**A:** The graph reports the number of unique complexes actually present in a simulated system (“cell”) as a function of time. Each point represents an average over 15 independent simulations. In all panels of this figure, the error bars represent approximately 95% confidence intervals.

**B:** The normalized distance between the complement of complexes (“complexomes”) generated by individual simulations is shown as a function of time. Each point is an average over all unique comparisons between 15 independent simulations. Using the parameters described in the text, the separation between steady states reaches

% of the maximal distance.

**C:** The stationary distance between cells is shown as a function of complex size, averaged over all of the unique comparisons between 15 independent simulations. The complexomes of cells are nearly identical with regard to small complexes, due to fewer combinational possibilities and the high relative abundance of small complexes (see below). However, complexomes differ dramatically for large complexes. This is the case for all combinations of parameters and ring closure scenarios we have tested (see below and ). Since other parameter sets do not substantially change the relationship shown here, much of the difference in inter-cell distances for these parameter sets derives from how heavily the dynamics sample large complexes.

**D:** The distance between a cell at time

and the same cell at time

is shown as a function of

. The first time point

is taken after cells have reached steady state (in this case,

= 2, see panels A and B). The blue line denotes the average inter-cell distance at steady state, taken from the last time point in panel A above. The red curve represents an exponential fit to the relaxation, with

.

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