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

Version: [ ReleaseNotes ] [ 1.0 ] [ 1.1 ] [ 2.0 ] [ 3.0 ] [ 3.1 ] [ 3.2 ] [ 4.0 ] [ 4.0.p1 ] [ 4.0.p2 ] [ 4.1 ] [ 4.1.p1 ] [ 5.0 ] [ 5.0.p1 ] [ 5.1 ] [ 5.1.p1 ] [ 5.2 ] [ 5.2.p1 ] [ 5.2.p2 ] [ 6.0 ] [ 6.0.p1 ] [ 6.1 ] [ 6.2 ] [ 6.2.p1 ] [ 6.2.p2 ] [ 7.0 ] [ 7.0.p1 ] [ 7.1 ] [ 7.1.p1 ] [ 8.0 ] [ 8.0.p1 ] [ 8.1 ] [ 8.1.p1 ] [ 8.1.p2 ] [ 8.2 ] [ 8.2.p1 ] [ 8.3 ] [ 8.3.p1 ] [ 8.3.p2 ] [ 9.0 ] [ 9.0.p1 ] [ 9.0.p2 ] [ 9.1 ] [ 9.1.p1 ] [ 9.1.p2 ] [ 9.1.p3 ] [ 9.2 ] [ 9.2.p1 ] [ 9.2.p2 ] [ 9.2.p3 ] [ 9.2.p4 ] [ 9.3 ] [ 9.3.p1 ] [ 9.3.p2 ] [ 9.4 ] [ 9.4.p1 ] [ 9.4.p2 ] [ 9.4.p3 ] [ 9.4.p4 ] [ 9.5 ] [ 9.5.p1 ] [ 9.5.p2 ] [ 9.6 ] [ 9.6.p1 ] [ 9.6.p2 ] [ 9.6.p3 ] [ 9.6.p4 ] [ 10.0 ] [ 10.0.p1 ] [ 10.0.p2 ] [ 10.0.p3 ] [ 10.0.p4 ] [ 10.1 ] [ 10.1.p1 ] [ 10.1.p2 ] [ 10.1.p3 ] [ 10.2 ] [ 10.2.p1 ] [ 10.2.p2 ] [ 10.2.p3 ] [ 10.3 ] [ 10.3.p1 ] [ 10.3.p2 ] [ 10.3.p3 ] [ 10.4 ] [ 10.4.p1 ] [ 10.4.p2 ] [ 10.4.p3 ] [ 10.5 ] [ 10.5.p1 ] [ 10.6 ] [ 10.6.p1 ] [ 10.6.p2 ] [ 10.6.p3 ] [ 10.7 ] [ 10.7.p1 ] [ 10.7.p2 ] [ 10.7.p3 ] [ 10.7.p4 ] [ 11.0 ] [ 11.0.p1 ] [ 11.0.p2 ] [ 11.0.p3, ] [ 11.0.p4 ] [ 11.1 ] [ 11.1.1 ] [ 11.1.2 ] [ 11.1.3 ] [ 11.2 ] [ 11.2.1 ] [ 11.2.2 ] [ 11.3.0 ]

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Differences between /examples/extended/medical/dna/dnadamage1/README.txt (Version 11.3.0) and /examples/extended/medical/dna/dnadamage1/README.txt (Version 11.1.2)


  1      =========================================      1      =========================================================
  2       Geant4 - dnadamage1 example                   2       Geant4 - dnadamage1 example
  3      =========================================      3      =========================================================
  4                                                     4 
  5                                 README file         5                                 README file
  6                           --------------------      6                           ----------------------
  7                                                     7 
  8                                                     8 
  9 This is a new example and it may contain bugs.      9 This is a new example and it may contain bugs.
 10 It was developed by Hoang Tran.                    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:            11 If you find a bug, please contact IRSN:
 13  yann.perrot@irsn.fr or carmen.villagrasa@irsn     12  yann.perrot@irsn.fr or carmen.villagrasa@irsn.fr
 14                                                    13 
 15 ---->0. INTRODUCTION.                              14 ---->0. INTRODUCTION.                                                    
 16                                                    15                                                                        
 17 The dnadamage1 example shows a simple way to s     16 The dnadamage1 example shows a simple way to simulate dna direct and indirect damages 
 18 using the Geant4-DNA physics and chemical proc     17 using the Geant4-DNA physics and chemical processes in a molecular DNA geometry. 
 19 Moreover, a clustering algorithm is introduced << 
 20                                                    18 
 21 This example is based on the work described in     19 This example is based on the work described in Sc. Rep. 7 (2017)11923 
 22 and is provided by the Geant4-DNA collaboratio     20 and is provided by the Geant4-DNA collaboration.
 23                                                    21 
 24 Any report or published results obtained using     22 Any report or published results obtained using the Geant4-DNA software shall 
 25 cite the following Geant4-DNA collaboration pu     23 cite the following Geant4-DNA collaboration publications:
 26 Phys. Med. 31 (2015) 861-874                       24 Phys. Med. 31 (2015) 861-874
 27 Med. Phys. 37 (2010) 4692-4708                     25 Med. Phys. 37 (2010) 4692-4708
 28                                                    26 
 29 ---->1. GEOMETRY SET-UP.                           27 ---->1. GEOMETRY SET-UP.
 30                                                    28  
 31 The geometry is chromatical fiber in a 40-nm s     29 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 ci     30 material). Particles are randomly shot in a cicle of 5 nm2 radius from left side of the cube.
 33                                                    31 
 34 The DNA chromatical fiber geometry is generate     32 The DNA chromatical fiber geometry is generated by DnaFabric tool(https://bitbucket.org/sylMeylan/opendnafabric). 
 35 For detail, please see: Sc. Rep. 7 (2017) 1192     33 For detail, please see: Sc. Rep. 7 (2017) 11923
 36                                                    34 
 37 ---->2. SET-UP                                     35 ---->2. SET-UP 
 38                                                    36                                                                         
 39 The code can be compiled with cmake.               37 The code can be compiled with cmake.
 40 It works in MT mode.                               38 It works in MT mode.
 41 Chemistry stage is automatically activated.        39 Chemistry stage is automatically activated. 
 42                                                    40 
 43 ---->3. HOW TO RUN THE EXAMPLE                     41 ---->3. HOW TO RUN THE EXAMPLE                                         
 44                                                    42 
 45 In interactive mode, run:                          43 In interactive mode, run:
 46                                                    44 
 47 ./dnadamage1                                       45 ./dnadamage1
 48 (Note: interactive mode needs at least 6Go of      46 (Note: interactive mode needs at least 6Go of RAM for visualization and may not work correctly in some plateformes)
 49                                                    47 
 50 In batch, the macro dnadamage1.in can be used      48 In batch, the macro dnadamage1.in can be used as bellows. It shows how to shoot different 
 51 particle types and energies.                       49 particle types and energies.
 52                                                    50 
 53 ./dnadamage1 dnadamage1.in                         51 ./dnadamage1 dnadamage1.in
 54                                                    52 
 55 ---->4. PHYSICS                                    53 ---->4. PHYSICS
 56                                                    54 
 57 This example shows:                                55 This example shows:
 58 - how to use the Geant4-DNA processes (physics     56 - how to use the Geant4-DNA processes (physics and chemistry) through G4EmDNAPhysics and G4EmDNAChemistry_option2 constructors
 59 (look at the PhysicsList.cc file)                  57 (look at the PhysicsList.cc file)
 60 - how to count and save energy depositions giv     58 - 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.      59 of 17.5 eV in teh nucleotide backbone region.
 62 (look at the SteppingAction.cc file)               60 (look at the SteppingAction.cc file)
 63 -how to forbid water radicals to be created at     61 -how to forbid water radicals to be created at the DNA molecule volume (look at the SteppingAction.cc file)
 64 )                                                  62 )
 65                                                    63 
 66 ---->5. CHEMISTRY                                  64 ---->5. CHEMISTRY
 67                                                    65 
 68 This example shows:                                66 This example shows: 
 69 - how to add a parallel world for chemistry        67 - how to add a parallel world for chemistry
 70 - how to add a new reaction of free radicals w     68 - how to add a new reaction of free radicals with a DNA molecule using <Step by step model> 
 71 (look at the G4EmDNAChemistry_option2)             69 (look at the G4EmDNAChemistry_option2)
 72 - how to count and save occurrences of chemica     70 - how to count and save occurrences of chemical reactions for indirect damages
 73 (look at to TimeStepAction.cc file)                71 (look at to TimeStepAction.cc file)
 74                                                    72 
 75                                                    73 
 76 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS      74 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS                                    
 77                                                    75 
 78 This file can be easily analyzed using the pro     76 This file can be easily analyzed using the provided ROOT macro 
 79 file analysis.C (and scandamges.C, molecule.C) <<  77 file analysis.C (and plot.C, molecule.C); The plot.C results in a text file using the SDD format:
 80  "A new standard DNA damage (SDD) data format"     78  "A new standard DNA damage (SDD) data format" J. Schuemann et al. Published in Rad. Res. 191 (2019) 76-92
 81  to do so :                                        79  to do so :
 82 * be sure to have ROOT installed on your machi     80 * be sure to have ROOT installed on your machine (version 6 series)
 83 * be sure to be in the directory containing th     81 * be sure to be in the directory containing the ROOT files created by dnadamage1
 84 * copy analysis.C (and scandamges.C, molecule. <<  82 * copy analysis.C (and plot.C, molecule.C) into this directory
 85 * from there, launch ROOT by typing root           83 * from there, launch ROOT by typing root
 86 * under your ROOT session, type in : .X analys     84 * under your ROOT session, type in : .X analysis.C to execute the macro file
 87 * alternatively you can type directly under yo     85 * alternatively you can type directly under your session : root -b analysis.C
 88                                                    86 
 89                                                << 
 90 Results will be obtained:                      << 
 91 * Count numbers of direct and indirect SB (str << 
 92 * Count numbers of SSB, DSB (simple, complex)  << 
 93 * In function scandamges(), users change:      << 
 94       * Break-energy to select direct damages  << 
 95       * probability to select indirect damages << 
 96       * minium distance between two clusters ( << 
 97 to see how they affect direct/indirect SB, SSB << 
 98 * Damages in SDD format                        << 
 99 ----------------------------------------------     87 ---------------------------------------------------------------------------
100                                                    88 
101 Contact: ngoc-hoang.tran@irsn.fr, carmen.villa     89 Contact: ngoc-hoang.tran@irsn.fr, carmen.villagrasa@irsn.fr
102                                                    90