% Reactants with initial conditions (see S5 Fig.)
numofelements=15;
X=zeros(1,numofelements);
X(1)=100; % UXP
X(2)=10; % CAP
X(3)=0; % UDPglucose
X(4)=10; % Activator
X(5)=0; % UXPActivator complex
X(6)=1; % DNAcap
X(7)=0; % DNAcapActivator complex
X(8)=0; % mRNAcap
X(9)=0; % Repressor
X(10)=0; % DNAcapRepressor complex
X(11)=0; % DNArepressorCAP complex
X(12)=0; % DNArepressorCAP2 complex (2 x CAP)
X(13)=0; % DNArepressorCAP11 complex (1 CAP attached to DNA, 1 not)
X(14)=0; % mRNArepressor
X(15)=1; % DNArepressor

% Reactions (first line is the reactants, second is the products)
numofreactions=23;
A=zeros(numofreactions,length(X));
A(1,[1 2])=[1 1];
Y(1,[1 3])=[-1 1];

A(2,[1 4])=[1 1];
Y(2,[1 4 5])=[-1 -1 1];

A(3,[5])=[1];
Y(3,[5 1 4])=[-1 1 1];

A(4,[6 4])=[1 1];
Y(4,[6 4 7])=[-1 -1 1];

A(5,[7])=[1];
Y(5,[6 4 7])=[1 1 -1];

A(6,[7])=[1];
Y(6,[8])=[1];

A(7,[8])=[1];
Y(7,[2])=[1];

A(8,[6 9])=[1 1];
Y(8,[6 9 10])=[-1 -1 1];

A(9,[10])=[1];
Y(9,[6 9 10])=[1 1 -1];

A(10,[6])=1;
Y(10,[8])=1;

A(11,[8])=[1];
Y(11,[8])=[-1];

A(12,[15 2])=[1 1];
Y(12,[15 2 11])=[-1 -1 1];

A(13,[11])=[1];
Y(13,[11 15 2])=[-1 1 1];

A(14,[11 2])=[1 1];
Y(14,[11 2 12])=[-1 -1 1];

A(15,[12])=[1];
Y(15,[12 13])=[-1 1];

A(16,[13])=[1];
Y(16,[13 15 2])=[-1 1 2];

A(17,[13])=[1];
Y(17,[13 12])=[-1 1];

A(18,[12])=[1];
Y(18,[14])=[1];

A(19,[14])=[1];
Y(19,[9])=[1];

A(20,[14])=[1];
Y(20,[14])=[-1];

A(21,[9])=[1];
Y(21,[9])=[-1];

A(22,[2])=[1];
Y(22,[2])=[-1];

A(23,[1])=[1];
Y(23,[1])=[-1];



% Rates of reactions (see Figure S3)
rates=zeros(size(A,1),1);
uflux=.3; % uxp flux (.003 for low, .3 for intermediate, 3 for high), rate for equation A1 
rates(1)=.0001; % A2 
rates(2)=.05; % A4 forward
rates(3)=.0005; % A4 backward
rates(4)=.05; % B1 forward
rates(5)=.00002; % B1 backward
rates(6)=.05; % B3
rates(7)=.01; % B4
rates(8)=.01; % C6 forwards
rates(9)=.00003; % C6 backwards
rates(10)=.01; % B2
rates(11)=.01; % D1
rates(12)=.00001; % C1 forwards
rates(13)=.001; % C1 backwards
rates(14)=.00001; % C2
rates(15)=.001; % C3 forwards
rates(16)=.001; % C7
rates(17)=.005; % C3 backwards
rates(18)=.05; % C4
rates(19)=.05; % C5
rates(20)=.01; % D2
rates(21)=.001; % D3
rates(22)=.001; % D4
rates(23)=.001; % A3 (assume PyrG is fixed)



% Parameters for simulation
tmax=2*10^5; % maximum time
t=0; % initial time
told=0; % counter for previous time step
datamat=zeros(tmax+1,length(X)+1); % store data of times and number of each molecule, may need to be extended
datamat(1,:)=[t X]; % initialize
ct=1; % counter for number of unique reactions simulated
rehisold=0; % counter for previous reaction
as=zeros(1,numofreactions+1); % reaction proclivities
as(end)=uflux;

% Simulation
while t<tmax;
    % Calculate proclivities
    for j1=1:numofreactions
        as(j1)=rates(j1)*prod(X(A(j1,:)>0));
    end
    % Calculate time
    told=t;
    t=t-1*log(rand())/sum(as);
    % Determine which reaction occurs
    ind=sum(rand()>cumsum(as./sum(as)))+1;
    if ind==numofreactions+1;
	% Add UTP
        X(1)=X(1)+1;
    else
        X=X+Y(ind,:); 
    end
    % Store data
    if ind~=rehisold
        ct=ct+1; % new reaction, add to counter
        if ct>size(datamat,1);
            % Extend size of data mat
            datamat=[datamat;zeros(100000,length(X)+1)];
        end
        datamat(ct,:)=[t X];
        rehisold=ind;
    end 
end

% Prune early burn-in phase for datamat
datamatold=datamat;
st=round(.05*ct);
datamat=datamat(st+1:ct,:);
datamat(:,1)=datamat(:,1)-datamatold(st,1); % adjust time


% Visualize colanic acid-like polymer levels
close all;plot(datamat(:,1)/60/60,datamat(:,3),'bo-','LineWidth',3);
xlabel('Time (hours)','FontSize',18)
ylabel('Amount of CAP','FontSize',18)
set(gca,'TickLength',[.025 .025],'LineWidth',2)
axis square
axis([0 48 -5 100]);