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

作者：Bernal M A^*; Sikansi D; Cavalcante F; Incerti S; Champion C; Ivanchenko V; Francis Z

来源：Computer Physics Communications, 2013, 184(12): 2840-2847.

DOI：10.1016/j.cpc.2013.07.015

• B-DNA
• Geometrical model
• Atomistic model

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.
Program summary
Program title: FindClosestAtom
Catalogue identifier: AEPZ_v1_0
Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 1245
No. of bytes in distributed program, including test data, etc.: 6574
Distribution format: tar.gz
Programming language: FORTRAN.
Computer: Any.
Operating system: Multi-platform.
RAM: 2 Gb
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 containing 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. In our tests, the current model took into account the explicit position of about 56 x 10(6) 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.

• 出版日期2013-12