Dissociation of membrane sp into two volume sp fails

[wxchew]

%matplotlib inline
from ecell4 import *
L=2
rv=0.01
D=1
h=0.5*L
h0=0
h1=h

with species_attributes():
A | B | {'radius':str(rv),"D": str(D), "location": "M"}
C | {'radius':str(rv),'D': str(D)}
with reaction_rules():
C > A+B | 10 #rule1
C > B | 10 #rule2

m = get_model()
w = spatiocyte.SpatiocyteWorld(Real3(L,h,L),rv)
w.bind_to(m)
upper = Real3(0,h1-2*rv,0)
lower = Real3(0,h0,0)
unit0 = Real3(0,0,L)
unit1 = Real3(L,0,0)
w.add_structure(Species("M"),PlanarSurface(upper,unit0,unit1))
w.add_structure(Species("W"),PlanarSurface(lower,unit0,unit1))
w.add_molecules(Species("C"),100)
sim = spatiocyte.SpatiocyteSimulator(w)
dt=50
duration=0.3
obs1 = FixedIntervalNumberObserver(duration/dt, ['C'])
sim.run(duration, obs1)
viz.plot_number_observer(obs1)

[wxchew]

rule2 in reaction rules() works, but rule1 fail.

[wxchew]

is this expected behavior?

[wxchew]

fail means fail to dissociate

[kaizu]

This looks due to the locations. C + M > A + B should work. However, an unit of the rate constant is different.

with reaction_rules():
    C + M > B | 10.0  # correct
    C > B | 10.0  # wrong

[kaizu]

The original problem mentioned here is

with species_attributes():
    A | B | {'radius':str(rv),"D": str(D)}
    C | {'radius':str(rv),'D': str(D), "location": "M"}

with reaction_rules():
    C > A+B | 10 #rule1

This doesn't work because the first order reaction with two products both on the different structure is not supported yet. See the following.

https://github.com/ecell/ecell4/blob/master/ecell4/spatiocyte/SpatiocyteReactions.cpp#L112-L116

One way to do this now is to place an intermediate state.

with reaction_rules():
    C > AB | 10 > A + B | 1e+20  # AB is at the same location with A or B

[kaizu]

Or

with species_attributes():
    A | B | {'radius':rv,"D": D}
    C | X | {'radius':rv,'D': D, "location": "M"}

with reaction_rules():
    C > X + A | 10
    X > B | 1e+20