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

Published: 1 June 2013| Version 1 | DOI: 10.17632/tsrx8x8hpc.1
M.A. Bernal,
D. Sikansi,
F. Cavalcante,
S. Incerti,
V. Ivanchenko,
Z. Francis


Abstract 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... Title of program: FindClosestAtom Catalogue Id: AEPZ_v1_0 Nature of problem The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Versions of this program held in the CPC repository in Mendeley Data AEPZ_v1_0; FindClosestAtom; 10.1016/j.cpc.2013.07.015 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Biological Sciences, Computational Physics