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[Licence| Download | New Version Template] aepz_v1_0.tar.gz(600 Kbytes)
Manuscript Title: An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
Authors: M.A. Bernal, D. Sikansi, F. Cavalcante, S. Incerti, C. Champion, V. Ivanchenko, Z. Francis
Program title: FindClosestAtom
Catalogue identifier: AEPZ_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 184(2013)2842
Programming language: FORTRAN.
Computer: Any.
Operating system: Multi-platform.
RAM: 2 Gb
Keywords: B-DNA, Geometrical model, Atomistic model.
Classification: 3.

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.

Solution method:
This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30-nm chromatin fiber. This subroutine carries out a series of coordinate transformations to find which is the closest atom to an arbitrary point in space. Atom sizes are according to the corresponding van der Waals radii.

Restrictions:
The geometrical model presented here does not include the chromosome organization level but it could be easily build up by using fragments of the 30-nm chromatin fiber.

Unusual features:
To our knowledge, this is the first open source atomic-resolution DNA geometrical model developed for DNA-radiation interaction Monte Carlo simulations. The current model takes into account the explicit position of about 56x106 atoms, although the user may enhance this amount according to the necessities.

Running time:
This subroutine can process about 2 million points within a few minutes in a typical current computer.