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0001 =========================================================
0002 Geant4 - dnadamage1 example
0003 =========================================================
0004
0005 README file
0006 ----------------------
0007
0008
0009 This is a new example and it may contain bugs.
0010 It was developed by Hoang Tran.
0011 Damage analysis was developed by Le Tuan Anh.
0012 If you find a bug, please contact IRSN:
0013 yann.perrot@irsn.fr or carmen.villagrasa@irsn.fr
0014
0015 ---->0. INTRODUCTION.
0016
0017 The dnadamage1 example shows a simple way to simulate dna direct and indirect damages
0018 using the Geant4-DNA physics and chemical processes in a molecular DNA geometry.
0019 Moreover, a clustering algorithm is introduced to demonstrate how to extract SSB, DSB (simple, complex).
0020
0021 This example is based on the work described in Sc. Rep. 7 (2017)11923
0022 and is provided by the Geant4-DNA collaboration.
0023
0024 Any report or published results obtained using the Geant4-DNA software shall
0025 cite the following Geant4-DNA collaboration publications:
0026 Phys. Med. 31 (2015) 861-874
0027 Med. Phys. 37 (2010) 4692-4708
0028
0029 ---->1. GEOMETRY SET-UP.
0030
0031 The geometry is chromatical fiber in a 40-nm side cube (Voxel<straight>) made of liquid water (G4_WATER
0032 material). Particles are randomly shot in a cicle of 5 nm2 radius from left side of the cube.
0033
0034 The DNA chromatical fiber geometry is generated by DnaFabric tool(https://bitbucket.org/sylMeylan/opendnafabric).
0035 For detail, please see: Sc. Rep. 7 (2017) 11923
0036
0037 ---->2. SET-UP
0038
0039 The code can be compiled with cmake.
0040 It works in MT mode.
0041 Chemistry stage is automatically activated.
0042
0043 ---->3. HOW TO RUN THE EXAMPLE
0044
0045 In interactive mode, run:
0046
0047 ./dnadamage1
0048 (Note: interactive mode needs at least 6Go of RAM for visualization and may not work correctly in some plateformes)
0049
0050 In batch, the macro dnadamage1.in can be used as bellows. It shows how to shoot different
0051 particle types and energies.
0052
0053 ./dnadamage1 dnadamage1.in
0054
0055 ---->4. PHYSICS
0056
0057 This example shows:
0058 - how to use the Geant4-DNA processes (physics and chemistry) through G4EmDNAPhysics and G4EmDNAChemistry_option2 constructors
0059 (look at the PhysicsList.cc file)
0060 - how to count and save energy depositions giving rise to direct damages using an energy thershold
0061 of 17.5 eV in teh nucleotide backbone region.
0062 (look at the SteppingAction.cc file)
0063 -how to forbid water radicals to be created at the DNA molecule volume (look at the SteppingAction.cc file)
0064 )
0065
0066 ---->5. CHEMISTRY
0067
0068 This example shows:
0069 - how to add a parallel world for chemistry
0070 - how to add a new reaction of free radicals with a DNA molecule using <Step by step model>
0071 (look at the G4EmDNAChemistry_option2)
0072 - how to count and save occurrences of chemical reactions for indirect damages
0073 (look at to TimeStepAction.cc file)
0074
0075
0076 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS
0077
0078 This file can be easily analyzed using the provided ROOT macro
0079 file analysis.C (and scandamges.C, molecule.C); The scandamges.C results in a text file using the SDD format:
0080 "A new standard DNA damage (SDD) data format" J. Schuemann et al. Published in Rad. Res. 191 (2019) 76-92
0081 to do so :
0082 * be sure to have ROOT installed on your machine (version 6 series)
0083 * be sure to be in the directory containing the ROOT files created by dnadamage1
0084 * copy analysis.C (and scandamges.C, molecule.C) into this directory
0085 * from there, launch ROOT by typing root
0086 * under your ROOT session, type in : .X analysis.C to execute the macro file
0087 * alternatively you can type directly under your session : root -b analysis.C
0088
0089
0090 Results will be obtained:
0091 * Count numbers of direct and indirect SB (strand break)
0092 * Count numbers of SSB, DSB (simple, complex)
0093 * In function scandamges(), users change:
0094 * Break-energy to select direct damages (default is 17.5 ev)
0095 * probability to select indirect damages (default is 40%)
0096 * minium distance between two clusters (default is 10 bp)
0097 to see how they affect direct/indirect SB, SSB, and DSB.
0098 * Damages in SDD format
0099 ---------------------------------------------------------------------------
0100
0101 Contact: ngoc-hoang.tran@irsn.fr, carmen.villagrasa@irsn.fr
0102
