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

Pablo de Vera*, Nigel J. Mason, Frederick Currell, Andrey V. Solov’yov

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)
184 Downloads (Pure)

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 is not possible with the analytical model.

Original languageEnglish
Article number183
Number of pages10
JournalEuropean Physical Journal D
Volume70
Issue number183
Early online date06 Sep 2016
DOIs
Publication statusEarly online date - 06 Sep 2016

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

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