# actin_simple_hpp.bngl
# Created by BioNetGen 2.2.4
version("2.2.4+")

begin model
begin parameters
  f                      0.01
  Vol                    f*1e-12
  NA                     6.02e23
  ActinConc              1e-6*(Vol*NA)
  ADFconc                1e-6*(Vol*NA)
  kOn_barbed_ATP         11.6e6/(NA*Vol)
  kOff_barbed_ATP        1.4
  kOff_barbed_ADP        7.2
  kOn_pointed_ATP        1.3e6/(NA*Vol)
  kOff_pointed_ATP       0.8
  kOff_pointed_ADP       0.27
  kOnADF                 0.0085e6/(NA*Vol)
  kOffADF                0.005
  kOnADF_coop            0.075e6/(NA*Vol)
  kHydrolysis            0.3
  kPiRelease             0.0019
  kPiReleaseADF          0.035
  kSevering              0.012
  InitialConc1           100*f
  rateLaw1               kPiReleaseADF-kPiRelease
  rateLaw2               10000
  rateLaw3               10000
  rateLaw4               10000
  k_lump                 10000
end parameters
begin molecule types
  X0002()                                               population
  ADF(a)                                              
  X0001()                                               population
  Actin(barbed,pointed,p~ATP~ADPp~ADP,d,c~CAPPED~OPEN)
end molecule types
begin observables
  Molecules Polymers Actin(pointed,barbed!1).Actin(pointed!1)
  Molecules ActinMonomer Actin(barbed,pointed) X0002()
  Molecules ActinMonomerAvailable Actin(barbed,pointed,p~ATP,d,c~OPEN) X0002()
  Molecules ActinSubunit Actin(barbed!+,pointed!+)
  Molecules ActinSubunit_ATP Actin(barbed!+,pointed!+,p~ATP)
  Molecules ActinSubunit_ADPp Actin(barbed!+,pointed!+,p~ADPp)
  Molecules ActinSubunit_ADP Actin(barbed!+,pointed!+,p~ADP)
  Molecules ActinBarbedEnd Actin(barbed,pointed!+)
  Molecules ActinPointedEnd Actin(barbed!+,pointed)
  Molecules Actin_ADF Actin(barbed!+,pointed!+,d!+)
  Molecules ActinCapped Actin(c~CAPPED)
  Molecules ActinTotal Actin() X0002()
  Molecules ADFfree ADF(a) X0001()
  Molecules ADFtotal ADF() X0001()
end observables
begin functions
  ActinGeneratorRate() = if((ActinMonomerAvailable<ActinConc),(100000*f),0)
  ADFGeneratorRate()   = if((ADFfree<ADFconc),(100000*f),0)
end functions
begin species
  X0002() ActinConc
  X0001() ADFconc
  Actin(barbed!1,c~OPEN,d,p~ATP,pointed).Actin(barbed,c~OPEN,d,p~ATP,pointed!1) InitialConc1
end species
begin reaction rules
  Rule1_v1:  Actin(barbed,pointed) + Actin(barbed,c~OPEN,pointed!+) -> Actin(barbed,pointed!1).Actin(barbed!1,c~OPEN,pointed!+)  kOn_barbed_ATP
  Rule1_v2:  X0002() + Actin(barbed,c~OPEN,pointed!+) -> Actin(barbed!1,c~OPEN,pointed!+).Actin(barbed,c~OPEN,d,p~ATP,pointed!1)  kOn_barbed_ATP
  Rule2_v1:  Actin(barbed!1,pointed!+).Actin(barbed,c~OPEN,p~ATP,pointed!1) -> Actin(barbed,c~OPEN,p~ATP,pointed) + Actin(barbed,pointed!+)  kOff_barbed_ATP
  Rule3_v1:  Actin(barbed!1,pointed!+).Actin(barbed,c~OPEN,p~ADPp,pointed!1) -> Actin(barbed,c~OPEN,p~ADPp,pointed) + Actin(barbed,pointed!+)  kOff_barbed_ADP
  Rule4_v1:  Actin(barbed!1,pointed!+).Actin(barbed,c~OPEN,p~ADP,pointed!1) -> Actin(barbed,c~OPEN,p~ADP,pointed) + Actin(barbed,pointed!+)  kOff_barbed_ADP
  Rule5_v1:  Actin(barbed!+,c~OPEN,pointed) + Actin(barbed,pointed) -> Actin(barbed!1,pointed).Actin(barbed!+,c~OPEN,pointed!1)  kOn_pointed_ATP
  Rule5_v2:  Actin(barbed!+,c~OPEN,pointed) + X0002() -> Actin(barbed!+,c~OPEN,pointed!1).Actin(barbed!1,c~OPEN,d,p~ATP,pointed)  kOn_pointed_ATP
  Rule6_v1:  Actin(barbed!+,pointed!1).Actin(barbed!1,c~OPEN,p~ATP,pointed) -> Actin(barbed!+,pointed) + Actin(barbed,c~OPEN,p~ATP,pointed)  kOff_pointed_ATP
  Rule7_v1:  Actin(barbed!+,pointed!1).Actin(barbed!1,c~OPEN,p~ADPp,pointed) -> Actin(barbed!+,pointed) + Actin(barbed,c~OPEN,p~ADPp,pointed)  kOff_pointed_ADP
  Rule8_v1:  Actin(barbed!+,pointed!1).Actin(barbed!1,c~OPEN,p~ADP,pointed) -> Actin(barbed!+,pointed) + Actin(barbed,c~OPEN,p~ADP,pointed)  kOff_pointed_ADP
  Rule9_v1:  Actin().Actin(p~ATP) -> Actin().Actin(p~ADPp)  kHydrolysis
  Rule10_v1:  Actin().Actin(p~ADPp) -> Actin().Actin(p~ADP)  kPiRelease
  Rule11_v1:  ADF().Actin(d,p~ADPp) -> ADF().Actin(d,p~ADP)  rateLaw1
  Rule12_v1:  Actin(barbed!1,d).Actin(d,pointed!2).Actin(barbed!2,d,p~ADP,pointed!1) + X0001() -> ADF(a!1).Actin(barbed!2,d).Actin(d,pointed!3).Actin(barbed!3,d!1,p~ADP,pointed!2)  kOnADF
  Rule13_v1:  Actin(d!+,pointed!1).Actin(barbed!1,d,p~ADP,pointed!+) + X0001() -> ADF(a!1).Actin(d!+,pointed!2).Actin(barbed!2,d!1,p~ADP,pointed!+)  kOnADF_coop
  Rule14_v1:  Actin(barbed!1,d!+).Actin(barbed!+,d,p~ADP,pointed!1) + X0001() -> ADF(a!1).Actin(barbed!2,d!+).Actin(barbed!+,d!1,p~ADP,pointed!2)  kOnADF_coop
  Rule15_v1:  ADF(a!1).Actin(d!1) -> Actin(d) + X0001()  kOffADF DeleteMolecules
  Rule16_v1:  Actin(d!+,pointed!1).Actin(barbed!1,c~OPEN,d!+) -> Actin(d!+,pointed) + Actin(barbed,c~CAPPED,d!+)  kSevering
  Rule17_v1:  0 -> X0002()  ActinGeneratorRate()
  Rule18_v1:  0 -> X0001()  ADFGeneratorRate()
  Rule19_v1:  Actin(c~CAPPED) -> 0  rateLaw2
  Rule20_v1:  Actin(barbed,p~ADP,pointed) -> 0  rateLaw3
  Rule21_v1:  Actin(barbed,p~ADPp,pointed) -> 0  rateLaw4
  MapRule0:  ADF(a) -> X0001()  k_lump
  MapRule1:  Actin(barbed,c~OPEN,d,p~ATP,pointed) -> X0002()  k_lump
end reaction rules
end model


## model actions ##
simulate_nf({ t_end=>1000, n_steps=>200, gml=>10000000, complex=>0 })