I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link leeds to the paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236362/) I know this is an old paper, but maybe someone here remembers it. I really need the answers of the following questions because the enzymatic model explained in the paper is very important for my master thesis.

First: The author defines a system of two ODEs but the initial conditions of these ODEs are not printed in the paper. The author just writes: "Initial conditions for the integration are determined by letting the network relax to steady state. " (see p. 1324 on the lower right) . But how is this meant? In this paper the author wants to optimize the mentioned ODEs , so how can I find initial conditions, when there are not all parameters of the ODEs given?

Second: On the top of page 1324 are two needstate functions defined, called $\xi_T$ and $\xi_F$. When I plot $\xi(F)$, the plot looks completely different from the one depicted in figure 3b in the paper. So the function defined in figure 3b) must be wrong. Did anyone realize that error and has a workaround for that? Of course I could define my own functions but I want to stay as close to the model in the paper as possible.

Thank you very much for your help.

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    $\begingroup$ Have you looked at the caption of figure 1? I believe all the constants you need for your model are stated there. Also the steady-state is $\dot A=\dot B = 0$, where $F$ and $T$ are externally set constants (the reservoir). $\endgroup$ – Deathbreath Jul 7 '16 at 14:52
  • $\begingroup$ Hi @Deathbreath , thank you for your comment. Yes I have looked at the caption. The problem is, that there still occur eight unknown parameters in the ODE system. Those parameters appear in the functions $\nu_{\alpha}$ and $\nu_{\beta}$ . But now I think in steady state it holds: $\nu_{\alpha} = \nu_{\beta}$ and, as you wrote $dA/dt = dB/dt = 0$. So $\nu_{\alpha}$ and $\nu_{\beta}$ cancel out each other. I think this might solve the problem. $\endgroup$ – maxE Jul 9 '16 at 15:43

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