// Created by libAntimony v2.8.0 model *Akman2008_Circadian_Clock_Model2() // Compartments and Species: compartment cytosol, nucleus; species E1F in cytosol, E1Fp in cytosol, E1W in cytosol, E2F in cytosol; species E2Fp in cytosol, E2W in cytosol, MF in nucleus, MW in nucleus, PF in nucleus; species PFp in nucleus, PW in nucleus, PWL in nucleus, $sFrq_tot in nucleus; species $lFrq_tot in nucleus, $Frq_tot in nucleus, $WC1_tot in nucleus; // Assignment Rules: sFrq_tot := PF + E2F + E1F; lFrq_tot := PFp + E2Fp + E1Fp; Frq_tot := sFrq_tot + lFrq_tot; WC1_tot := PW + PWL + E1W + E2W; // Reactions: MFtrn: => MF; (a1*PWL^n)/((1 + (PF + PFp)/b1)*(PWL^n + b2^n)) + (a2*PW^m)/((1 + (PF + PFp)/b3)*(PW^m + b4^m)); MFdeg: MF => ; (d1*MF)/(MF + b5); E1Ftrl: => E1F; a3*MF; E1Fdeg: E1F => ; gam1*E1F; E2Ftrl: E1F => E2F; f1*E1F; E2Fdeg: E2F => ; gam1*E2F; PFtrl: E2F => PF; f1*E2F; PFdeg: PF => ; d2*PF; MWtrn: => MW; a4 + (a5*PWL^k)/(PWL^k + b7^k); MWdeg: MW => ; (d3*MW)/(MW + b8); E1Wtrl: => E1W; (a6 + a7*(PF + PFp))*MW; E1Wdeg: E1W => ; gam2*E1W; E2Wtrl: E1W => E2W; f2*E1W; E2Wdeg: E2W => ; gam2*E2W; PWtrl: E2W => PW; f2*E2W; PWdeg: PW => ; (d4*PW)/(PW + b9); PWtrs: PW -> PWL; (r1*amp*PW*(1 + tanh(24*(time - 24*floor(time/24) - dawn)))*(1 - tanh(24*(time - 24*floor(time/24) - dusk))))/4 - r2*PWL; PWLdeg: PWL => ; (d5*PWL)/(PWL + b10); E1Fptrl: => E1Fp; a3p*MF; E1Fpdeg: E1Fp => ; gam1p*E1Fp; E2Fptrl: E1Fp => E2Fp; f1p*E1Fp; E2Fpdeg: E2Fp => ; gam1p*E2Fp; PFptrl: E2Fp => PFp; f1p*E2Fp; PFpdeg: PFp => ; d2p*PFp; // Species initializations: E1F = 0.43076; E1Fp = 0.45583; E1W = 5.84748; E2F = 0.10647; E2Fp = 0.09872; E2W = 5.70265; MF = 0.6935; MW = 1.2689; PF = 0.06565; PFp = 0.07719; PW = 26.4393; PWL = 0; // Compartment initializations: cytosol = 1; nucleus = 1; // Variable initializations: a1 = 24.9736; a2 = 3.59797; a3 = 0.2834; a4 = 0.46227; a5 = 0.02917; a6 = 0.20695; a7 = 3.02856; b1 = 0.00209; b2 = 2.13476; b3 = 0.08039; b4 = 0.45859; b5 = 0.13056; b7 = 2.96739; b8 = 0.11167; b9 = 81.10381; b10 = 93.03664; b6 = 0; d1 = 1.43549; d2 = 0.21251; d3 = 0.50309; d4 = 3.36641; d5 = 0.41085; f1 = 0.09292; f2 = 0.14979; gam1 = 0.34603; gam2 = 0.00028; r1 = 2.71574; r2 = 35.40005; n = 1.02419; m = 1.34979; k = 2.18234; a3p = 0.34578; d2p = 0.18191; f1p = 0.09588; gam1p = 0.40119; amp = 0; dawn = 12; dusk = 24; // Other declarations: const cytosol, nucleus, a1, a2, a3, a4, a5, a6, a7, b1, b2, b3, b4, b5; const b7, b8, b9, b10, b6, d1, d2, d3, d4, d5, f1, f2, gam1, gam2, r1, r2; const n, m, k, a3p, d2p, f1p, gam1p, amp, dawn, dusk; // Unit definitions: unit time_unit = 3600 second; unit substance = dimensionless; // Display Names: time_unit is "hours"; substance is "arbitrary_units"; E1F is "s-Frq_1"; E1Fp is "l-Frq_1"; E1W is "WC-1_1"; E2F is "s-Frq_2"; E2Fp is "l-Frq_2"; E2W is "WC-1_2"; MF is "Frq mRNA"; MW is "WC-1 mRNA"; PF is "s-Frq"; PFp is "l-Frq"; PW is "WC-1"; PWL is "WC-1*"; sFrq_tot is "tot s-Frq"; lFrq_tot is "tot l-Frq"; Frq_tot is "tot Frq"; WC1_tot is "tot WC-1"; end