  We propose a stochastic Gillespie scheme to describe the temporal
fluctuations of local denaturation zones in double-stranded DNA as a single
molecule time series. It is demonstrated that the model recovers the
equilibrium properties. We also study measurable dynamical quantities such as
the bubble size autocorrelation function. This efficient computational approach
will be useful to analyse in detail recent single molecule experiments on
clamped homopolymer breathing domains, to probe the parameter values of the
underlying Poland-Scheraga model, as well as to design experimental conditions
for similar setups.
