  Understanding the inherent timescales of large bubbles in DNA is critical to
a thorough comprehension of its physicochemical characteristics, as well as
their potential role on helix opening and biological function. In this work we
employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study
relaxation dynamics of large bubbles in homopolymer DNA, using simulations up
to the microsecond time scale. By studying energy autocorrelation functions of
relatively large bubbles inserted into thermalised DNA molecules, we extract
characteristic relaxation times from the equilibration process for both
adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of
different amplitudes and widths are investigated through extensive statistics
and appropriate fittings of their relaxation. Characteristic relaxation times
increase with bubble height and width. We show that, within the model,
relaxation times are two orders of magnitude longer in GC sequences than in AT
sequences. Overall, our results confirm that large bubbles leave a lasting
impact on the molecule's dynamics, for times between 0.4-200ns depending on the
homopolymer type and bubble shape, thus clearly affecting long-time evolutions
of the molecule.
