An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
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DOI：
10.1016/j.cpc.2013.07.015
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发表时间：
2013-12-01
影响因子：
6.3
通讯作者：
Francis, Z.
中科院分区：
文献类型：
--
作者：
Bernal, M. A.;Sikansi, D.;Francis, Z.
本文解释了B-DNA结构的原子几何模型。这个模型解释了DNA的五个组织水平，直到30纳米的染色质纤维。然而，这种纤维的片段可以用来构建整个基因组。在这项工作中开发的算法能够确定哪个是相对于空间中的任意点最近的原子。它可以用于任何需要DNA几何模型的应用中，例如，在与电离辐射对人类遗传物质的影响有关的研究中。进行了成功的一致性检查来测试所提出的模型。项目摘要项目名称：findclosestatomcatalog标识符：aepz_v1_0项目摘要URL: http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.htmlProgram可从：爱尔兰贝尔法斯特女王大学CPC项目图书馆获得许可条款：标准CPC许可，http://cpc.cs.qub.ac.uk/licence/licence.htmlNo。分布式程序的行数，包括测试数据等：1245分布程序中包含测试数据等的字节数：6574分布格式：tar。编程语言：FORTRAN。计算机:任何。操作系统：多平台。内存：2gb分类：3。问题性质：蒙特卡罗方法用于模拟电离辐射与人类遗传物质的相互作用，以确定每单位吸收剂量的DNA损伤量。为了完成这项任务，需要一种算法来确定给定的能量沉积是否位于给定的目标内。这个目标可以是一个原子或遗传物质的任何其他结构。解决方法：这是一个独立的子程序，描述了B-DNA结构的原子分辨率几何模型。它能够确定离空间中任意一点最近的原子。这个模型解释了人类遗传物质的五个组织水平，从核苷酸对到30纳米的染色质纤维。这个子程序执行一系列坐标变换，以找出包含空间中任意点的最近原子。原子的大小根据相应的范德华半径。限制：这里提出的几何模型不包括染色体组织水平，但它可以很容易地通过使用30纳米染色质纤维的片段建立。不寻常的特点：据我们所知，这是第一个为DNA-辐射相互作用蒙特卡罗模拟开发的开源原子分辨率DNA几何模型。在我们的测试中，目前的模型考虑了大约56 x 10(6)个原子的明确位置，尽管用户可以根据需要增加这个数量。运行时间：这个子程序可以在几分钟内在一台典型的当前计算机上处理大约200万个点。(C) 2013 Elsevier B.V.版权所有
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 summaryProgram title: FindClosestAtomCatalogue identifier: AEPZ_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 1245No. of bytes in distributed program, including test data, etc.: 6574Distribution format: tar.gzProgramming language: FORTRAN.Computer: Any.Operating system: Multi-platform.RAM: 2 GbClassification: 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. (C) 2013 Elsevier B.V. All rights reserved.