// Created by libAntimony v2.8.0 model *Friedland2009_Ara_Counter_RC3_events() // Compartments and Species: compartment cell; species taRNA in cell, mT7cr in cell, mGFPcr in cell, pT7 in cell, pGFP in cell; species ara in cell, pT3 in cell, mT3cr in cell; // Assignment Rules: pulse2_start := pulse1_start + pulse1_length + pulse_interval; pulse3_start := pulse2_start + pulse2_length + pulse_interval; // Reactions: r0: ara => ; cell*piecewise(cAra, pulse_flag == 1 && ara > 0, dAra*ara); r1a: => taRNA; cell*((sT*ara)/(ara + k_ara) + s0_taRNA); r1b: taRNA => ; cell*d_taRNA*taRNA; r2a: => mT7cr; cell*s0_mT7cr; r2b: mT7cr => ; cell*d_mT7*mT7cr; r3a: => mGFPcr; cell*(s0_mGFPcr + (k_pT3*pT3^n3)/(km3^n3 + pT3^n3)); r3b: mGFPcr => ; cell*d_mGFP*mGFPcr; r6: => pT7; cell*(s0_pT7*mT7cr + s_pT7k*mT7cr*taRNA); r7: => pGFP; cell*(s0_pGFP*mGFPcr + s_pGFPk*mGFPcr*taRNA); r8: pT7 => ; cell*d_pT7*pT7; r9: pGFP => ; cell*d_pGFP*pGFP; r10a: => mT3cr; cell*(s0_mT3cr + (k_pT7*pT7^n7)/(km7^n7 + pT7^n7)); r10b: mT3cr => ; cell*d_mT3*mT3cr; r11: => pT3; cell*(s0_pT3*mT3cr + s_pT3k*taRNA*mT3cr); r12: pT3 => ; cell*d_pT3*pT3; // Events: pulse_start1: at time >= pulse1_start && time <= pulse1_start + pulse1_length: ara = pulse_conc, pulse_flag = 1; pulse_start2: at time >= pulse2_start && time <= pulse2_start + pulse2_length: ara = pulse_conc, pulse_flag = 1; pulse_start3: at time >= pulse3_start && time <= pulse3_start + pulse3_length: ara = pulse_conc, pulse_flag = 1; pulse_end1: at time < pulse2_start && time > pulse1_start + pulse1_length: pulse_flag = 0; pulse_end2: at time < pulse3_start && time > pulse2_start + pulse2_length: pulse_flag = 0; pulse_end3: at time > pulse3_start + pulse3_length: pulse_flag = 0; // Species initializations: taRNA = 0.006796941377; mT7cr = 0.3569405099; mGFPcr = 0.176991329; pT7 = 0.05230744612; pGFP = 6.338921181; ara = 0; pT3 = 6.41674e-005; mT3cr = 0.00566438; // Compartment initializations: cell = 1; // Variable initializations: pulse1_start = 0.01; pulse1_length = 11; pulse_flag = 0; pulse_conc = 0.01; pulse2_length = 11; pulse3_length = 22; cAra = 0.0003; dAra = 0.1201; sT = 0.8467; k_ara = 0.0571; s0_taRNA = 0.0008; d_taRNA = 0.1177; s0_mT7cr = 0.0252; d_mT7 = 0.0706; s0_mGFPcr = 0.0123; k_pT3 = 3.006; n3 = 0.8892; km3 = 7.9075; d_mGFP = 0.07; s0_pT7 = 0.0003; s_pT7k = 0.0766; s0_pGFP = 0.1007; s_pGFPk = 0.9923; d_pT7 = 0.0056; d_pGFP = 0.003; s0_mT3cr = 0.0003; k_pT7 = 3.8009; n7 = 2.602; km7 = 3.0455; d_mT3 = 0.0701; s0_pT3 = 0; s_pT3k = 0.0115; d_pT3 = 0.0069; pulse_interval = 20; // Other declarations: var pulse_flag, pulse2_start, pulse3_start; const cell, pulse1_start, pulse1_length, pulse_conc, pulse2_length, pulse3_length; const cAra, dAra, sT, k_ara, s0_taRNA, d_taRNA, s0_mT7cr, d_mT7, s0_mGFPcr; const k_pT3, n3, km3, d_mGFP, s0_pT7, s_pT7k, s0_pGFP, s_pGFPk, d_pT7, d_pGFP; const s0_mT3cr, k_pT7, n7, km7, d_mT3, s0_pT3, s_pT3k, d_pT3, pulse_interval; end