dna/dnadamage1/README.md

0001 \page Examplednadamage1 Example dnadamage1
0002
0003 This is a new example and it may contain bugs.
0004 It was developed by Hoang Tran.
0005 Damage analysis was developed by Le Tuan Anh.
0006 If you find a bug, please contact IRSN:
0007 yann.perrot@irsn.fr or carmen.villagrasa@irsn.fr
0008
0009 ## INTRODUCTION
0010
0011 The dnadamage1 example shows a simple way to simulate dna direct and indirect damages
0012 using the Geant4-DNA physics and chemical processes in a molecular DNA geometry.
0013 Moreover, a clustering algorithm is introduced to demonstrate how to extract SSB, DSB (simple, complex).
0014
0015 This example is based on the work described in Sc. Rep. 7 (2017)11923
0016 and is provided by the Geant4-DNA collaboration.
0017
0018 Any report or published results obtained using the Geant4-DNA software shall
0019 cite the following Geant4-DNA collaboration publications:
0020 - Phys. Med. 31 (2015) 861-874
0021 - Med. Phys. 37 (2010) 4692-4708
0022
0023 ## GEOMETRY SET-UP
0024
0025 The geometry is chromatical fiber in a 40-nm side cube (Voxel<straight>) made of liquid water (G4_WATER
0026 material). Particles are randomly shot in a cicle of 5 nm2 radius from left side of the cube.
0027
0028 The DNA chromatical fiber geometry is generated by DnaFabric tool(https://bitbucket.org/sylMeylan/opendnafabric).
0029 For detail, please see: Sc. Rep. 7 (2017) 11923
0030
0031 ## SET-UP
0032
0033 The code can be compiled with cmake.
0034 It works in MT mode.
0035 Chemistry stage is automatically activated.
0036
0037 ## HOW TO RUN THE EXAMPLE
0038
0039 In interactive mode, run:
0040
0041 ```
0042 ./dnadamage1
0043 ```
0044
0045 Note: interactive mode needs at least 6Go of RAM for visualization and may not work correctly in some plateformes.
0046
0047 In batch, the macro dnadamage1.in can be used as bellows. It shows how to shoot different
0048 particle types and energies.
0049
0050 ```
0051 ./dnadamage1 dnadamage1.in
0052 ```
0053
0054 ## PHYSICS
0055
0056 This example shows:
0057 - how to use the Geant4-DNA processes (physics and chemistry) through G4EmDNAPhysics and G4EmDNAChemistry_option2 constructors
0058 (look at the PhysicsList class)
0059 - how to count and save energy depositions giving rise to direct damages using an energy thershold
0060 of 17.5 eV in teh nucleotide backbone region.
0061 (look at the SteppingAction class)
0062 -how to forbid water radicals to be created at the DNA molecule volume (look at the SteppingAction class)
0063 )
0064
0065 ## CHEMISTRY
0066
0067 This example shows:
0068 - how to add a parallel world for chemistry
0069 - how to add a new reaction of free radicals with a DNA molecule using "Step by step model"
0070 (look at the G4EmDNAChemistry_option2)
0071 - how to count and save occurrences of chemical reactions for indirect damages
0072 (look at to TimeStepAction class)
0073
0074
0075 ## SIMULATION OUTPUT AND RESULT ANALYSIS
0076
0077 This file can be easily analyzed using the provided ROOT macro
0078 file analysis.C (and scandamages.C, molecule.C); The scandamages.C results in a text file using the SDD format: \n
0079  "A new standard DNA damage (SDD) data format" J. Schuemann et al. Published in Rad. Res. 191 (2019) 76-92
0080
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 Results will be obtained:
0090 - Count numbers of direct and indirect SB (strand break)
0091 - Count numbers of SSB, DSB (simple, complex)
0092 - In function scandamges(), users change:
0093     - Break-energy to select direct damages (default is 17.5 ev)
0094     - probability to select indirect damages (default is 40%)
0095     - minium distance between two clusters (default is 10 bp)
0096 to see how they affect direct/indirect SB, SSB, and DSB.
0097 - Damages in SDD format
0098 ---------------------------------------------------------------------------
0099
0100 Contact: ngoc-hoang.tran@irsn.fr, carmen.villagrasa@irsn.fr