  We present a molecular dynamics study of the effects of carbon- and iron-ion
induced shock waves in DNA duplexes in liquid water. We use the CHARMM force
field implemented within the MBN Explorer simulation package to optimize and
equilibrate DNA duplexes in liquid water boxes of different sizes and shapes.
The translational and vibrational degrees of freedom of water molecules are
excited according to the energy deposited by the ions and the subsequent shock
waves in liquid water are simulated. The pressure waves generated are studied
and compared with an analytical hydrodynamics model which serves as a benchmark
for evaluating the suitability of the simulation boxes. The energy deposition
in the DNA backbone bonds is also monitored as an estimation of biological
damage, something which lies beyond the possibilities of the analytical model.
