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calculatePropensity0x8E_TI.m
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calculatePropensity0x8E_TI.m
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function h = calculatePropensity0x8E_TI(X)
% Define ks:
ka = 0.25; % Activated production rate
ka_f = 0.0033; % Forward activation binding rate
ka_r = 1.0; % Reverse activation binding rate
kao_f = 1.0; % Forward activated RNAP binding rate
kao_r = 1.0; % Reverse activated RNAP binding rate
kb = 1.0E-4; % Basal production rate
kc_f = 0.05; % Forward complex formation rate
kc_r = 1.0; % Reverse complex formation rate
kd = 7.5E-4; % Degradation rate
ko = 0.05; % Open complex production rate
ko_f = 0.033; % Forward RNAP binding rate
ko_r = 1.0; % Reverse RNAP binding rate
kr_f = 0.5; % Forward repression binding rate
kr_r = 1.0; % Reverse repression binding rate
nc = 2.0; % Stoichiometry of binding
ng = 2.0; % Initial promoter count
np = 10.0; % Stoichiometry of production
nr = 30.0; % Initial RNAP count
topModel_AmtRpart_module_sub__ka = 0.25;
topModel_AmtRpart_module_sub__ka_f = 0.0033;
topModel_AmtRpart_module_sub__ka_r = 1;
topModel_AmtRpart_module_sub__kao_f = 1;
topModel_AmtRpart_module_sub__kao_r = 1;
topModel_AmtRpart_module_sub__kb = 1.0E-4;
topModel_AmtRpart_module_sub__ko = 0.05;
topModel_AmtRpart_module_sub__ko_f = 0.033;
topModel_AmtRpart_module_sub__ko_r = 1;
topModel_AmtRpart_module_sub__kr_f = 0.5;
topModel_AmtRpart_module_sub__kr_r = 1;
topModel_AmtRpart_module_sub__nc = 2;
topModel_AmtRpart_module_sub__ng = 2;
topModel_AmtRpart_module_sub__np = 10;
topModel_AmtRpart_module_sub__nr = 30;
topModel_BetIpart_module_sub__ka = 0.25;
topModel_BetIpart_module_sub__ka_f = 0.0033;
topModel_BetIpart_module_sub__ka_r = 1;
topModel_BetIpart_module_sub__kao_f = 1;
topModel_BetIpart_module_sub__kao_r = 1;
topModel_BetIpart_module_sub__kb = 1.0E-4;
topModel_BetIpart_module_sub__ko = 0.05;
topModel_BetIpart_module_sub__ko_f = 0.033;
topModel_BetIpart_module_sub__ko_r = 1;
topModel_BetIpart_module_sub__kr_f = 0.5;
topModel_BetIpart_module_sub__kr_r = 1;
topModel_BetIpart_module_sub__nc = 2;
topModel_BetIpart_module_sub__ng = 2;
topModel_BetIpart_module_sub__np = 10;
topModel_BetIpart_module_sub__nr = 30;
topModel_HlyIIRpart_module_sub__ka = 0.25;
topModel_HlyIIRpart_module_sub__ka_f = 0.0033;
topModel_HlyIIRpart_module_sub__ka_r = 1.0;
topModel_HlyIIRpart_module_sub__kao_f = 1.0;
topModel_HlyIIRpart_module_sub__kao_r = 1.0;
topModel_HlyIIRpart_module_sub__kb = 1.0E-4;
topModel_HlyIIRpart_module_sub__ko = 0.05;
topModel_HlyIIRpart_module_sub__ko_f = 0.033;
topModel_HlyIIRpart_module_sub__ko_r = 1.0;
topModel_HlyIIRpart_module_sub__kr_f = 0.5;
topModel_HlyIIRpart_module_sub__kr_r = 1.0;
topModel_HlyIIRpart_module_sub__nc = 2.0;
topModel_HlyIIRpart_module_sub__ng = 2.0;
topModel_HlyIIRpart_module_sub__np = 10;
topModel_HlyIIRpart_module_sub__nr = 30;
topModel_Inverter1_module_sub__ka = 0.25;
topModel_Inverter1_module_sub__ka_f = 0.0033;
topModel_Inverter1_module_sub__ka_r = 1.0;
topModel_Inverter1_module_sub__kao_f = 1.0;
topModel_Inverter1_module_sub__kao_r = 1.0;
topModel_Inverter1_module_sub__kb = 1.0E-4;
topModel_Inverter1_module_sub__ko = 0.05;
topModel_Inverter1_module_sub__ko_f = 0.033;
topModel_Inverter1_module_sub__ko_r = 1.0;
topModel_Inverter1_module_sub__kr_f = 0.5;
topModel_Inverter1_module_sub__kr_r = 1.0;
topModel_Inverter1_module_sub__nc = 2.0;
topModel_Inverter1_module_sub__ng = 2.0;
topModel_Inverter1_module_sub__np = 10.0;
topModel_Inverter1_module_sub__nr = 30.0;
topModel_Inverter2_module_sub__ka = 0.25;
topModel_Inverter2_module_sub__ka_f = 0.0033;
topModel_Inverter2_module_sub__ka_r = 1.0;
topModel_Inverter2_module_sub__kao_f = 1.0;
topModel_Inverter2_module_sub__kao_r = 1.0;
topModel_Inverter2_module_sub__kb = 1.0E-4;
topModel_Inverter2_module_sub__ko = 0.05;
topModel_Inverter2_module_sub__ko_f = 0.033;
topModel_Inverter2_module_sub__ko_r = 1.0;
topModel_Inverter2_module_sub__kr_f = 0.5;
topModel_Inverter2_module_sub__kr_r = 1.0;
topModel_Inverter2_module_sub__nc = 2.0;
topModel_Inverter2_module_sub__ng = 2.0;
topModel_Inverter2_module_sub__np = 10.0;
topModel_Inverter2_module_sub__nr = 30.0;
topModel_PhlFpart_module_sub__ka = 0.25;
topModel_PhlFpart_module_sub__ka_f = 0.0033;
topModel_PhlFpart_module_sub__ka_r = 1;
topModel_PhlFpart_module_sub__kao_f = 1;
topModel_PhlFpart_module_sub__kao_r = 1;
topModel_PhlFpart_module_sub__kb = 1.0E-4;
topModel_PhlFpart_module_sub__ko = 0.05;
topModel_PhlFpart_module_sub__ko_f = 0.033;
topModel_PhlFpart_module_sub__ko_r = 1;
topModel_PhlFpart_module_sub__kr_f = 0.5;
topModel_PhlFpart_module_sub__kr_r = 1;
topModel_PhlFpart_module_sub__nc = 2;
topModel_PhlFpart_module_sub__ng = 2;
topModel_PhlFpart_module_sub__np = 10;
topModel_PhlFpart_module_sub__nr = 30;
topModel_YFPpart_module_sub__ka = 0.25;
topModel_YFPpart_module_sub__ka_f = 0.0033;
topModel_YFPpart_module_sub__ka_r = 1;
topModel_YFPpart_module_sub__kao_f = 1;
topModel_YFPpart_module_sub__kao_r = 1;
topModel_YFPpart_module_sub__kb = 1.0E-4;
topModel_YFPpart_module_sub__ko = 0.05;
topModel_YFPpart_module_sub__ko_f = 0.033;
topModel_YFPpart_module_sub__ko_r = 1;
topModel_YFPpart_module_sub__kr_f = 0.5;
topModel_YFPpart_module_sub__kr_r = 1;
topModel_YFPpart_module_sub__nc = 2;
topModel_YFPpart_module_sub__ng = 2;
topModel_YFPpart_module_sub__np = 10;
topModel_YFPpart_module_sub__nr = 30;
% Reaction Propensities
h(1,1) = kd*X(1); % AmtR_degradation_interaction
h(2,1) = kd*X(3); % BetI_degradation_interaction
h(3,1) = kd*X(4); % BM3R1_degradation_interaction
h(4,1) = kd*X(5); % HlyIIR_degradation_interaction
h(5,1) = kd*X(7); % PhlF_degradation_interaction
h(6,1) = kd*X(8); % SrpR_degradation_interaction
h(7,1) = X(12)*(topModel_AmtRpart_module_sub__kb*topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r*topModel_AmtRpart_module_sub__nr+topModel_AmtRpart_module_sub__ka*topModel_AmtRpart_module_sub__kao_f/topModel_AmtRpart_module_sub__kao_r*topModel_AmtRpart_module_sub__nr*(topModel_AmtRpart_module_sub__ka_f/topModel_AmtRpart_module_sub__ka_r*X(2))^topModel_AmtRpart_module_sub__nc)/(1+topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r*topModel_AmtRpart_module_sub__nr+topModel_AmtRpart_module_sub__kao_f/topModel_AmtRpart_module_sub__kao_r*topModel_AmtRpart_module_sub__nr*(topModel_AmtRpart_module_sub__ka_f/topModel_AmtRpart_module_sub__ka_r*X(2))^topModel_AmtRpart_module_sub__nc); % topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
h(8,1) = X(11)*topModel_AmtRpart_module_sub__ko*topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r*topModel_AmtRpart_module_sub__nr/(1+topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r*topModel_AmtRpart_module_sub__nr+(topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r*X(5))^topModel_AmtRpart_module_sub__nc); % topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
h(9,1) = X(13)*topModel_BetIpart_module_sub__ko*topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r*topModel_BetIpart_module_sub__nr/(1+topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r*topModel_BetIpart_module_sub__nr+(topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r*X(5))^topModel_BetIpart_module_sub__nc); % topModel_BetIpart_module_sub__BetI_protein_interaction_0
h(10,1) = X(14)*topModel_BetIpart_module_sub__ko*topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r*topModel_BetIpart_module_sub__nr/(1+topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r*topModel_BetIpart_module_sub__nr+(topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r*X(9))^topModel_BetIpart_module_sub__nc); % topModel_BetIpart_module_sub__BetI_protein_interaction_1
h(11,1) = X(15)*(topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r*topModel_HlyIIRpart_module_sub__nr+topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r*topModel_HlyIIRpart_module_sub__nr*(topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r*X(2))^topModel_HlyIIRpart_module_sub__nc)/(1+topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r*topModel_HlyIIRpart_module_sub__nr+topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r*topModel_HlyIIRpart_module_sub__nr*(topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r*X(2))^topModel_HlyIIRpart_module_sub__nc); % topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
h(12,1) = X(16)*topModel_HlyIIRpart_module_sub__ko*topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r*topModel_HlyIIRpart_module_sub__nr/(1+topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r*topModel_HlyIIRpart_module_sub__nr+(topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r*X(9))^topModel_HlyIIRpart_module_sub__nc); % topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
h(13,1) = X(17)*topModel_Inverter1_module_sub__ko*topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r*topModel_Inverter1_module_sub__nr/(1+topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r*topModel_Inverter1_module_sub__nr+(topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r*X(6))^topModel_Inverter1_module_sub__nc); % topModel_Inverter1_module_sub__BM3R1_protein_interaction
h(14,1) = X(18)*topModel_Inverter2_module_sub__ko*topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r*topModel_Inverter2_module_sub__nr/(1+topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r*topModel_Inverter2_module_sub__nr+(topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r*X(4))^topModel_Inverter2_module_sub__nc); % topModel_Inverter2_module_sub__SrpR_protein_interaction
h(15,1) = X(19)*topModel_PhlFpart_module_sub__ko*topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r*topModel_PhlFpart_module_sub__nr/(1+topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r*topModel_PhlFpart_module_sub__nr+(topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r*X(8))^topModel_PhlFpart_module_sub__nc); % topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
h(16,1) = X(20)*topModel_PhlFpart_module_sub__ko*topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r*topModel_PhlFpart_module_sub__nr/(1+topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r*topModel_PhlFpart_module_sub__nr+(topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r*X(1))^topModel_PhlFpart_module_sub__nc); % topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
h(17,1) = X(22)*topModel_YFPpart_module_sub__ko*topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r*topModel_YFPpart_module_sub__nr/(1+topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r*topModel_YFPpart_module_sub__nr+(topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r*X(7))^topModel_YFPpart_module_sub__nc); % topModel_YFPpart_module_sub__YFP_protein_interaction_0
h(18,1) = X(21)*topModel_YFPpart_module_sub__ko*topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r*topModel_YFPpart_module_sub__nr/(1+topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r*topModel_YFPpart_module_sub__nr+(topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r*X(3))^topModel_YFPpart_module_sub__nc); % topModel_YFPpart_module_sub__YFP_protein_interaction_1
h(19,1) = kd*X(10); % YFP_degradation_interaction
end