PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule in Geant4 Monte Carlo particle transport simulations. For the evaluation of direct damage induced on the DNA molecule by ionizing particles, the application makes use of an algorithm able to determine the closest atom in the DNA molecule to energy depositions. Both the PDB4DNA application and the PDBlib library are available as free and open source under the Geant4 license. Program summary Program title: PDB4DNA Catalogue identifier: AEWB_v1_0 Program summary URL: http://.cpc.cs.qub.ac.uk/summaries/AEWB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Geant4 license, http://geant4.web.cern.ch/geant4/license/LICENSE.html No. of lines in distributed program, including test data, etc.: 34714 No. of bytes in distributed program, including test data, etc.: 515359 Distribution format: tar.gz Programming language: C++. Computer: All. Operating system: Cross-Platform. Classification: 3. External routines: Geant4 10.0 or later Nature of problem: To evaluate strand breaks induced on the DNA molecule by ionizing particles using Monte Carlo method. It requires the implementation of DNA geometry, physical processes adapted to nanodosimetry simulations and an algorithm to determine the closest atom in the DNA molecule to energy depositions. Solution method: PDB4DNA is a Geant4 user application that simulates energy deposition in a target volume generated from a Protein Data Bank file representing the geometry of DNA molecule. Energy depositions are allocated to DNA geometry in order to compute DNA strand breaks. Restrictions: The algorithm for finding the closest atom to energy depositions has been optimized for DNA molecule and is not proposed for other stereochemistry conformation. Running time: Depending on the particle type/energy, PDB4DNA is able to track in the target volume: similar to 5000 particles/min (100 key protons), 120000 particles/min (100 keV electrons), Geant4.10.0 using one thread, Intel(R) Core(TM) i5-4570 CPU @3.20 GHz, RAM 4096 MB 1600 MHz. (C) 2015 Published by Elsevier B.V.