// Created by libAntimony v2.8.0 function function_1(V, substrate, Km) (V*substrate)/(Km + substrate); end function LightFunction(t, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod) (lightOffset + 0.5*lightAmplitude*(1 + tanh((cyclePeriod*((t + phase)/cyclePeriod - floor(floor(t + phase)/cyclePeriod)))/twilightPeriod))) - 0.5*lightAmplitude*(1 + tanh((cyclePeriod*((t + phase)/cyclePeriod - floor(floor(t + phase)/cyclePeriod)) - photoPeriod)/twilightPeriod)) + 0.5*lightAmplitude*(1 + tanh((cyclePeriod*((t + phase)/cyclePeriod - floor(floor(t + phase)/cyclePeriod)) - cyclePeriod)/twilightPeriod)); end model *MODEL1001130000() // Compartments and Species: compartment compartment_; species cLm in compartment_, cLc in compartment_, cLn in compartment_, cTm in compartment_; species cTc in compartment_, cTn in compartment_, cXm in compartment_, cXc in compartment_; species cXn in compartment_, cYm in compartment_, cYc in compartment_, cYn in compartment_; species cPn in compartment_, cAm in compartment_, cAc in compartment_, cAn in compartment_; // Reactions: reaction_1: => cLm; (compartment_*g0^alpha)/(g0^alpha + cAn^alpha)*(LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod)*(q1*cPn + n0) + (n1*cXn^a)/(g1^a + cXn^a)); reaction_0: cLm => ; compartment_*function_1(m1, cLm, k1); reaction_2: => cLc; compartment_*p1*cLm; reaction_3: cLc -> cLn; compartment_*(r1*cLc - r2*cLn); reaction_4: cLc => ; compartment_*function_1(m2, cLc, k2); reaction_5: cLn => ; compartment_*function_1(m3, cLn, k3); reaction_6: => cTm; (compartment_*n2*cYn^b)/(g2^b + cYn^b)*(g3^c/(g3^c + cLn^c)); reaction_7: cTm => ; compartment_*function_1(m4, cTm, k4); reaction_9: cYc -> cYn; compartment_*(r7*cYc - r8*cYn); reaction_10: cYn => ; compartment_*function_1(m14, cYn, k12); reaction_11: => cYc; compartment_*p4*cYm; reaction_12: cYc => ; compartment_*function_1(m13, cYc, k11); reaction_13: cXc -> cXn; compartment_*(r5*cXc - r6*cXn); reaction_14: cXc => ; compartment_*function_1(m10, cXc, k8); reaction_15: => cXc; compartment_*p3*cXm; reaction_16: cXn => ; compartment_*function_1(m11, cXn, k9); reaction_17: => cAc; compartment_*p6*cAm; reaction_18: cAc -> cAn; compartment_*(r9*cAc - r10*cAn); reaction_19: cAc => ; compartment_*function_1(m17, cAc, k15); reaction_20: cAn => ; compartment_*function_1(m18, cAn, k16); reaction_21: => cPn; (1 - LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod))*p5*compartment_; reaction_22: cPn => ; LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod)*q3*cPn*compartment_; reaction_23: cPn => ; (compartment_*m15*cPn)/(k13 + cPn); reaction_25: => cAm; LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod)*q4*cPn*compartment_; reaction_26: => cAm; (compartment_*n6*cLn^g)/(g7^g + cLn^g); reaction_27: cAm => ; (compartment_*m16*cAm)/(k14 + cAm); reaction_28: => cXm; (compartment_*n3*cTn^d)/(g4^d + cTn^d); reaction_29: cXm => ; (compartment_*m9*cXm)/(k7 + cXm); reaction_30: => cTc; p2*compartment_*cTm; reaction_31: cTc -> cTn; compartment_*(-r4*cTn + r3*cTc); reaction_32: cTc => ; (compartment_*(1 - LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod))*m5*cTc)/(k5 + cTc); reaction_33: cTc => ; (m6*compartment_*cTc)/(k5 + cTc); reaction_34: cTn => ; (compartment_*(1 - LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod))*m7*cTn)/(k6 + cTn); reaction_38: cTn => ; (m8*compartment_*cTn)/(k6 + cTn); reaction_39: => cYm; compartment_*(LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod)*q2*cPn + ((LightFunction(time, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod)*n4 + n5)*g5^e)/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f)); reaction_40: cYm => ; (compartment_*m12*cYm)/(k10 + cYm); // Species initializations: cLm = 0.4625; cLc = 0.0132; cLn = 0.0699; cTm = 0.4303; cTc = 10.2965; cTn = 0.5402; cXm = 0.0957; cXc = 1.5413; cXn = 0.4585; cYm = 0.0303; cYc = 0.0041; cYn = 0.0122; cPn = 0.8476; cAm = 14.6921; cAc = 0.7027; cAn = 0.8648; // Compartment initializations: compartment_ = 1; // Variable initializations: q1 = 4.1954; n0 = 0.05; g0 = 1; alpha = 4; n1 = 7.8142; a = 1.2479; g1 = 3.1383; m1 = 1.999; k1 = 2.392; p1 = 0.8295; r1 = 16.8363; r2 = 0.1687; m2 = 20.44; k2 = 1.5644; m3 = 3.6888; k3 = 1.2765; n2 = 3.0087; b = 1.0258; g2 = 0.0368; g3 = 0.2658; c = 1.0258; m4 = 3.8231; k4 = 2.5734; p2 = 4.324; r3 = 0.3166; r4 = 2.1509; m5 = 0.0013; m6 = 3.1741; k5 = 2.7454; m7 = 0.0492; m8 = 4.0424; k6 = 0.4033; n3 = 0.2431; d = 1.4422; g4 = 0.5388; m9 = 10.1132; k7 = 6.5585; p3 = 2.147; r5 = 1.0352; r6 = 3.3017; m10 = 0.2179; k8 = 0.6632; m11 = 3.3442; k9 = 17.1111; q2 = 2.4017; n4 = 0.0857; n5 = 0.1649; g5 = 1.178; g6 = 0.0645; e = 3.6064; f = 1.0237; m12 = 4.297; k10 = 1.7303; p4 = 0.2485; r7 = 2.2123; r8 = 0.2002; m13 = 0.1347; k11 = 1.8258; m14 = 0.6114; k12 = 1.8066; p5 = 0.5; k13 = 1.2; m15 = 1.2; q3 = 1; q4 = 2.4514; g = 1.0258; n6 = 8.0706; g7 = 0.0004; m16 = 12.2398; k14 = 10.3617; p6 = 0.2907; r9 = 0.2528; r10 = 0.2212; m17 = 4.4505; k15 = 0.0703; m18 = 0.0156; k16 = 0.6104; lightAmplitude = 1; lightOffset = 0; cyclePeriod = 24; photoPeriod = 12; phase = 0; twilightPeriod = 0.0416666667; // Other declarations: const compartment_, q1, n0, g0, alpha, n1, a, g1, m1, k1, p1, r1, r2, m2; const k2, m3, k3, n2, b, g2, g3, c, m4, k4, p2, r3, r4, m5, m6, k5, m7; const m8, k6, n3, d, g4, m9, k7, p3, r5, r6, m10, k8, m11, k9, q2, n4, n5; const g5, g6, e, f, m12, k10, p4, r7, r8, m13, k11, m14, k12, p5, k13, m15; const q3, q4, g, n6, g7, m16, k14, p6, r9, r10, m17, k15, m18, k16, lightAmplitude; const lightOffset, cyclePeriod, photoPeriod, phase, twilightPeriod; // Unit definitions: unit time_unit = 3600 second; unit substance = 1e-9 mole; // Display Names: substance is "nM"; compartment_ is "cell"; cLm is "LHY mRNA"; cLc is "LHY protein in cytoplasm"; cLn is "LHY protein in nucleus"; cTm is "TOC1 mRNA"; cTc is "TOC1 protein in cytoplasm"; cTn is "TOC1 protein in nucleus"; cXm is "X mRNA"; cXc is "X protein in cytoplasm"; cXn is "X protein in nucleus"; cYm is "Y mRNA"; cYc is "Y protein in the cytoplasm"; cYn is "Y protein in nucleus"; cPn is "light sensitive protein P"; cAm is "PPR7/9 mRNA"; cAc is "PPR7/9 protein in cytoplasm"; cAn is "PPR7/9 protein in nucleus"; reaction_1 is "cLm transcription"; reaction_0 is "cLm degradation"; reaction_2 is "cLc translation"; reaction_3 is "LHY protein translocation"; reaction_4 is "cLc degradation"; reaction_5 is "cLn degradation"; reaction_6 is "cTm transcription "; reaction_7 is "cTm degradation"; reaction_9 is "Y protein translocation"; reaction_10 is "cYn degradation"; reaction_11 is "cYc translation"; reaction_12 is "cYc degradation"; reaction_13 is "X protein translocation"; reaction_14 is "cXc degradation"; reaction_15 is "cXc translation"; reaction_16 is "cXn degradation"; reaction_17 is "cAc translation"; reaction_18 is "PPR7/9 protein translocation"; reaction_19 is "cAc degradation"; reaction_20 is "cAn degradation"; reaction_21 is "light dependent production of protein P"; reaction_22 is "light activation protein P degradation"; reaction_23 is "cPn degradation"; reaction_25 is "light activation of cAm transcription"; reaction_26 is "light independent cAm transcription"; reaction_27 is "cAm degradation"; reaction_28 is "cXm transcription"; reaction_29 is "cXm degradation"; reaction_30 is "cTc translation"; reaction_31 is "TOC1 protein translocation"; reaction_32 is "light activation degradation of cTc"; reaction_33 is "light independent degradation of cTc"; reaction_34 is "light activation degradation of cTn"; reaction_38 is "light independent degradation cTn"; reaction_39 is "cYm transcription"; reaction_40 is "cYm degradation"; end