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

TL;DR

This study uses molecular dynamics simulations to analyze how ion-induced shock waves in water affect DNA, providing insights into biological damage mechanisms caused by ion irradiation.

Contribution

It introduces a detailed molecular dynamics approach to simulate ion-induced shock waves in biological media and compares results with hydrodynamics models.

Findings

Shock waves in water can be accurately simulated with molecular dynamics.

Energy deposition correlates with potential biological damage.

Simulation results align with hydrodynamics models for pressure wave analysis.

Abstract

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.