Molecular dynamics study of accelerated ion-induced shock waves in biological media*
1 School of Mathematics and Physics,
Queen’s University Belfast, BT7 1NN
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
b On leave from A. F. Ioffe Physical Technical Institute, 194021 St. Petersburg, Russian Federation.
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.
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