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output.json
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time_step = 1.0e-6
TIME_STEP = time_step
TIME_STEP_MAX = time_step
ITERATIONS = 1e-2/time_step
EFFECTOR_GRID_DENSITY = 10000
INTERACTION_RADIUS = 0.001
nEndo = 5.0
vol_EC = 20.0
vol_CP = 4.0
vol_NU = 1.0
vol_EN = 0.5
sa_PM = 0.4
sa_NM = 0.1
sa_EM = 0.05
eff_width = 1.0
L0 = 1000.0
R0 = 200.0
TF0 = 200.0
DNA0 = 2.0
Im0 = 40.0
NP0 = 4.0
kp_LR = 0.1
km_LR = 1.0
kp_LL = 0.1
km_LL = 1.0
k_R_endo = 1.0
k_recycle = 0.1
k_R_transphos = 1.0
k_R_dephos = 0.1
kp_R_TF = 0.1
km_R_TF = 0.1
kp_R_TFp = 0.1
km_R_TFp = 10.0
k_TF_transphos = 1.0
k_TF_dephos = 1.0
kp_TF_TF = 0.1
km_TF_TF = 1.0
kp_TF_p1 = 0.1
km_TF_p1 = 1.0
k_transcribe = 1.0
k_translate = 1.0
k_mRNA_to_CP = 1.0
k_mRNA_deg = 1.0
k_P_deg = 0.1
k_Im_bind_CP = 0.1
k_Im_unbind_CP = 0.1
k_Im_bind_NU = 0.1
k_Im_unbind_NU = 10.0
k_Im_enters_NP = 0.1
k_Im_exits_NP = 1.0
k_Im_cross_NP = 1.0
kp_P1_p2 = 0.1
km_P1_p2 = 1.0
DEFINE_MOLECULES{
S76 { D_3D = 100e-8 } /*@NU::mRNA2()*/
S48 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~pY,dna,im,r!4)@CP*/
S58 { D_3D = 100e-8 } /*@CP::TF(d~pY!1,dna,im,r).TF(d~pY!1,dna,im,r)*/
S54 { D_3D = 100e-8 } /*@EM::L(d,r!1)@EN.R(l!1,tf~pY!2).TF(d~pY,dna,im,r!2)@CP*/
S25 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~Y,dna,im,r!4)@CP*/
S26 { D_3D = 100e-8 } /*@EN::L(d!1,r).L(d!1,r)*/
S49 { D_3D = 100e-8 } /*@CP::TF(d~pY,dna,im,r)*/
S18 { D_3D = 100e-8 } /*@EM::R(l,tf~Y)*/
S5 { D_3D = 100e-8 } /*@CP::Im(cargo,fg)*/
S73 { D_3D = 100e-8 } /*@NU::Im(cargo!1,fg).P1(dna,im!1)*/
S62 { D_3D = 100e-8 } /*@NU::TF(d~pY!1,dna,im,r).TF(d~pY!1,dna,im,r)*/
S50 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~pY,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP*/
S9 { D_3D = 100e-8 } /*@EC::L(d!1,r).L(d!1,r)*/
S61 { D_3D = 100e-8 } /*@NM::Im(cargo!1!2,fg!3)@NU.NP(fg!3).TF(d~pY!4,dna,im!1,r)@NU.TF(d~pY!4,dna,im!2,r)@NU*/
S71 { D_3D = 100e-8 } /*@NM::Im(cargo!1,fg!2)@NU.NP(fg!2).P1(dna,im!1)@NU*/
S63 { D_3D = 100e-8 } /*@NU::Im(cargo!1!2,fg).TF(d~pY!3,dna,im!1,r).TF(d~pY!3,dna,im!2,r)*/
S65 { D_3D = 100e-8 } /*@NU::DNA(p1!1!2,p2).TF(d~pY!3,dna!1,im,r).TF(d~pY!3,dna!2,im,r)*/
S55 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~pY,dna,im,r!4)@CP*/
S67 { D_3D = 100e-8 } /*@CP::mRNA1()*/
S10 { D_3D = 100e-8 } /*@NM::Im(cargo,fg!1)@CP.NP(fg!1)*/
S77 { D_3D = 100e-8 } /*@CP::mRNA2()*/
S13 { D_3D = 100e-8 } /*@NM::Im(cargo,fg!1)@NU.NP(fg!1)*/
S6 { D_3D = 100e-8 } /*@NM::NP(fg)*/
S12 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~Y)*/
S24 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY).R(l!3,tf~pY)*/
S34 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY).R(l!3,tf~pY)*/
S35 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~Y,dna,im,r!4)@CP*/
S3 { D_3D = 100e-8 } /*@CP::TF(d~Y,dna,im,r)*/
S4 { D_3D = 100e-8 } /*@NU::DNA(p1,p2)*/
S39 { D_3D = 100e-8 } /*@EM::R(l,tf~pY!1).TF(d~Y,dna,im,r!1)@CP*/
S57 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~pY,dna,im,r!4)@CP*/
S23 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~pY)*/
S38 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY!3).TF(d~Y,dna,im,r!3)@CP*/
S70 { D_3D = 100e-8 } /*@NM::Im(cargo!1,fg!2)@CP.NP(fg!2).P1(dna,im!1)@CP*/
S53 { D_3D = 100e-8 } /*@EM::R(l,tf~pY!1).TF(d~pY,dna,im,r!1)@CP*/
S31 { D_3D = 100e-8 } /*@PM::R(l,tf~pY!1).TF(d~Y,dna,im,r!1)@CP*/
S69 { D_3D = 100e-8 } /*@CP::Im(cargo!1,fg).P1(dna,im!1)*/
S52 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY!3).TF(d~pY,dna,im,r!3)@CP*/
S44 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY!3).TF(d~pY,dna,im,r!3)@CP*/
S75 { D_3D = 100e-8 } /*@NU::DNA(p1!1!2,p2!3).P1(dna!3,im).TF(d~pY!4,dna!1,im,r).TF(d~pY!4,dna!2,im,r)*/
S45 { D_3D = 100e-8 } /*@PM::R(l,tf~pY!1).TF(d~pY,dna,im,r!1)@CP*/
S16 { D_3D = 100e-8 } /*@NU::Im(cargo,fg)*/
S78 { D_3D = 100e-8 } /*@CP::P2()*/
S68 { D_3D = 100e-8 } /*@CP::P1(dna,im)*/
S43 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP*/
S64 { D_3D = 100e-8 } /*@NU::TF(d~pY,dna,im,r)*/
S51 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY!4).TF(d~pY,dna,im,r!4)@CP*/
S32 { D_3D = 100e-8 } /*@EM::L(d,r!1)@EN.R(l!1,tf~pY)*/
S36 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~Y,dna,im,r!4)@CP*/
S7 { D_3D = 100e-8 } /*@CP::$Sink()*/
S60 { D_3D = 100e-8 } /*@NM::Im(cargo!1!2,fg!3)@CP.NP(fg!3).TF(d~pY!4,dna,im!1,r)@CP.TF(d~pY!4,dna,im!2,r)@CP*/
S37 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~Y,dna,im,r!5)@CP*/
S59 { D_3D = 100e-8 } /*@CP::Im(cargo!1!2,fg).TF(d~pY!3,dna,im!1,r).TF(d~pY!3,dna,im!2,r)*/
S27 { D_3D = 100e-8 } /*@EN::L(d,r)*/
S2 { D_3D = 100e-8 } /*@PM::R(l,tf~Y)*/
S1 { D_3D = 100e-8 } /*@EC::L(d,r)*/
S47 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP*/
S33 { D_3D = 100e-8 } /*@PM::L(d,r!1)@EC.R(l!1,tf~pY!2).TF(d~Y,dna,im,r!2)@CP*/
S17 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~Y)*/
S21 { D_3D = 100e-8 } /*@EM::L(d,r!1)@EN.R(l!1,tf~Y)*/
S20 { D_3D = 100e-8 } /*@PM::R(l,tf~pY)*/
S30 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY!3).TF(d~Y,dna,im,r!3)@CP*/
S72 { D_3D = 100e-8 } /*@NU::P1(dna,im)*/
S46 { D_3D = 100e-8 } /*@PM::L(d,r!1)@EC.R(l!1,tf~pY!2).TF(d~pY,dna,im,r!2)@CP*/
S15 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r!3)@EC.R(l!2,tf~Y).R(l!3,tf~pY)*/
S11 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~Y)*/
S22 { D_3D = 100e-8 } /*@PM::L(d,r!1)@EC.R(l!1,tf~pY)*/
S74 { D_3D = 100e-8 } /*@NU::DNA(p1,p2!1).P1(dna!1,im)*/
S8 { D_3D = 100e-8 } /*@PM::L(d,r!1)@EC.R(l!1,tf~Y)*/
S28 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r)@EN.R(l!2,tf~pY)*/
S66 { D_3D = 100e-8 } /*@NU::mRNA1()*/
S56 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~pY,dna,im,r!4)@CP.TF(d~pY,dna,im,r!5)@CP*/
S40 { D_3D = 100e-8 } /*@EM::L(d,r!1)@EN.R(l!1,tf~pY!2).TF(d~Y,dna,im,r!2)@CP*/
S42 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~pY!4).R(l!3,tf~pY!5).TF(d~Y,dna,im,r!4)@CP.TF(d~Y,dna,im,r!5)@CP*/
S29 { D_3D = 100e-8 } /*@EM::R(l,tf~pY)*/
S19 { D_3D = 100e-8 } /*@PM::L(d!1,r!2)@EC.L(d!1,r)@EC.R(l!2,tf~pY)*/
S41 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!3,tf~pY!4).R(l!2,tf~pY).TF(d~Y,dna,im,r!4)@CP*/
S14 { D_3D = 100e-8 } /*@EM::L(d!1,r!2)@EN.L(d!1,r!3)@EN.R(l!2,tf~Y).R(l!3,tf~Y)*/
}
small_box BOX
{
CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
}
INSTANTIATE my_world OBJECT
{
S1_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S1
NUMBER_TO_RELEASE = L0
SITE_DIAMETER = 0.196
}
S2_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S2
NUMBER_TO_RELEASE = R0
SITE_DIAMETER = 0.196
}
S3_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S3
NUMBER_TO_RELEASE = TF0
SITE_DIAMETER = 0.196
}
S4_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S4
NUMBER_TO_RELEASE = DNA0
SITE_DIAMETER = 0.196
}
S5_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S5
NUMBER_TO_RELEASE = Im0
SITE_DIAMETER = 0.196
}
S6_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S6
NUMBER_TO_RELEASE = NP0
SITE_DIAMETER = 0.196
}
S7_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S7
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S8_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S8
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S9_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S9
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S10_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S10
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S11_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S11
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S12_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S12
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S13_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S13
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S14_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S14
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S15_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S15
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S16_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S16
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S17_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S17
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S18_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S18
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S19_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S19
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S20_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S20
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S21_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S21
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S22_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S22
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S23_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S23
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S24_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S24
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S25_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S25
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S26_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S26
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S27_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S27
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S28_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S28
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S29_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S29
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S30_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S30
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S31_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S31
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S32_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S32
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S33_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S33
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S34_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S34
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S35_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S35
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S36_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S36
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S37_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S37
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S38_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S38
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S39_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S39
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S40_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S40
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S41_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S41
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S42_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S42
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S43_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S43
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S44_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S44
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S45_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S45
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S46_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S46
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S47_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S47
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S48_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S48
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S49_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S49
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S50_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S50
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S51_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S51
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S52_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S52
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S53_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S53
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S54_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S54
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S55_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S55
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S56_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S56
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S57_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S57
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S58_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S58
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S59_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S59
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S60_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S60
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S61_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S61
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S62_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S62
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S63_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S63
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S64_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S64
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S65_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S65
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S66_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S66
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S67_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S67
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S68_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S68
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S69_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S69
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S70_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S70
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S71_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S71
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S72_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S72
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S73_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S73
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S74_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S74
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S75_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S75
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S76_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S76
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S77_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S77
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
S78_release CUBIC_RELEASE_SITE {
LOCATION = [0,0,0]
MOLECULE = S78
NUMBER_TO_RELEASE = 0
SITE_DIAMETER = 0.196
}
my_box OBJECT small_box {}
}
DEFINE_REACTIONS
{
S1+S2 -> S8 [0.05*kp_LR]
S1+S1 -> S9 [0.025*kp_LL]
S5+S6 -> S10 [0.25*k_Im_enters_NP]
S2+S9 -> S11 [0.1*kp_LR]
S8 -> S1+S2 [km_LR]
S1+S8 -> S11 [0.05*kp_LL]
S8+S8 -> S12 [1.25*kp_LL]
S9 -> S1+S1 [km_LL]
S10 -> S5+S6 [k_Im_exits_NP]
S10 -> S13 [k_Im_cross_NP]
S2+S11 -> S12 [2.5*kp_LR]
S11 -> S2+S9 [km_LR]
S12 -> S2+S11 [2*km_LR]
S11 -> S1+S8 [km_LL]
S12 -> S8+S8 [km_LL]
S12 -> S14 [k_R_endo]
S12 -> S15 [2*k_R_transphos]
S13 -> S6+S16 [k_Im_exits_NP]
S13 -> S10 [k_Im_cross_NP]
S14 -> S17+S18 [2*km_LR]
S15 -> S2+S19 [km_LR]
S15 -> S11+S20 [km_LR]
S14 -> S21+S21 [km_LL]
S15 -> S8+S22 [km_LL]
S15 -> S23 [k_R_endo]
S14 -> S12 [k_recycle]
S14 -> S23 [2*k_R_transphos]
S15 -> S24 [k_R_transphos]
S15 -> S12 [k_R_dephos]
S3+S15 -> S25 [0.25*kp_R_TF]
S6+S16 -> S13 [k_Im_enters_NP]
S1+S20 -> S22 [0.05*kp_LR]
S9+S20 -> S19 [0.1*kp_LR]
S11+S20 -> S15 [2.5*kp_LR]
S17+S18 -> S14 [20*kp_LR]
S2+S19 -> S15 [2.5*kp_LR]
S19+S20 -> S24 [2.5*kp_LR]
S17 -> S18+S26 [km_LR]
S19 -> S9+S20 [km_LR]
S21 -> S18+S27 [km_LR]
S22 -> S1+S20 [km_LR]
S23 -> S18+S28 [km_LR]
S23 -> S17+S29 [km_LR]
S24 -> S19+S20 [2*km_LR]
S25 -> S2+S30 [km_LR]
S25 -> S11+S31 [km_LR]
S1+S22 -> S19 [0.05*kp_LL]
S8+S22 -> S15 [2.5*kp_LL]
S21+S21 -> S14 [10*kp_LL]
S22+S22 -> S24 [1.25*kp_LL]
S17 -> S21+S27 [km_LL]
S19 -> S1+S22 [km_LL]
S23 -> S21+S32 [km_LL]
S24 -> S22+S22 [km_LL]
S25 -> S8+S33 [km_LL]
S24 -> S34 [k_R_endo]
S25 -> S35 [k_R_endo]
S17 -> S11 [k_recycle]
S18 -> S2 [k_recycle]
S21 -> S8 [k_recycle]
S23 -> S15 [k_recycle]
S23 -> S34 [k_R_transphos]
S25 -> S36 [k_R_transphos]
S19 -> S11 [k_R_dephos]
S20 -> S2 [k_R_dephos]
S22 -> S8 [k_R_dephos]
S23 -> S14 [k_R_dephos]
S24 -> S15 [2*k_R_dephos]
S3+S19 -> S30 [0.25*kp_R_TF]
S3+S20 -> S31 [0.25*kp_R_TF]
S3+S22 -> S33 [0.25*kp_R_TF]
S3+S23 -> S35 [0.25*kp_R_TF]
S3+S24 -> S36 [0.5*kp_R_TF]
S25 -> S3+S15 [km_R_TF]
S1+S31 -> S33 [0.05*kp_LR]
S9+S31 -> S30 [0.1*kp_LR]
S11+S31 -> S25 [2.5*kp_LR]
S17+S29 -> S23 [20*kp_LR]
S19+S31 -> S36 [2.5*kp_LR]
S18+S26 -> S17 [4*kp_LR]
S26+S29 -> S28 [4*kp_LR]
S18+S27 -> S21 [2*kp_LR]
S27+S29 -> S32 [2*kp_LR]
S18+S28 -> S23 [20*kp_LR]
S28+S29 -> S34 [20*kp_LR]
S2+S30 -> S25 [2.5*kp_LR]
S20+S30 -> S36 [2.5*kp_LR]
S30+S31 -> S37 [2.5*kp_LR]
S28 -> S26+S29 [km_LR]
S30 -> S9+S31 [km_LR]
S32 -> S27+S29 [km_LR]
S33 -> S1+S31 [km_LR]
S34 -> S28+S29 [2*km_LR]
S35 -> S18+S38 [km_LR]
S35 -> S17+S39 [km_LR]
S36 -> S20+S30 [km_LR]
S36 -> S19+S31 [km_LR]
S1+S33 -> S30 [0.05*kp_LL]
S8+S33 -> S25 [2.5*kp_LL]
S21+S27 -> S17 [2*kp_LL]
S21+S32 -> S23 [20*kp_LL]
S22+S33 -> S36 [2.5*kp_LL]
S27+S27 -> S26 [kp_LL]
S27+S32 -> S28 [2*kp_LL]
S32+S32 -> S34 [10*kp_LL]
S33+S33 -> S37 [1.25*kp_LL]
S26 -> S27+S27 [km_LL]
S28 -> S27+S32 [km_LL]
S30 -> S1+S33 [km_LL]
S34 -> S32+S32 [km_LL]
S35 -> S21+S40 [km_LL]
S36 -> S22+S33 [km_LL]
S36 -> S41 [k_R_endo]
S28 -> S19 [k_recycle]
S29 -> S20 [k_recycle]
S32 -> S22 [k_recycle]
S34 -> S24 [k_recycle]
S35 -> S25 [k_recycle]
S26 -> S9 [k_recycle]
S27 -> S1 [k_recycle]
S35 -> S41 [k_R_transphos]
S28 -> S17 [k_R_dephos]
S29 -> S18 [k_R_dephos]
S32 -> S21 [k_R_dephos]
S34 -> S23 [2*k_R_dephos]
S36 -> S25 [k_R_dephos]
S3+S28 -> S38 [0.25*kp_R_TF]
S3+S29 -> S39 [0.25*kp_R_TF]
S3+S32 -> S40 [0.25*kp_R_TF]
S3+S34 -> S41 [0.5*kp_R_TF]
S3+S36 -> S37 [0.25*kp_R_TF]
S30 -> S3+S19 [km_R_TF]
S31 -> S3+S20 [km_R_TF]
S33 -> S3+S22 [km_R_TF]
S35 -> S3+S23 [km_R_TF]
S36 -> S3+S24 [km_R_TF]
S17+S39 -> S35 [20*kp_LR]
S26+S39 -> S38 [4*kp_LR]
S27+S39 -> S40 [2*kp_LR]
S28+S39 -> S41 [20*kp_LR]
S18+S38 -> S35 [20*kp_LR]
S29+S38 -> S41 [20*kp_LR]
S38+S39 -> S42 [20*kp_LR]
S37 -> S30+S31 [2*km_LR]
S38 -> S26+S39 [km_LR]
S40 -> S27+S39 [km_LR]
S41 -> S29+S38 [km_LR]
S41 -> S28+S39 [km_LR]
S21+S40 -> S35 [20*kp_LL]
S27+S40 -> S38 [2*kp_LL]
S32+S40 -> S41 [20*kp_LL]
S40+S40 -> S42 [10*kp_LL]
S37 -> S33+S33 [km_LL]
S38 -> S27+S40 [km_LL]
S41 -> S32+S40 [km_LL]
S37 -> S42 [k_R_endo]
S38 -> S30 [k_recycle]
S39 -> S31 [k_recycle]
S40 -> S33 [k_recycle]
S41 -> S36 [k_recycle]
S41 -> S35 [k_R_dephos]
S3+S41 -> S42 [0.25*kp_R_TF]
S37 -> S3+S36 [2*km_R_TF]
S38 -> S3+S28 [km_R_TF]
S39 -> S3+S29 [km_R_TF]
S40 -> S3+S32 [km_R_TF]
S41 -> S3+S34 [km_R_TF]
S37 -> S43 [2*k_TF_transphos]
S42 -> S38+S39 [2*km_LR]
S43 -> S31+S44 [km_LR]
S43 -> S30+S45 [km_LR]
S42 -> S40+S40 [km_LL]
S43 -> S33+S46 [km_LL]
S43 -> S47 [k_R_endo]
S42 -> S37 [k_recycle]
S42 -> S3+S41 [2*km_R_TF]
S43 -> S3+S48 [km_R_TF]
S43 -> S36+S49 [km_R_TFp]
S42 -> S47 [2*k_TF_transphos]
S43 -> S50 [k_TF_transphos]
S43 -> S37 [k_TF_dephos]
S1+S45 -> S46 [0.05*kp_LR]
S9+S45 -> S44 [0.1*kp_LR]
S11+S45 -> S51 [2.5*kp_LR]
S19+S45 -> S48 [2.5*kp_LR]
S30+S45 -> S43 [2.5*kp_LR]
S2+S44 -> S51 [2.5*kp_LR]
S20+S44 -> S48 [2.5*kp_LR]
S31+S44 -> S43 [2.5*kp_LR]
S44+S45 -> S50 [2.5*kp_LR]
S44 -> S9+S45 [km_LR]
S46 -> S1+S45 [km_LR]
S47 -> S39+S52 [km_LR]
S47 -> S38+S53 [km_LR]
S48 -> S20+S44 [km_LR]
S48 -> S19+S45 [km_LR]
S50 -> S44+S45 [2*km_LR]
S1+S46 -> S44 [0.05*kp_LL]
S8+S46 -> S51 [2.5*kp_LL]
S22+S46 -> S48 [2.5*kp_LL]
S33+S46 -> S43 [2.5*kp_LL]
S46+S46 -> S50 [1.25*kp_LL]
S44 -> S1+S46 [km_LL]
S47 -> S40+S54 [km_LL]
S48 -> S22+S46 [km_LL]
S50 -> S46+S46 [km_LL]
S48 -> S55 [k_R_endo]
S50 -> S56 [k_R_endo]
S47 -> S43 [k_recycle]
S48 -> S51 [k_R_dephos]
S3+S48 -> S43 [0.25*kp_R_TF]
S47 -> S3+S55 [km_R_TF]
S15+S49 -> S51 [0.25*kp_R_TFp]
S19+S49 -> S44 [0.25*kp_R_TFp]
S20+S49 -> S45 [0.25*kp_R_TFp]
S22+S49 -> S46 [0.25*kp_R_TFp]
S23+S49 -> S57 [0.25*kp_R_TFp]
S24+S49 -> S48 [0.5*kp_R_TFp]
S28+S49 -> S52 [0.25*kp_R_TFp]
S29+S49 -> S53 [0.25*kp_R_TFp]
S32+S49 -> S54 [0.25*kp_R_TFp]
S34+S49 -> S55 [0.5*kp_R_TFp]
S36+S49 -> S43 [0.25*kp_R_TFp]
S41+S49 -> S47 [0.25*kp_R_TFp]
S48+S49 -> S50 [0.25*kp_R_TFp]
S44 -> S19+S49 [km_R_TFp]
S45 -> S20+S49 [km_R_TFp]
S46 -> S22+S49 [km_R_TFp]
S47 -> S41+S49 [km_R_TFp]
S48 -> S24+S49 [km_R_TFp]
S50 -> S48+S49 [2*km_R_TFp]
S47 -> S56 [k_TF_transphos]
S44 -> S30 [k_TF_dephos]