paul wants to display inhibitors as cyan and yellow channels

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currently activators R,S are displayed as cyan and yellow respectively which results in a display of full cyan and yellow if there are no signalling molecules c,c'. We would like to display L,T instead, which have a steady state of (0,0) when c,c' are not present

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Figure 1 : Steady state levels of L,T in cyan,yellow respectively as a function of c,c' with parameters taken from CRN file demonstrating neither bistability nor exclusivity are present

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Figure 2 : Steady state levels of L,T in cyan,yellow respectively as a function of c,c' demonstrating both bistability and exclusivity with other parameter sets

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The simulations carried out with crn tool with this code demonstrate that no matter the initialisation with c6 or c12 the system will tend towards expressing only cfp, consistent with analytical results in Figure 1.

Here we have plotted ([cfp]-[yfp])/([cfp]+[yfp]) which is a measure between -1 and 1 reveals to us the relative dominance of concentration regardless of magnitudes. The worrying thing is that Figure 4 suggests that the observed boundary sharpening may actually be a transient in a longer timescale equilibration process.

Figure 3 : Spacetime plot of L,T in one dimensional simulation, with only c6 initialised as a central core

Figure 4 : Spacetime plot of L,T in one dimensional simulation, initialised with mutually exclusive domains of c6 and c12 showing transient sharp boundary dissolving into a sea of cfp

Figure 5 : Spacetime plot of L,T in one dimensional simulation, with only c12 initialised as a central core