| Geant4 Cross Reference |
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3 3
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5 Geant4 - Microbeam example 5 Geant4 - Microbeam example
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7 7
8 README file 8 README file
9 -------------------- 9 ----------------------
10 10
11 CORRESPONDING AUTHO 11 CORRESPONDING AUTHOR
12 12
13 S. Incerti (a, *) et al. 13 S. Incerti (a, *) et al.
14 a. Centre d'Etudes Nucleaires de Bordeaux-Grad 14 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
15 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 15 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
16 * e-mail:incerti@cenbg.in2p3.fr 16 * e-mail:incerti@cenbg.in2p3.fr
17 17
18 ---->0. INTRODUCTION. 18 ---->0. INTRODUCTION.
19 19
20 The microbeam example simulates the cellular i 20 The microbeam example simulates the cellular irradiation beam line
21 installed on the AIFIRA electrostatic accelera 21 installed on the AIFIRA electrostatic accelerator facility located at
22 CENBG, Bordeaux-Gradignan, France. For more in 22 CENBG, Bordeaux-Gradignan, France. For more information on this facility,
23 please visit : 23 please visit :
24 http://www.cenbg.in2p3.fr/ 24 http://www.cenbg.in2p3.fr/
25 25
26 ---->1. GEOMETRY SET-UP. 26 ---->1. GEOMETRY SET-UP.
27 27
28 The elements simulated are: 28 The elements simulated are:
29 29
30 1. A switching dipole magnet with fringing fie 30 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
31 beam generated by the electrostatic accelerato 31 beam generated by the electrostatic accelerator into the microbeam line,
32 oriented at 10 degrees from the main beam dire 32 oriented at 10 degrees from the main beam direction;
33 33
34 2. A circular collimator object, defining the 34 2. A circular collimator object, defining the incident beam size at the
35 microbeam line entrance; 35 microbeam line entrance;
36 36
37 3. A quadrupole based magnetic symmetric focus 37 3. A quadrupole based magnetic symmetric focusing system allowing equal
38 transverse demagnifications of 10. Fringe fiel 38 transverse demagnifications of 10. Fringe fields are calculated from Enge's
39 model. 39 model.
40 40
41 4. A dedicated cellular irradiation chamber se 41 4. A dedicated cellular irradiation chamber setup;
42 42
43 5. A set of horizontal and vertical electrosta 43 5. A set of horizontal and vertical electrostatic deflecting plates which can
44 be turned on or off to deflect the beam on tar 44 be turned on or off to deflect the beam on target;
45 45
46 6. A realistic human keratinocyte voxellized c 46 6. A realistic human keratinocyte voxellized cell observed from confocal
47 microscopy and taking into account realistic n 47 microscopy and taking into account realistic nucleus and cytoplasm chemical
48 compositions. 48 compositions.
49 49
50 50
51 ---->2. EXPERIMENTAL SET-UP. 51 ---->2. EXPERIMENTAL SET-UP.
52 52
53 The beam is defined at the microbeam line entr 53 The beam is defined at the microbeam line entrance through a collimator
54 5 micrometer in diameter. The beam is then foc 54 5 micrometer in diameter. The beam is then focused onto target using a
55 quadruplet of quadrupoles in the so-called Dym 55 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
56 The beam is sent to the irradiation chamber wh 56 The beam is sent to the irradiation chamber where it travels through a
57 isobutane gas detector for counting purpose be 57 isobutane gas detector for counting purpose before reaching the polypropylene
58 culture foil of the target cell which is immer 58 culture foil of the target cell which is immersed in the growing medium and
59 enclosed within a dish. 59 enclosed within a dish.
60 60
61 A cell is placed on the polypropylene foil and 61 A cell is placed on the polypropylene foil and is irradiated using the
62 microbeam. The cell is represented through a 3 62 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
63 obtained from confocal microscopy. In the prov 63 obtained from confocal microscopy. In the provided example, the voxels sizes
64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) 64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
65 65
66 The primary particle beam parameters are gener 66 The primary particle beam parameters are generated from experimental
67 measurements performed on the AIFIRA facility. 67 measurements performed on the AIFIRA facility. Incident particle used for
68 cellular irradiation are 3 MeV alpha particles 68 cellular irradiation are 3 MeV alpha particles.
69 69
70 More details on the experimental setup and its 70 More details on the experimental setup and its simulation with Geant4 can
71 be found in the following papers: 71 be found in the following papers:
72 72
73 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO N 73 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO NON-TARGETED BIOLOGICAL RESPONSES TO
74 RADIATION 74 RADIATION
75 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. 75 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti
76 Publsihed in Comp. Math. Meth. Med. (2012) 147 76 Publsihed in Comp. Math. Meth. Med. (2012) 147252
77 77
78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRA 78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
79 A MICROBEAM FACILITY 79 A MICROBEAM FACILITY
80 By S. Incerti, H. Seznec, M. Simon, Ph. Barber 80 By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
82 82
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA 83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
84 GEANT4 TOOLKIT 84 GEANT4 TOOLKIT
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor 85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout 86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
87 Published in Nucl. Instrum. and Meth. B 260 (2 87 Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
88 88
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ 89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT 90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa 91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. 92 T. Pouthier, H. Seznec. Dec 2006. 3pp.
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) 93 Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
94 94
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND 95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv 96 By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp.
97 Published in Nucl.Instrum.Meth.B249:738-742, 2 97 Published in Nucl.Instrum.Meth.B249:738-742, 2006
98 98
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE 99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
100 SYSTEMS 100 SYSTEMS
101 By S. Incerti et al., 101 By S. Incerti et al.,
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 102 Published in Nucl.Instrum.Meth.B231:76-85, 2005
103 103
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI 104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
105 INDIVIDUAL CELLS. 105 INDIVIDUAL CELLS.
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic 106 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
107 Th. Pouthier. Dec 2004. 6pp. 107 Th. Pouthier. Dec 2004. 6pp.
108 Published in Rev.Sci.Instrum.76:015101, 2005 108 Published in Rev.Sci.Instrum.76:015101, 2005
109 109
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE 110 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
111 GEANT4. 111 GEANT4.
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. 112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, 113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp.
114 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 114 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
115 115
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE 116 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
117 GEANT4. 117 GEANT4.
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M 118 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
119 Ph. Moretto. Sep 2003. 119 Ph. Moretto. Sep 2003.
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 120 Published in Nucl.Instrum.Meth.B210:92-97, 2003
121 121
122 122
123 ---->3 VISUALIZATION 123 ---->3 VISUALIZATION
124 124
125 The user can visualize the targeted cell thank 125 The user can visualize the targeted cell thanks to the Qt interface.
126 126
127 ---->4. HOW TO RUN THE EXAMPLE 127 ---->4. HOW TO RUN THE EXAMPLE
128 128
129 The code should be compiled with cmake. 129 The code should be compiled with cmake.
130 130
131 Run the example from your build directory with 131 Run the example from your build directory with:
132 ./microbeam microbeam.mac 132 ./microbeam microbeam.mac
133 133
134 or in interactive mode: 134 or in interactive mode:
135 ./microbeam 135 ./microbeam
136 136
137 The example works in MT mode. 137 The example works in MT mode.
138 138
139 ---->5. PHYSICS 139 ---->5. PHYSICS
140 140
141 Livermore physics list is used by default. 141 Livermore physics list is used by default.
142 142
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS 143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
144 144
145 The output results consist in a microbeam.root 145 The output results consist in a microbeam.root file per thread,
146 containing several ntuples: 146 containing several ntuples:
147 147
148 * total deposited dose in the cell nucleus and 148 * total deposited dose in the cell nucleus and in the cell
149 cytoplasm by each incident alpha particle; 149 cytoplasm by each incident alpha particle;
150 150
151 * average on the whole run of the dose deposit 151 * average on the whole run of the dose deposited per
152 Voxel per incident alpha particle; 152 Voxel per incident alpha particle;
153 153
154 * final stopping (x,y,z) position of the incid 154 * final stopping (x,y,z) position of the incident
155 alpha particle within the irradiated medium (c 155 alpha particle within the irradiated medium (cell or culture medium);
156 156
157 * stopping power dE/dx of the incident 157 * stopping power dE/dx of the incident
158 alpha particle just before penetrating into th 158 alpha particle just before penetrating into the targeted cell;
159 159
160 * beam transverse position distribution (X and 160 * beam transverse position distribution (X and Y)
161 just before penetrating into the targeted cell 161 just before penetrating into the targeted cell;
162 162
163 These results can be easily analyzed using for 163 These results can be easily analyzed using for example the provided ROOT macro
164 file plot.C; to do so : 164 file plot.C; to do so :
165 * be sure to have ROOT installed on your machi 165 * be sure to have ROOT installed on your machine
166 * be sure to be in the directory where the out 166 * be sure to be in the directory where the output ROOT files have been created
167 * do: root plot.C 167 * do: root plot.C
168 * or under your ROOT session, type in : .X plo 168 * or under your ROOT session, type in : .X plot.C to execute the macro file
169 169
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171 171
172 Should you have any enquiry, please do not hes 172 Should you have any enquiry, please do not hesitate to contact:
173 incerti@cenbg.in2p3.fr 173 incerti@cenbg.in2p3.fr