Molecular dynamics study of accelerated ion-induced shock waves in biological media

Abstract: We present a molecular dynamics study of the effects of carbon- and iron-ion inducedshock waves in DNA duplexes in liquid water. We use the CHARMM force field implementedwithin the MBN Explorer simulation package to optimize and equilibrate DNA duplexes inliquid water boxes of different sizes and shapes. The translational and vibrationaldegrees of freedom of water molecules are excited according to the energy deposited by theions and the subsequent shock waves in liquid water are simulated. The pressure wavesgenerated are studied and compared with an analytical hydrodynamics model which serves asa benchmark for evaluating the suitability of the simulation boxes. The energy depositionin the DNA backbone bonds is also monitored as an estimation of biological damage,something which is not possible with the analytical model.