https://doi.org/10.1140/epjd/e2016-70281-7
Regular Article
Molecular dynamics study of accelerated ion-induced shock waves in biological media*
1 School of Mathematics and Physics,
Queen’s University Belfast, BT7 1NN
Belfast, Northern
Ireland, UK
2 Department of Physical Sciences, The
Open University, Walton Hall, MK7
6AA Milton Keynes, England, UK
3 MBN Research Center, Altenhöferallee
3, 60438
Frankfurt am Main,
Germany
a
e-mail: p.devera@qub.ac.uk
b
On leave from A. F. Ioffe Physical Technical Institute, 194021 St. Petersburg, Russian
Federation.
Received:
20
April
2016
Received in final form:
28
June
2016
Published online:
6
September
2016
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.
© The Author(s) 2016. This article is published with open access at Springerlink.com
Open Access This is an open access article distributed
under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/4.0), which
permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
