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 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.

arXiv comment10 pages, 6 figures

References in corpus (2)

• Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology
• Transport of secondary electrons and reactive species in ion tracks

Cited by in corpus (13)

• Frontiers, challenges, and solutions in modeling of swift heavy ion effects in materials
• Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment
• Modeling time-resolved kinetics in solids induced by extreme electronic excitation
• Radial doses around energetic ion tracks and the onset of shock waves on the nanoscale
• The effect of ion-induced shock waves on the transport of reacting species around energetic ion tracks
• Lethal DNA damages caused by ion-induced shock waves in cells
• Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field
• Phenomenon-based prediction of relative biological effectiveness of ion beams by means of the MultiScale Approach
• Irradiation driven molecular dynamics: A review
• A TDDFT-based Study on the Proton-DNA Collision
• Calculation of survival probabilities for cells exposed to high ion fluences
• Advances in multiscale modeling for novel and emerging technologies
• Creating mixed-phase states in cadmium sulfide by swift heavy ion irradiation