viscosity=self.parameters['viscosity'],
+            actin_segmentation=self.parameters['actin_segmentation'],
             confine=self.parameters['confine'],
             bounds_x=box_extent[0],
             bounds_y=box_extent[1],

vivarium_models/templates/actin.cym

@@ -0,0 +1,37 @@
+% Actin filaments with advanced rendering
+% F. Nedelec, November 2015
+
+set simul system
+{
+    time_step = 0.001
+    viscosity = 1
+    display = ( point_value=0.001; style=3; )
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 0.125
+}
+
+set fiber actin
+{
+    rigidity = 0.05
+    segmentation = 0.0055      %that is 4 monomers
+    confine = inside, 200
+    display = ( style=actin; color=red, dark_red; end_color=yellow; )
+}
+
+new 10 actin
+{
+    length = 0.25
+}
+
+run 5000 system
+{
+    nb_frames = 10
+}

vivarium_models/templates/cytosim-buckling.cym

@@ -4,8 +4,8 @@
 set simul system
 {
     time_step = {{internal_timestep}}
-    viscosity = 0.01
-    kT = 0.001
+    viscosity = {{viscosity}}
+    kT = {{kT}}
 }
 
 set space cell
@@ -21,7 +21,7 @@ new cell
 set fiber actin
 {
     rigidity = 10
-    segmentation = 0.1
+    segmentation = {{actin_segmentation}}
     display = ( point=6,1; line=10,2; )
     {% if confine %}
     confine = {{confine.side}}, {{confine.force}}, {{confine.space}}