function [ dQ ] = incubate37( ~,Q )
%INCUBATE37 Model of cells at 37 degrees in mid-log stage 
%           after adding IPTG
%   Notes:
%   --Assuming 0.01 mW light during storage because culture is 
%     covered in foil
%   --Reduced translation rate by three orders of magnitute to reflect codon
%     non-optimization

%SPECIES
mRNA = Q(1);        %mRNA transcript
immature = Q(2);    %KR without mature chromophore
KR_S = Q(3);        %KR with mature chromophore (singlet state)
KR_S_ex = Q(4);     %KR in singlet excited state (S*)
KR_T_ex = Q(5);     %KR in triplet excited state (T*)
KR_deac = Q(6);     %KR deactivated (photobleached)
SOx = max(Q(7),0);         %Superoxide

%Basic parameters
N_a = 6.022e23;
Vcell = 6.7e-16;                %cytoplasmic volume in liters
copyNo = 5e1;

%SOD kinetics
SOD_conc = 1e3 / (N_a*Vcell);   %est. 1000 molecules/cell
SOD_Kcat = 1667;                %turnover rate
SOD_Km = 2e-6;
SOD_Vmax = SOD_Kcat*SOD_conc;   %maximum rate

%CONSTANTS  for reaction rates 
k_RNAsynth = 0.347/(N_a*Vcell); %mRNA synthesis: 0 -> mRNA
k_RNAdeg = 0.0039;              %mRNA degradation: mRNA -> 0
k_KRsynth = .0032;              %KR synthesis: mRNA -> immature + mRNA
k_KRmature = 4.81e-5;           %KR chrom. maturation: immature -> KR_S
k_KRdeg1 = 7.7e-6;              %KR immature degradation: immature -> 0
k_KRdeg2 = 7.7e-6;              %KR mature degradation: S -> 0
k_KRdeg3 = 7.7e-6;              %KR mature degradation: S* -> 0
k_KRdeg4 = 7.7e-6;              %KR mature degradation: T* -> 0
k_KRact = 1.72e3;               %activation by light: S + hv -> S*
k_KRflo = 3.5e8;                %fluorescence: S* -> S + hv 
k_KRiconv = 6.9e10;             %internal conversion: S* -> S
k_KRisc = 6.6e6;                %intersys. crossing: S* -> T*
k_KRrd = 50;                    %radiationless deactivation: T* -> S
k_KRsox1 = 9*1e-4/.15; %superoxide production: T* + 2H2O -> S + SOx
k_KRsox2 = 1e-4/.15; %superoxide production: T* + 2H2O -> Deac + SOx

%REACTIONS
RNAsynth = k_RNAsynth*copyNo;       %mRNA synthesis treated as zero order
RNAdeg = mRNA*k_RNAdeg;
KRsynth = mRNA*k_KRsynth;
KRmature = immature*k_KRmature;
KRdeg1 = immature*k_KRdeg1;
KRdeg2 = KR_S*k_KRdeg2;
KRdeg3 = KR_S_ex*k_KRdeg3;
KRdeg4 = KR_T_ex*k_KRdeg4;
KRact = KR_S*k_KRact;
KRflo = KR_S_ex*k_KRflo;
KRiconv = KR_S_ex*k_KRiconv;
KRisc = KR_S_ex*k_KRisc;
KRrd = KR_T_ex*k_KRrd;
KRsox1 = KR_T_ex*k_KRsox1;
KRsox2 = KR_T_ex*k_KRsox2;

dQ = zeros(7,1);

dQ(1) = RNAsynth - (RNAdeg);
dQ(2) = KRsynth - (KRmature + KRdeg1);
dQ(3) = KRmature + KRflo + KRiconv + KRrd + KRsox1 - (KRact + KRdeg2);
dQ(4) = KRact - (KRflo + KRiconv + KRisc + KRdeg3);
dQ(5) = KRisc - (KRrd + KRsox1 + KRsox2 + KRdeg4);
dQ(6) = KRsox2;
dQ(7) = KRsox1 + KRsox2 - .001*SOD_Vmax*SOx/(SOD_Km+SOx);
end

