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Manuscript Title: PDB4DNA: implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations
Authors: E. Delage, Q.T. Pham, M. Karamitros, H. Payno, V. Stepan, S. Incerti, L. Maigne, Y. Perrot
Program title: PDB4DNA
Catalogue identifier: AEWB_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 192(2015)282
Programming language: C++.
Computer: All.
Operating system: Cross-Platform.
Keywords: DNA geometry, Protein Data Bank file, Monte Carlo simulations.
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.

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: ~5000 particles / min (100 keV 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.