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