October 12, 2016
An image highlighting the recent molecular dynamics study exploiting MBN Explorer has been chosen as a cover for the September issue of the European Physical Journal D (EPJD).
The paper by Pablo de Vera, Nigel Mason, Fred Currell and Andrey V. Solov'yov [1] explored radiation damage of DNA molecules in liquid water due to ion-induced shock waves. In this work, MBN Explorer was used to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes and to simulate the dynamics of the biological medium in the vicinity of an ion track leading to the creation and the propagation of a cylindrical shock wave capable to produce biodamage.
The concrete simulations and analysis of the shock wave effects have been performed for the Bragg peak region of carbon ions, being used in ion-beam cancer therapy, as well as for heavier iron ions. The dependencies of several quantities, namely pressure waves and energy deposition in DNA bonds, on the size and other parameters of the system, were studied, and the significant effects of ion-induced thermo-mechanical damage have been characterized on the molecular level.
This work represents a contribution to the Topical Issue “Atomic Cluster Collisions (7th International Symposium)” of EPJD.
[1] Pablo de Vera, Nigel J. Mason, Fred J. Currell, and Andrey V. Solov’yov, Molecular dynamics study of accelerated ion-induced shock waves in biological media, Eur. Phys. J. D 70, 183 (2016).