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

de Vera Gomis, Pablo; Mason, Nigel J.; Currell, Fred J. and Solov’yov, Andrey V. (2016). Molecular dynamics study of accelerated ion-induced shock waves in biological media. The European Physical Journal D, 70(9) p. 183.

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DOI (Digital Object Identifier) Link: https://doi.org/10.1140/epjd/e2016-70281-7
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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.

Item Type: Journal Item
Copyright Holders: 2016 The Author(s)
ISSN: 1434-6079
Project Funding Details:
Funded Project NameProject IDFunding Body
FP7-People Program608163European Union
Not SetNot SetEuropean Regional Development Fund
Not SetFIS2014-58849-PSpanish Ministerio de Econom´ıa y Competitividad
Keywords: Regular Article
Academic Unit/School: Faculty of Science, Technology, Engineering and Mathematics (STEM) > Physical Sciences
Faculty of Science, Technology, Engineering and Mathematics (STEM)
Item ID: 52031
SWORD Depositor: Jisc Publications-Router
Depositing User: Jisc Publications-Router
Date Deposited: 08 Mar 2018 09:54
Last Modified: 05 May 2019 11:33
URI: http://oro.open.ac.uk/id/eprint/52031
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