/* * This code is generated by BioUML FrameWork * for BIOMD0000000013.xml diagram at 2008.03.20 15:03:28 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000013 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_J0 = Light_on*J0_Rbco_vm*x[14]/(x[14] + J0_Rbco_km*(1 + x[10]/J0_Rbco_KiPGA + x[6]/J0_Rbco_KiFBP + x[16]/J0_Rbco_KiSBP + x[11]/J0_Rbco_KiPi + _uVol_x_NADPH_ch_/J0_Rbco_KiNADPH)); rate_J1 = J1_TPI_v*(x[9] - x[3]/J1_q4); rate_J10 = J10_PGI_v*(x[5] - x[8]/J10_q14); rate_J11 = J11_PGM_v*(x[8] - x[7]/J11_q15); rate_J12 = Light_on*J12_LR_vm*x[0]*x[11]/((x[0] + J12_LR_kmADP)*(x[11] + J12_LR_kmPi)); rate_J13 = Light_on*J13_Ru5Pk_ch_vm*x[13]*x[1]/((x[13] + J13_Ru5Pk_ch_km1*(1 + x[10]/J13_Ru5Pk_ch_KiPGA + x[14]/J13_Ru5Pk_ch_KiRuBP + x[11]/J13_Ru5Pk_ch_KiPi))*(x[1]*(1 + x[0]/J13_Ru5Pk_ch_KiADP1) + J13_Ru5Pk_ch_km2*(1 + x[0]/J13_Ru5Pk_ch_KiADP2))); rate_J14 = Light_on*J14_PGK_v*(x[10]*x[1] - x[2]*x[0]/J14_q2); rate_J15 = J15_StSyn_vm*x[7]*x[1]/((x[7] + J15_stsyn_ch_km1)*(1 + x[0]/J15_stsyn_ch_Ki)*(x[1] + J15_stsyn_ch_km2) + J15_stsyn_ch_km2*x[11]/(J15_stsyn_ch_ka1*x[10]) + J15_stsyn_ch_ka2*x[5] + J15_stsyn_ch_ka3*x[6]); rate_J16 = J16_StPase_Vm*x[11]/(x[11] + J16_StPase_km*(1 + x[7]/J16_StPase_kiG1P)); rate_J17 = Light_on*J17_FBPase_ch_vm*x[6]/(x[6] + J17_FBPase_ch_km*(1 + x[5]/J17_FBPase_ch_KiF6P + x[11]/J17_FBPase_ch_KiPi)); rate_J18 = J18_TP_Piap_vm*x[3]/(J18_TP_Piap_kDHAP_ch*(1 + (1 + J18_TP_Piap_kPi_cyt/_uVol_x_Pi_cyt_)*(x[11]/J18_TP_Piap_kPi_ch + x[10]/J18_TP_Piap_kPGA_ch + x[3]/J18_TP_Piap_kDHAP_ch + x[9]/J18_TP_Piap_kGAP_ch))); rate_J19 = Light_on*J19_G3Pdh_v*(x[2]*_uVol_x_NADPH_ch_*_uVol_x_Proton_ch_ - _uVol_x_NADP_ch_*x[9]*x[11]/J19_q3); rate_J2 = J2_F_Aldo_v*(x[3]*x[9] - x[6]/J2_q5); rate_J20 = Light_on*J20_SBPase_ch_vm*x[16]/(x[16] + J20_SBPase_ch_km*(1 + x[11]/J20_SBPase_ch_KiPi)); rate_J3 = J3_F_TKL_v*(x[5]*x[9] - x[4]*x[17]/J3_q7); rate_J4 = J4_E_Aldo_v*(x[4]*x[3] - x[16]/J4_q8); rate_J5 = J5_G_TKL_v*(x[9]*x[15] - x[17]*x[12]/J5_q10); rate_J6 = J6_R5Piso_v*(x[12] - x[13]/J6_q11); rate_J7 = J7_X5Pepi_v*(x[17] - x[13]/J7_q12); rate_J8 = J8_PGA_xpMult*J8_TP_Piap_vm*x[10]/(J8_TP_Piap_kPGA_ch*(1 + (1 + J8_TP_Piap_kPi_cyt/_uVol_x_Pi_cyt_)*(x[11]/J8_TP_Piap_kPi_ch + x[10]/J8_TP_Piap_kPGA_ch + x[3]/J8_TP_Piap_kDHAP_ch + x[9]/J8_TP_Piap_kGAP_ch))); rate_J9 = J9_TP_Piap_vm*x[9]/(J9_TP_Piap_kGAP_ch*(1 + (1 + J9_TP_Piap_kPi_cyt/_uVol_x_Pi_cyt_)*(x[11]/J9_TP_Piap_kPi_ch + x[10]/J9_TP_Piap_kPGA_ch + x[3]/J9_TP_Piap_kDHAP_ch + x[9]/J9_TP_Piap_kGAP_ch))); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _uVol_x_CO2_ = 1.0; // initial value of $"uVol.x_CO2" _uVol_x_DHAP_cyt_ = 1.0; // initial value of $"uVol.x_DHAP_cyt" _uVol_x_GAP_cyt_ = 1.0; // initial value of $"uVol.x_GAP_cyt" _uVol_x_NADPH_ch_ = 0.21; // initial value of $"uVol.x_NADPH_ch" _uVol_x_NADP_ch_ = 0.29; // initial value of $"uVol.x_NADP_ch" _uVol_x_PGA_cyt_ = 1.0; // initial value of $"uVol.x_PGA_cyt" _uVol_x_Pi_cyt_ = 0.5; // initial value of $"uVol.x_Pi_cyt" _uVol_x_Proton_ch_ = 1.26E-5; // initial value of $"uVol.x_Proton_ch" _uVol_x_Starch_ch_ = 1.0; // initial value of $"uVol.x_Starch_ch" J0_Rbco_KiFBP = 0.04; // initial value of J0_Rbco_KiFBP J0_Rbco_KiNADPH = 0.07; // initial value of J0_Rbco_KiNADPH J0_Rbco_KiPGA = 0.84; // initial value of J0_Rbco_KiPGA J0_Rbco_KiPi = 0.9; // initial value of J0_Rbco_KiPi J0_Rbco_KiSBP = 0.075; // initial value of J0_Rbco_KiSBP J0_Rbco_km = 0.02; // initial value of J0_Rbco_km J0_Rbco_vm = 340.0; // initial value of J0_Rbco_vm J10_PGI_v = 5.0E9; // initial value of J10_PGI_v J10_q14 = 2.3; // initial value of J10_q14 J11_PGM_v = 5.0E9; // initial value of J11_PGM_v J11_q15 = 0.058; // initial value of J11_q15 J12_LR_kmADP = 0.014; // initial value of J12_LR_kmADP J12_LR_kmPi = 0.3; // initial value of J12_LR_kmPi J12_LR_vm = 1500.0; // initial value of J12_LR_vm J13_Ru5Pk_ch_KiADP1 = 2.5; // initial value of J13_Ru5Pk_ch_KiADP1 J13_Ru5Pk_ch_KiADP2 = 0.4; // initial value of J13_Ru5Pk_ch_KiADP2 J13_Ru5Pk_ch_KiPGA = 2.0; // initial value of J13_Ru5Pk_ch_KiPGA J13_Ru5Pk_ch_KiPi = 4.0; // initial value of J13_Ru5Pk_ch_KiPi J13_Ru5Pk_ch_KiRuBP = 0.7; // initial value of J13_Ru5Pk_ch_KiRuBP J13_Ru5Pk_ch_km1 = 0.05; // initial value of J13_Ru5Pk_ch_km1 J13_Ru5Pk_ch_km2 = 0.05; // initial value of J13_Ru5Pk_ch_km2 J13_Ru5Pk_ch_vm = 10000.0; // initial value of J13_Ru5Pk_ch_vm J14_PGK_v = 5.0E9; // initial value of J14_PGK_v J14_q2 = 3.1E-4; // initial value of J14_q2 J15_StSyn_vm = 40.0; // initial value of J15_StSyn_vm J15_stsyn_ch_Ki = 10.0; // initial value of J15_stsyn_ch_Ki J15_stsyn_ch_ka1 = 0.1; // initial value of J15_stsyn_ch_ka1 J15_stsyn_ch_ka2 = 0.02; // initial value of J15_stsyn_ch_ka2 J15_stsyn_ch_ka3 = 0.02; // initial value of J15_stsyn_ch_ka3 J15_stsyn_ch_km1 = 0.08; // initial value of J15_stsyn_ch_km1 J15_stsyn_ch_km2 = 0.08; // initial value of J15_stsyn_ch_km2 J16_StPase_Vm = 40.0; // initial value of J16_StPase_Vm J16_StPase_kiG1P = 3.12; // initial value of J16_StPase_kiG1P J16_StPase_km = 5.0; // initial value of J16_StPase_km J17_FBPase_ch_KiF6P = 0.7; // initial value of J17_FBPase_ch_KiF6P J17_FBPase_ch_KiPi = 12.0; // initial value of J17_FBPase_ch_KiPi J17_FBPase_ch_km = 0.03; // initial value of J17_FBPase_ch_km J17_FBPase_ch_vm = 200.0; // initial value of J17_FBPase_ch_vm J18_TP_Piap_kDHAP_ch = 0.077; // initial value of J18_TP_Piap_kDHAP_ch J18_TP_Piap_kGAP_ch = 0.075; // initial value of J18_TP_Piap_kGAP_ch J18_TP_Piap_kPGA_ch = 0.25; // initial value of J18_TP_Piap_kPGA_ch J18_TP_Piap_kPi_ch = 0.63; // initial value of J18_TP_Piap_kPi_ch J18_TP_Piap_kPi_cyt = 0.74; // initial value of J18_TP_Piap_kPi_cyt J18_TP_Piap_vm = 250.0; // initial value of J18_TP_Piap_vm J19_G3Pdh_v = 5.0E9; // initial value of J19_G3Pdh_v J19_q3 = 1.6E7; // initial value of J19_q3 J1_TPI_v = 5.0E9; // initial value of J1_TPI_v J1_q4 = 22.0; // initial value of J1_q4 J20_SBPase_ch_KiPi = 12.0; // initial value of J20_SBPase_ch_KiPi J20_SBPase_ch_km = 0.013; // initial value of J20_SBPase_ch_km J20_SBPase_ch_vm = 40.0; // initial value of J20_SBPase_ch_vm J2_F_Aldo_v = 5.0E9; // initial value of J2_F_Aldo_v J2_q5 = 7.1; // initial value of J2_q5 J3_F_TKL_v = 5.0E9; // initial value of J3_F_TKL_v J3_q7 = 0.084; // initial value of J3_q7 J4_E_Aldo_v = 5.0E9; // initial value of J4_E_Aldo_v J4_q8 = 13.0; // initial value of J4_q8 J5_G_TKL_v = 5.0E9; // initial value of J5_G_TKL_v J5_q10 = 0.85; // initial value of J5_q10 J6_R5Piso_v = 5.0E9; // initial value of J6_R5Piso_v J6_q11 = 0.4; // initial value of J6_q11 J7_X5Pepi_v = 5.0E9; // initial value of J7_X5Pepi_v J7_q12 = 0.67; // initial value of J7_q12 J8_PGA_xpMult = 0.2; // initial value of J8_PGA_xpMult J8_TP_Piap_kDHAP_ch = 0.077; // initial value of J8_TP_Piap_kDHAP_ch J8_TP_Piap_kGAP_ch = 0.075; // initial value of J8_TP_Piap_kGAP_ch J8_TP_Piap_kPGA_ch = 0.25; // initial value of J8_TP_Piap_kPGA_ch J8_TP_Piap_kPi_ch = 0.63; // initial value of J8_TP_Piap_kPi_ch J8_TP_Piap_kPi_cyt = 0.74; // initial value of J8_TP_Piap_kPi_cyt J8_TP_Piap_vm = 250.0; // initial value of J8_TP_Piap_vm J9_TP_Piap_kDHAP_ch = 0.077; // initial value of J9_TP_Piap_kDHAP_ch J9_TP_Piap_kGAP_ch = 0.075; // initial value of J9_TP_Piap_kGAP_ch J9_TP_Piap_kPGA_ch = 0.25; // initial value of J9_TP_Piap_kPGA_ch J9_TP_Piap_kPi_ch = 0.63; // initial value of J9_TP_Piap_kPi_ch J9_TP_Piap_kPi_cyt = 0.74; // initial value of J9_TP_Piap_kPi_cyt J9_TP_Piap_vm = 250.0; // initial value of J9_TP_Piap_vm Light_on = 1.0; // initial value of Light_on } /* * Model variables initial values */ protected double _uVol_x_CO2_; protected double _uVol_x_DHAP_cyt_; protected double _uVol_x_GAP_cyt_; protected double _uVol_x_NADPH_ch_; protected double _uVol_x_NADP_ch_; protected double _uVol_x_PGA_cyt_; protected double _uVol_x_Pi_cyt_; protected double _uVol_x_Proton_ch_; protected double _uVol_x_Starch_ch_; protected double rate_J0; protected double rate_J1; protected double rate_J10; protected double rate_J11; protected double rate_J12; protected double rate_J13; protected double rate_J14; protected double rate_J15; protected double rate_J16; protected double rate_J17; protected double rate_J18; protected double rate_J19; protected double rate_J2; protected double rate_J20; protected double rate_J3; protected double rate_J4; protected double rate_J5; protected double rate_J6; protected double rate_J7; protected double rate_J8; protected double rate_J9; protected double J0_Rbco_KiFBP; protected double J0_Rbco_KiNADPH; protected double J0_Rbco_KiPGA; protected double J0_Rbco_KiPi; protected double J0_Rbco_KiSBP; protected double J0_Rbco_km; protected double J0_Rbco_vm; protected double J10_PGI_v; protected double J10_q14; protected double J11_PGM_v; protected double J11_q15; protected double J12_LR_kmADP; protected double J12_LR_kmPi; protected double J12_LR_vm; protected double J13_Ru5Pk_ch_KiADP1; protected double J13_Ru5Pk_ch_KiADP2; protected double J13_Ru5Pk_ch_KiPGA; protected double J13_Ru5Pk_ch_KiPi; protected double J13_Ru5Pk_ch_KiRuBP; protected double J13_Ru5Pk_ch_km1; protected double J13_Ru5Pk_ch_km2; protected double J13_Ru5Pk_ch_vm; protected double J14_PGK_v; protected double J14_q2; protected double J15_StSyn_vm; protected double J15_stsyn_ch_Ki; protected double J15_stsyn_ch_ka1; protected double J15_stsyn_ch_ka2; protected double J15_stsyn_ch_ka3; protected double J15_stsyn_ch_km1; protected double J15_stsyn_ch_km2; protected double J16_StPase_Vm; protected double J16_StPase_kiG1P; protected double J16_StPase_km; protected double J17_FBPase_ch_KiF6P; protected double J17_FBPase_ch_KiPi; protected double J17_FBPase_ch_km; protected double J17_FBPase_ch_vm; protected double J18_TP_Piap_kDHAP_ch; protected double J18_TP_Piap_kGAP_ch; protected double J18_TP_Piap_kPGA_ch; protected double J18_TP_Piap_kPi_ch; protected double J18_TP_Piap_kPi_cyt; protected double J18_TP_Piap_vm; protected double J19_G3Pdh_v; protected double J19_q3; protected double J1_TPI_v; protected double J1_q4; protected double J20_SBPase_ch_KiPi; protected double J20_SBPase_ch_km; protected double J20_SBPase_ch_vm; protected double J2_F_Aldo_v; protected double J2_q5; protected double J3_F_TKL_v; protected double J3_q7; protected double J4_E_Aldo_v; protected double J4_q8; protected double J5_G_TKL_v; protected double J5_q10; protected double J6_R5Piso_v; protected double J6_q11; protected double J7_X5Pepi_v; protected double J7_q12; protected double J8_PGA_xpMult; protected double J8_TP_Piap_kDHAP_ch; protected double J8_TP_Piap_kGAP_ch; protected double J8_TP_Piap_kPGA_ch; protected double J8_TP_Piap_kPi_ch; protected double J8_TP_Piap_kPi_cyt; protected double J8_TP_Piap_vm; protected double J9_TP_Piap_kDHAP_ch; protected double J9_TP_Piap_kGAP_ch; protected double J9_TP_Piap_kPGA_ch; protected double J9_TP_Piap_kPi_ch; protected double J9_TP_Piap_kPi_cyt; protected double J9_TP_Piap_vm; protected double Light_on; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[18]; y[0] = x[0]; y[1] = x[1]; y[2] = x[2]; y[3] = x[3]; y[4] = x[4]; y[5] = x[5]; y[6] = x[6]; y[7] = x[7]; y[8] = x[8]; y[9] = x[9]; y[10] = x[10]; y[11] = x[11]; y[12] = x[12]; y[13] = x[13]; y[14] = x[14]; y[15] = x[15]; y[16] = x[16]; y[17] = x[17]; return y; } public double[] getInitialValues() { double [] x = new double[18]; this.time = 0.0; x[0] = 0.00149; // - $"uVol.ADP_ch" x[1] = 0.49806; // - $"uVol.ATP_ch" x[2] = 0.14825; // - $"uVol.BPGA_ch" x[3] = 0.29345; // - $"uVol.DHAP_ch" x[4] = 0.41021; // - $"uVol.E4P_ch" x[5] = 1.36481; // - $"uVol.F6P_ch" x[6] = 0.02776; // - $"uVol.FBP_ch" x[7] = 0.18206; // - $"uVol.G1P_ch" x[8] = 3.1396; // - $"uVol.G6P_ch" x[9] = 0.01334; // - $"uVol.GAP_ch" x[10] = 3.35479; // - $"uVol.PGA_ch" x[11] = 1.5662; // - $"uVol.Pi_ch" x[12] = 0.00599; // - $"uVol.R5P_ch" x[13] = 0.00235; // - $"uVol.Ru5P_ch" x[14] = 0.33644; // - $"uVol.RuBP_ch" x[15] = 0.00541; // - $"uVol.S7P_ch" x[16] = 1.56486; // - $"uVol.SBP_ch" x[17] = 0.00363; // - $"uVol.X5P_ch" __internalRateVarInitFunc_0(time, x); return x; } /* * code for algebraic rules calculations */ /* * end of code for algebraic rules calculations */ protected void calculateRates(double time, double[] x) { __internalRateVarInitFunc_0(time, x); } /* * calculate dy/dt for 'BIOMD0000000013.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate_J12+rate_J13+rate_J14+rate_J15; result[1] = +rate_J12-rate_J13-rate_J14-rate_J15; result[2] = +rate_J14-rate_J19; result[3] = -rate_J18+rate_J1-rate_J2-rate_J4; result[4] = +rate_J3-rate_J4; result[5] = -rate_J10+rate_J17-rate_J3; result[6] = -rate_J17+rate_J2; result[7] = +rate_J11-rate_J15+rate_J16; result[8] = +rate_J10-rate_J11; result[9] = +rate_J19-rate_J1-rate_J2-rate_J3-rate_J5-rate_J9; result[10] = +rate_J0*2-rate_J14-rate_J8; result[11] = -rate_J12+rate_J15-rate_J16+rate_J17+rate_J18+rate_J19+rate_J20+rate_J8+rate_J9; result[12] = +rate_J5-rate_J6; result[13] = -rate_J13+rate_J6+rate_J7; result[14] = -rate_J0+rate_J13; result[15] = +rate_J20-rate_J5; result[16] = -rate_J20+rate_J4; result[17] = +rate_J3+rate_J5-rate_J7; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[18]; __internalDyDt_0(time, x, result); return result; } public double[] dy_dt(double time, double[] x) { this.time = time; calculateRates( time,x ); return calculateResult( time,x ); } } // class ...