// Created by libAntimony v2.8.0 model *DellOrco2009_phototransduction() // Compartments and Species: compartment cytosol; species Arr in cytosol, Ca2_buff in cytosol, Ca2_free in cytosol, G_GTP in cytosol; species Ga_GDP in cytosol, Ga_GTP in cytosol, Ga_GTP_PDE_a_Ga_GTP in cytosol; species Ga_GTP_a_PDE_a_Ga_GTP in cytosol, Gbg in cytosol, Gt_ in cytosol; species Ops in cytosol, Ops_G in cytosol, Ops_G_GTP in cytosol, Ops_Gt in cytosol; species PDE in cytosol, PDE_Ga_GTP in cytosol, PDE_a_Ga_GTP in cytosol; species R in cytosol, R0 in cytosol, R0_G in cytosol, R0_G_GTP in cytosol; species R0_Gt in cytosol, R0_RKpre in cytosol, R1 in cytosol, R1_Arr in cytosol; species R1_G in cytosol, R1_G_GTP in cytosol, R1_Gt in cytosol, R1_RKpost in cytosol; species R1_RKpre in cytosol, R2 in cytosol, R2_Arr in cytosol, R2_G in cytosol; species R2_G_GTP in cytosol, R2_Gt in cytosol, R2_RKpost in cytosol, R2_RKpre in cytosol; species R3 in cytosol, R3_Arr in cytosol, R3_G in cytosol, R3_G_GTP in cytosol; species R3_Gt in cytosol, R3_RKpost in cytosol, R3_RKpre in cytosol, R4 in cytosol; species R4_Arr in cytosol, R4_G in cytosol, R4_G_GTP in cytosol, R4_Gt in cytosol; species R4_RKpost in cytosol, R4_RKpre in cytosol, R5 in cytosol, R5_Arr in cytosol; species R5_G in cytosol, R5_G_GTP in cytosol, R5_Gt in cytosol, R5_RKpost in cytosol; species R5_RKpre in cytosol, R6 in cytosol, R6_Arr in cytosol, R6_G in cytosol; species R6_G_GTP in cytosol, R6_Gt in cytosol, R6_RKpost in cytosol, R6_RKpre in cytosol; species RGS in cytosol, RGS_Ga_GTP_a_PDE_a_Ga_GTP in cytosol, RGS_PDE_a_Ga_GTP in cytosol; species RK in cytosol, Rec_wCa2_RK in cytosol, cGMP in cytosol; // Assignment Rules: background := flashBG; premag := flash0Mag/flash0Dur; mag := flashMag/flashDur; predur := flash0Dur; dur := flashDur; del := flashDel; preflash := piecewise(premag, time <= predur, 0); testflash := piecewise(mag, time >= del && time <= del + dur, 0); stimulus := background + preflash + testflash + otherstimulus; numConcFactor := 1/(6.022000e+005*Vcyto); kRK1_1 := kRK1_0*exp(-omega); kRK1_2 := kRK1_0*exp(-omega*2); kRK1_3 := kRK1_0*exp(-omega*3); kRK1_4 := kRK1_0*exp(-omega*4); kRK1_5 := kRK1_0*exp(-omega*5); kRK1_6 := 0; kA1_1 := kArr*exp(omega_arr); kA1_2 := kArr*exp(omega_arr*2); kA1_3 := kArr*exp(omega_arr*3); kA1_4 := kArr*exp(omega_arr*4); kA1_5 := kArr*exp(omega_arr*5); kA1_6 := kArr*exp(omega_arr*6); kG1_1 := kG1_0*exp(-omega); kG1_2 := kG1_0*exp(-omega*2); kG1_3 := kG1_0*exp(-omega*3); kG1_4 := kG1_0*exp(-omega*4); kG1_5 := kG1_0*exp(-omega*5); kG1_6 := kG1_0*exp(-omega*6); E := PDE_a_Ga_GTP + 2*Ga_GTP_a_PDE_a_Ga_GTP; Rec_wCa2 := (Rectot - Rec_wCa2_RK*numConcFactor)/(1 + (Kp/Ca2_free)^w); alfamax := betadark*cGMPdark*(1 + (Ca2dark/Kc)^m); J := 2/(2 + fCa)*(cGMP/cGMPdark)^ncg*Jdark + (fCa/(fCa + 2)*(Ca2_free - Ca2_0))/(Ca2dark - Ca2_0)*Jdark; deltaJ := Jdark - J; // Reactions: v_r1: R => R0; (stimulus*R)/Rtot; v_r2_0: R0 + RK -> R0_RKpre; kRK1_0*RK*R0 - kRK2*R0_RKpre; v_r2_1: R1 + RK -> R1_RKpre; kRK1_1*RK*R1 - kRK2*R1_RKpre; v_r2_2: R2 + RK -> R2_RKpre; kRK1_2*RK*R2 - kRK2*R2_RKpre; v_r2_3: R3 + RK -> R3_RKpre; kRK1_3*RK*R3 - kRK2*R3_RKpre; v_r2_4: R4 + RK -> R4_RKpre; kRK1_4*RK*R4 - kRK2*R4_RKpre; v_r2_5: R5 + RK -> R5_RKpre; kRK1_5*RK*R5 - kRK2*R5_RKpre; v_r2_6: R6 + RK -> R6_RKpre; kRK1_6*RK*R6 - kRK2*R6_RKpre; v_r3_0: R0_RKpre => R1_RKpost; kRK3_ATP*R0_RKpre; v_r3_1: R1_RKpre => R2_RKpost; kRK3_ATP*R1_RKpre; v_r3_2: R2_RKpre => R3_RKpost; kRK3_ATP*R2_RKpre; v_r3_3: R3_RKpre => R4_RKpost; kRK3_ATP*R3_RKpre; v_r3_4: R4_RKpre => R5_RKpost; kRK3_ATP*R4_RKpre; v_r3_5: R5_RKpre => R6_RKpost; kRK3_ATP*R5_RKpre; v_r4_1: R1_RKpost => R1 + RK; kRK4*R1_RKpost; v_r4_2: R2_RKpost => R2 + RK; kRK4*R2_RKpost; v_r4_3: R3_RKpost => R3 + RK; kRK4*R3_RKpost; v_r4_4: R4_RKpost => R4 + RK; kRK4*R4_RKpost; v_r4_5: R5_RKpost => R5 + RK; kRK4*R5_RKpost; v_r4_6: R6_RKpost => R6 + RK; kRK4*R6_RKpost; v_r5_1: Arr + R1 -> R1_Arr; kA1_1*Arr*R1 - kA2*R1_Arr; v_r5_2: Arr + R2 -> R2_Arr; kA1_2*Arr*R2 - kA2*R2_Arr; v_r5_3: Arr + R3 -> R3_Arr; kA1_3*Arr*R3 - kA2*R3_Arr; v_r5_4: Arr + R4 -> R4_Arr; kA1_4*Arr*R4 - kA2*R4_Arr; v_r5_5: Arr + R5 -> R5_Arr; kA1_5*Arr*R5 - kA2*R5_Arr; v_r5_6: Arr + R6 -> R6_Arr; kA1_6*Arr*R6 - kA2*R6_Arr; v_r6_1: R1_Arr => Arr + Ops; kA3*R1_Arr; v_r6_2: R2_Arr => Arr + Ops; kA3*R2_Arr; v_r6_3: R3_Arr => Arr + Ops; kA3*R3_Arr; v_r6_4: R4_Arr => Arr + Ops; kA3*R4_Arr; v_r6_5: R5_Arr => Arr + Ops; kA3*R5_Arr; v_r6_6: R6_Arr => Arr + Ops; kA3*R6_Arr; v_r7_0: R0 => Ops; ktherm*R0; v_r7_1: R1 => Ops; ktherm*R1; v_r7_2: R2 => Ops; ktherm*R2; v_r7_3: R3 => Ops; ktherm*R3; v_r7_4: R4 => Ops; ktherm*R4; v_r7_5: R5 => Ops; ktherm*R5; v_r7_6: R6 => Ops; ktherm*R6; v_r8: Gt_ + Ops -> Ops_Gt; kOps*Ops*Gt_ - kG2*Ops_Gt; v_r9: Ops_Gt -> Ops_G; kG3*Ops_Gt - kG4_GDP*Ops_G; v_r10: Ops_G => Ops_G_GTP; kG5_GTP*Ops_G; v_r11: Ops_G_GTP => G_GTP + Ops; kG6*Ops_G_GTP; v_r12: Ops => R; kRrecyc*Ops; v_r13_0: Gt_ + R0 -> R0_Gt; kG1_0*Gt_*R0 - kG2*R0_Gt; v_r13_1: Gt_ + R1 -> R1_Gt; kG1_1*Gt_*R1 - kG2*R1_Gt; v_r13_2: Gt_ + R2 -> R2_Gt; kG1_2*Gt_*R2 - kG2*R2_Gt; v_r13_3: Gt_ + R3 -> R3_Gt; kG1_3*Gt_*R3 - kG2*R3_Gt; v_r13_4: Gt_ + R4 -> R4_Gt; kG1_4*Gt_*R4 - kG2*R4_Gt; v_r13_5: Gt_ + R5 -> R5_Gt; kG1_5*Gt_*R5 - kG2*R5_Gt; v_r13_6: Gt_ + R6 -> R6_Gt; kG1_6*Gt_*R6 - kG2*R6_Gt; v_r14_0: R0_Gt -> R0_G; kG3*R0_Gt - kG4_GDP*R0_G; v_r14_1: R1_Gt -> R1_G; kG3*R1_Gt - kG4_GDP*R1_G; v_r14_2: R2_Gt -> R2_G; kG3*R2_Gt - kG4_GDP*R2_G; v_r14_3: R3_Gt -> R3_G; kG3*R3_Gt - kG4_GDP*R3_G; v_r14_4: R4_Gt -> R4_G; kG3*R4_Gt - kG4_GDP*R4_G; v_r14_5: R5_Gt -> R5_G; kG3*R5_Gt - kG4_GDP*R5_G; v_r14_6: R6_Gt -> R6_G; kG3*R6_Gt - kG4_GDP*R6_G; v_r15_0: R0_G => R0_G_GTP; kG5_GTP*R0_G; v_r15_1: R1_G => R1_G_GTP; kG5_GTP*R1_G; v_r15_2: R2_G => R2_G_GTP; kG5_GTP*R2_G; v_r15_3: R3_G => R3_G_GTP; kG5_GTP*R3_G; v_r15_4: R4_G => R4_G_GTP; kG5_GTP*R4_G; v_r15_5: R5_G => R5_G_GTP; kG5_GTP*R5_G; v_r15_6: R6_G => R6_G_GTP; kG5_GTP*R6_G; v_r16_0: R0_G_GTP => G_GTP + R0; kG6*R0_G_GTP; v_r16_1: R1_G_GTP => G_GTP + R1; kG6*R1_G_GTP; v_r16_2: R2_G_GTP => G_GTP + R2; kG6*R2_G_GTP; v_r16_3: R3_G_GTP => G_GTP + R3; kG6*R3_G_GTP; v_r16_4: R4_G_GTP => G_GTP + R4; kG6*R4_G_GTP; v_r16_5: R5_G_GTP => G_GTP + R5; kG6*R5_G_GTP; v_r16_6: R6_G_GTP => G_GTP + R6; kG6*R6_G_GTP; v_r17: G_GTP => Ga_GTP + Gbg; kG7*G_GTP; v_r18: Ga_GTP + PDE -> PDE_Ga_GTP; kP1*PDE*Ga_GTP - kP1_rev*PDE_Ga_GTP; v_r19: PDE_Ga_GTP => PDE_a_Ga_GTP; kP2*PDE_Ga_GTP; v_r20: Ga_GTP + PDE_a_Ga_GTP => Ga_GTP_PDE_a_Ga_GTP; kP3*PDE_a_Ga_GTP*Ga_GTP; v_r21: Ga_GTP_PDE_a_Ga_GTP => Ga_GTP_a_PDE_a_Ga_GTP; kP4*Ga_GTP_PDE_a_Ga_GTP; v_r22: Ga_GTP_a_PDE_a_Ga_GTP + RGS => RGS_Ga_GTP_a_PDE_a_Ga_GTP; kRGS1*RGS*Ga_GTP_a_PDE_a_Ga_GTP; v_r23: RGS_Ga_GTP_a_PDE_a_Ga_GTP => Ga_GDP + PDE_a_Ga_GTP + RGS; kRGS2*RGS_Ga_GTP_a_PDE_a_Ga_GTP; v_r24: PDE_a_Ga_GTP + RGS => RGS_PDE_a_Ga_GTP; kRGS1*RGS*PDE_a_Ga_GTP; v_r25: RGS_PDE_a_Ga_GTP => Ga_GDP + PDE + RGS; kRGS2*RGS_PDE_a_Ga_GTP; v_r26: PDE_a_Ga_GTP => Ga_GDP + PDE; kPDEshutoff*PDE_a_Ga_GTP; v_r27: Ga_GTP_a_PDE_a_Ga_GTP => Ga_GDP + PDE_a_Ga_GTP; kPDEshutoff*Ga_GTP_a_PDE_a_Ga_GTP; v_r28: Ga_GTP => Ga_GDP; kGshutoff*Ga_GTP; v_r29: Ga_GDP + Gbg => Gt_; kGrecyc*Gbg*Ga_GDP; v_r30: RK -> Rec_wCa2_RK; kRec3*Rec_wCa2*RK - kRec4*Rec_wCa2_RK; v_r31: Ca2_free -> Ca2_buff; k1*(eT - Ca2_buff)*Ca2_free - k2*Ca2_buff; v_r32: Ca2_free => ; gammaCa*(Ca2_free - Ca2_0); v_r33: => Ca2_free; (1.000000e+006*fCa*Jdark)/((2 + fCa)*F*Vcyto)*(cGMP/cGMPdark)^ncg; v_r34: => cGMP; alfamax/(1 + (Ca2_free/Kc)^m); v_r35: cGMP => ; (betadark + betasub*E)*cGMP; // Species initializations: Arr = 31300000; Ca2_buff = 42.857; Ca2_free = 0.6; G_GTP = 0; Ga_GDP = 0; Ga_GTP = 0; Ga_GTP_PDE_a_Ga_GTP = 0; Ga_GTP_a_PDE_a_Ga_GTP = 0; Gbg = 0; Gt_ = 360000000; Ops = 0; Ops_G = 0; Ops_G_GTP = 0; Ops_Gt = 0; PDE = 13350000; PDE_Ga_GTP = 0; PDE_a_Ga_GTP = 0; R = 3600000000; R0 = 0; R0_G = 0; R0_G_GTP = 0; R0_Gt = 0; R0_RKpre = 0; R1 = 0; R1_Arr = 0; R1_G = 0; R1_G_GTP = 0; R1_Gt = 0; R1_RKpost = 0; R1_RKpre = 0; R2 = 0; R2_Arr = 0; R2_G = 0; R2_G_GTP = 0; R2_Gt = 0; R2_RKpost = 0; R2_RKpre = 0; R3 = 0; R3_Arr = 0; R3_G = 0; R3_G_GTP = 0; R3_Gt = 0; R3_RKpost = 0; R3_RKpre = 0; R4 = 0; R4_Arr = 0; R4_G = 0; R4_G_GTP = 0; R4_Gt = 0; R4_RKpost = 0; R4_RKpre = 0; R5 = 0; R5_Arr = 0; R5_G = 0; R5_G_GTP = 0; R5_Gt = 0; R5_RKpost = 0; R5_RKpre = 0; R6 = 0; R6_Arr = 0; R6_G = 0; R6_G_GTP = 0; R6_Gt = 0; R6_RKpost = 0; R6_RKpre = 0; RGS = 3000000; RGS_Ga_GTP_a_PDE_a_Ga_GTP = 0; RGS_PDE_a_Ga_GTP = 0; RK = 10838; Rec_wCa2_RK = 4204560; cGMP = 4; // Compartment initializations: cytosol = 1; // Variable initializations: Rtot = 3600000000; PDEtot = 13350000; Gtot = 360000000; Rectot = 35; RGStot = 3000000; ArrTot = 31300000; flashBG = 0; flash0Dur = 0.001; flash0Mag = 0; flashDel = 0; flashDur = 0.001; flashMag = 0; otherstimulus = 0; kRK1_0 = 0.0076429599557114; omega = 0.6; kRK2 = 250; RKdark = 10838; kRK3_ATP = 400; kRK4 = 20; omega_arr = 0.81323; kArr = 6.0918e-010; kA2 = 0.00323198; kA3 = 0.0445091; kOps = 6.1172e-013; kRrecyc = 0.0007; kG1_0 = 3.0586111111e-005; kG2 = 2250.34; kG3 = 2000; kG4_GDP = 600; kG5_GTP = 750; kG6 = 2000; kG7 = 200; kGrecyc = 2; kGshutoff = 0.05; kP1 = 0.0549715; kP1_rev = 0; kP2 = 940.706; kP3 = 1.49834e-009; kP4 = 21.0881; kPDEshutoff = 0.033; kRGS1 = 1.57e-007; kRGS2 = 256.07; kRec3 = 9.68777; kRec4 = 0.610084; Kp = 0.425272; w = 2; Vcyto = 1; Kc = 0.17; m = 2.5; betadark = 1.2; betasub = 0.00043; fCa = 0.2; Jdark = 29.7778; F = 96485.3415; cGMPdark = 4; ncg = 3; gammaCa = 47.554; Ca2dark = 0.6; Ca2_0 = 0.01; k1 = 0.381529; k2 = 1.9094; eT = 400; ktherm = 0.0238; // Other declarations: var background, premag, mag, predur, dur, del, preflash, testflash, stimulus; var numConcFactor, kRK1_1, kRK1_2, kRK1_3, kRK1_4, kRK1_5, kRK1_6, kA1_1; var kA1_2, kA1_3, kA1_4, kA1_5, kA1_6, kG1_1, kG1_2, kG1_3, kG1_4, kG1_5; var kG1_6, E, Rec_wCa2, alfamax, J, deltaJ; const cytosol, Rtot, PDEtot, Gtot, Rectot, RGStot, ArrTot, flashBG, flash0Dur; const flash0Mag, flashDel, flashDur, flashMag, otherstimulus, kRK1_0, omega; const kRK2, RKdark, kRK3_ATP, kRK4, omega_arr, kArr, kA2, kA3, kOps, kRrecyc; const kG1_0, kG2, kG3, kG4_GDP, kG5_GTP, kG6, kG7, kGrecyc, kGshutoff, kP1; const kP1_rev, kP2, kP3, kP4, kPDEshutoff, kRGS1, kRGS2, kRec3, kRec4, Kp; const w, Vcyto, Kc, m, betadark, betasub, fCa, Jdark, F, cGMPdark, ncg; const gammaCa, Ca2dark, Ca2_0, k1, k2, eT, ktherm; end