Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool

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• 作者：S. Meylan^a ; ¹ ; ^{sylvain.meylan@irsn.fr" class="auth_mail" title="E-mail the corresponding author} ; U. Vimont^b ; S. Incerti^c ; ^d ; ¹ ; I. Clairand^a ; ¹ ; C. Villagrasa^a ; ¹ ; ^{carmen.villagrasa@irsn.fr" class="auth_mail" title="E-mail the corresponding author}
• 关键词：DNA model ; Real-time rendering ; DNA damage ; Geant4-DNA
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：July 2016
• 年：2016
• 卷：204
• 期：Complete
• 页码：159-169
• 全文大小：3705 K

文摘

Several DNA representations are used to study radio-induced complex DNA damages depending on the approach and the required level of granularity. Among all approaches, the mechanistic one requires the most resolved DNA models that can go down to atomistic DNA descriptions. The complexity of such DNA models make them hard to modify and adapt in order to take into account different biological conditions. The DnaFabric project was started to provide a tool to generate, visualise and modify such complex DNA models. In the current version of DnaFabric, the models can be exported to the Geant4 code to be used as targets in the Monte Carlo simulation. In this work, the project was used to generate two DNA fibre models corresponding to two DNA compaction levels representing the hetero and the euchromatin. The fibres were imported in a Geant4 application where computations were performed to estimate the influence of the DNA compaction on the amount of calculated DNA damage. The relative difference of the DNA damage computed in the two fibres for the same number of projectiles was found to be constant and equal to 1.3 for the considered primary particles (protons from 300 keV to 50 MeV). However, if only the tracks hitting the DNA target are taken into account, then the relative difference is more important for low energies and decreases to reach zero around 10 MeV. The computations were performed with models that contain up to 18,000 DNA nucleotide pairs. Nevertheless, DnaFabric will be extended to manipulate multi-scale models that go from the molecular to the cellular levels.

Program summary

Program title: DnaFabric

Catalogue identifier: AEZV_v1_0

Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZV_v1_0.html

Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland

Licensing provisions: Apache License, 2.0

No. of lines in distributed program, including test data, etc.: 13514

No. of bytes in distributed program, including test data, etc.: 186753

Distribution format: tar.gz

Programming language: C++.

Computer: Computer with a GPU and OpenGL3.3 compatible drivers.

Operating system: Linux (Ubuntu).

RAM: 4 gigabytes

Classification: 3, 14, 20.

External routines: Qt5 and OpenGL3.3

Nature of problem:

Simulations implying DNA geometrical models often show limitations to support the huge number of DNA constituents. In order to allow users to build, visualise and perform calculations on detailed DNA models including hundreds of thousands of DNA elements, a dedicated framework is needed.

Solution method:

The DnaFabric library is a framework that allows users to easily build their own DNA models, display them and perform calculations. The DnaFabric includes: hierarchically organised DNA models (binary-executable example named “Fibre”), a dedicated 3D render engine, an optimised OpenGL interface and some multi-threading facilities.

Unusual features:

The DnaFabric uses 3D technologies from the computer graphics world allowing the rendering of huge DNA models in real-time.

Additional comments:

Three examples are provided in the Examples folder. The “Basic” example describes how to set-up a simple DnaFabric user-application. The “Fibre” example shows the two DNA fibre models used for the calculations in this paper. The “MovingSpheres” example, demonstrates how to implement a simulation interacting with the DNA geometrical model.

Running time:

Once a user application is started, an auto-generated window will show the 3D model. The efficiency of the rendering depends highly on the user hardware. However, the user can customise each of the rendered elements contained in its application to adjust the required computer power.