  We demonstrate how the stochastic global optimization scheme of Simulated
Annealing can be used to evaluate optimum parameters in the problem of DNA
breathing dynamics. The breathing dynamics is followed in accordance with the
stochastic Gillespie scheme with the denaturation zones in double stranded DNA
studied as a single molecule time series. Simulated Annealing is used to find
the optimum value of the activation energy for which the equilibrium bubble
size distribution matches with a given value. It is demonstrated that the
method overcomes even large noise in the input surrogate data.
