An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

M.A. Bernal , D. Sikansi , F. Cavalcante , S. Incerti (1) , C. Champion (1) , V. Ivanchenko , Z. Francis

1 IPCV - Interface Physique et Chimie pour le Vivant

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model.

Mots clés: B-DNA Geometrical model Atomistic model

Domaines: Physique Médicale [physics.med-ph]

M.A. Bernal, D. Sikansi, F. Cavalcante, S. Incerti, C. Champion, et al.. An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations. Computer Physics Communications, 2013, 184, pp.2840-2847. ⟨10.1016/j.cpc.2013.07.015⟩. ⟨in2p3-00918490⟩