  We investigate the distribution of bubble lifetimes and bubble lengths in DNA
at physiological temperature, by performing extensive molecular dynamics
simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended
version (ePBD) having a sequence-dependent stacking interaction, emphasizing
the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content
on these distributions. For both models we find that base pair-dependent (GC vs
AT) thresholds for considering complementary nucleotides to be separated are
able to reproduce the observed dependence of the melting temperature on the GC
content of the DNA sequence. Using these thresholds for base pair openings, we
obtain bubble lifetime distributions for bubbles of lengths up to ten base
pairs as the GC content of the sequences is varied, which are accurately fitted
with stretched exponential functions. We find that for both models the average
bubble lifetime decreases with increasing either the bubble length or the GC
content. In addition, the obtained bubble length distributions are also fitted
by appropriate stretched exponential functions and our results show that short
bubbles have similar likelihoods for any GC content, but longer ones are
substantially more likely to occur in AT-rich sequences. We also show that the
ePBD model permits more, longer-lived, bubbles than the PBD system.
