Effect of kinetic rate constants upon the equilibrium state in microarray simulations. The fractional occupancies of probes at equilibrium (Eq. 27) are unaffected by random perturbations of rate constants as t → ∞. Each point represents a pair of results for each of the 6256 Agilent probes targeting yeast ORFs. The CPU time required for equilibration of simulated systems (4 h, 100 h, above), like the hybridization time (not shown) does, however, depend upon the rates. Our methodology for estimating rate constants yields rapidly converging simulations.