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Geant4/examples/extended/medical/dna/dnadamage1/README.txt

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  1      =========================================================
  2       Geant4 - dnadamage1 example
  3      =========================================================
  4 
  5                                 README file
  6                           ----------------------
  7 
  8 
  9 This is a new example and it may contain bugs.
 10 It was developed by Hoang Tran.
 11 Damage analysis was developed by Le Tuan Anh.
 12 If you find a bug, please contact IRSN:
 13  yann.perrot@irsn.fr or carmen.villagrasa@irsn.fr
 14 
 15 ---->0. INTRODUCTION.                                                    
 16                                                                        
 17 The dnadamage1 example shows a simple way to simulate dna direct and indirect damages 
 18 using the Geant4-DNA physics and chemical processes in a molecular DNA geometry. 
 19 Moreover, a clustering algorithm is introduced to demonstrate how to extract SSB, DSB (simple, complex).
 20 
 21 This example is based on the work described in Sc. Rep. 7 (2017)11923 
 22 and is provided by the Geant4-DNA collaboration.
 23 
 24 Any report or published results obtained using the Geant4-DNA software shall 
 25 cite the following Geant4-DNA collaboration publications:
 26 Phys. Med. 31 (2015) 861-874
 27 Med. Phys. 37 (2010) 4692-4708
 28 
 29 ---->1. GEOMETRY SET-UP.
 30  
 31 The geometry is chromatical fiber in a 40-nm side cube (Voxel<straight>) made of liquid water (G4_WATER
 32 material). Particles are randomly shot in a cicle of 5 nm2 radius from left side of the cube.
 33 
 34 The DNA chromatical fiber geometry is generated by DnaFabric tool(https://bitbucket.org/sylMeylan/opendnafabric). 
 35 For detail, please see: Sc. Rep. 7 (2017) 11923
 36 
 37 ---->2. SET-UP 
 38                                                                         
 39 The code can be compiled with cmake.
 40 It works in MT mode.
 41 Chemistry stage is automatically activated. 
 42 
 43 ---->3. HOW TO RUN THE EXAMPLE                                         
 44 
 45 In interactive mode, run:
 46 
 47 ./dnadamage1
 48 (Note: interactive mode needs at least 6Go of RAM for visualization and may not work correctly in some plateformes)
 49 
 50 In batch, the macro dnadamage1.in can be used as bellows. It shows how to shoot different 
 51 particle types and energies.
 52 
 53 ./dnadamage1 dnadamage1.in
 54 
 55 ---->4. PHYSICS
 56 
 57 This example shows:
 58 - how to use the Geant4-DNA processes (physics and chemistry) through G4EmDNAPhysics and G4EmDNAChemistry_option2 constructors
 59 (look at the PhysicsList.cc file)
 60 - how to count and save energy depositions giving rise to direct damages using an energy thershold 
 61 of 17.5 eV in teh nucleotide backbone region.
 62 (look at the SteppingAction.cc file)
 63 -how to forbid water radicals to be created at the DNA molecule volume (look at the SteppingAction.cc file)
 64 )
 65 
 66 ---->5. CHEMISTRY
 67 
 68 This example shows: 
 69 - how to add a parallel world for chemistry
 70 - how to add a new reaction of free radicals with a DNA molecule using <Step by step model> 
 71 (look at the G4EmDNAChemistry_option2)
 72 - how to count and save occurrences of chemical reactions for indirect damages
 73 (look at to TimeStepAction.cc file)
 74 
 75 
 76 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS                                    
 77 
 78 This file can be easily analyzed using the provided ROOT macro 
 79 file analysis.C (and scandamges.C, molecule.C); The scandamges.C results in a text file using the SDD format:
 80  "A new standard DNA damage (SDD) data format" J. Schuemann et al. Published in Rad. Res. 191 (2019) 76-92
 81  to do so :
 82 * be sure to have ROOT installed on your machine (version 6 series)
 83 * be sure to be in the directory containing the ROOT files created by dnadamage1
 84 * copy analysis.C (and scandamges.C, molecule.C) into this directory
 85 * from there, launch ROOT by typing root
 86 * under your ROOT session, type in : .X analysis.C to execute the macro file
 87 * alternatively you can type directly under your session : root -b analysis.C
 88 
 89 
 90 Results will be obtained:
 91 * Count numbers of direct and indirect SB (strand break)
 92 * Count numbers of SSB, DSB (simple, complex)
 93 * In function scandamges(), users change:
 94       * Break-energy to select direct damages (default is 17.5 ev)
 95       * probability to select indirect damages (default is 40%)
 96       * minium distance between two clusters (default is 10 bp)
 97 to see how they affect direct/indirect SB, SSB, and DSB.
 98 * Damages in SDD format
 99 ---------------------------------------------------------------------------
100 
101 Contact: ngoc-hoang.tran@irsn.fr, carmen.villagrasa@irsn.fr
102