| Geant4 Cross Reference |
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>> 2 $Id: README 70524 2013-05-31 16:36:26Z gcosmo $
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3 4
4 ========================================= 5 =========================================================
5 Geant4 - Microbeam example 6 Geant4 - Microbeam example
6 ========================================= 7 =========================================================
7 8
8 README file 9 README file
9 -------------------- 10 ----------------------
10 11
11 CORRESPONDING AUTHO 12 CORRESPONDING AUTHOR
12 13
13 S. Incerti (a, *) et al. 14 S. Incerti (a, *) et al.
14 a. Centre d'Etudes Nucleaires de Bordeaux-Grad 15 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
15 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 16 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
16 * e-mail:incerti@cenbg.in2p3.fr 17 * e-mail:incerti@cenbg.in2p3.fr
17 18
18 ---->0. INTRODUCTION. 19 ---->0. INTRODUCTION.
19 20
20 The microbeam example simulates the cellular i 21 The microbeam example simulates the cellular irradiation beam line
21 installed on the AIFIRA electrostatic accelera 22 installed on the AIFIRA electrostatic accelerator facility located at
22 CENBG, Bordeaux-Gradignan, France. For more in 23 CENBG, Bordeaux-Gradignan, France. For more information on this facility,
23 please visit : 24 please visit :
24 http://www.cenbg.in2p3.fr/ 25 http://www.cenbg.in2p3.fr/
25 26
26 ---->1. GEOMETRY SET-UP. 27 ---->1. GEOMETRY SET-UP.
27 28
28 The elements simulated are: 29 The elements simulated are:
29 30
30 1. A switching dipole magnet with fringing fie 31 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
31 beam generated by the electrostatic accelerato 32 beam generated by the electrostatic accelerator into the microbeam line,
32 oriented at 10 degrees from the main beam dire 33 oriented at 10 degrees from the main beam direction;
33 34
34 2. A circular collimator object, defining the 35 2. A circular collimator object, defining the incident beam size at the
35 microbeam line entrance; 36 microbeam line entrance;
36 37
37 3. A quadrupole based magnetic symmetric focus 38 3. A quadrupole based magnetic symmetric focusing system allowing equal
38 transverse demagnifications of 10. Fringe fiel 39 transverse demagnifications of 10. Fringe fields are calculated from Enge's
39 model. 40 model.
40 41
41 4. A dedicated cellular irradiation chamber se 42 4. A dedicated cellular irradiation chamber setup;
42 43
43 5. A set of horizontal and vertical electrosta 44 5. A set of horizontal and vertical electrostatic deflecting plates which can
44 be turned on or off to deflect the beam on tar 45 be turned on or off to deflect the beam on target;
45 46
46 6. A realistic human keratinocyte voxellized c 47 6. A realistic human keratinocyte voxellized cell observed from confocal
47 microscopy and taking into account realistic n 48 microscopy and taking into account realistic nucleus and cytoplasm chemical
48 compositions. << 49 compositions
49 50
50 51
51 ---->2. EXPERIMENTAL SET-UP. 52 ---->2. EXPERIMENTAL SET-UP.
52 53
53 The beam is defined at the microbeam line entr 54 The beam is defined at the microbeam line entrance through a collimator
54 5 micrometer in diameter. The beam is then foc 55 5 micrometer in diameter. The beam is then focused onto target using a
55 quadruplet of quadrupoles in the so-called Dym 56 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
56 The beam is sent to the irradiation chamber wh 57 The beam is sent to the irradiation chamber where it travels through a
57 isobutane gas detector for counting purpose be 58 isobutane gas detector for counting purpose before reaching the polypropylene
58 culture foil of the target cell which is immer 59 culture foil of the target cell which is immersed in the growing medium and
59 enclosed within a dish. 60 enclosed within a dish.
60 61
61 A cell is placed on the polypropylene foil and 62 A cell is placed on the polypropylene foil and is irradiated using the
62 microbeam. The cell is represented through a 3 63 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
63 obtained from confocal microscopy. In the prov 64 obtained from confocal microscopy. In the provided example, the voxels sizes
64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) 65 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
65 66
66 The primary particle beam parameters are gener 67 The primary particle beam parameters are generated from experimental
67 measurements performed on the AIFIRA facility. 68 measurements performed on the AIFIRA facility. Incident particle used for
68 cellular irradiation are 3 MeV alpha particles 69 cellular irradiation are 3 MeV alpha particles.
69 70
70 More details on the experimental setup and its 71 More details on the experimental setup and its simulation with Geant4 can
71 be found in the following papers: 72 be found in the following papers:
72 73
73 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO N 74 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO NON-TARGETED BIOLOGICAL RESPONSES TO
74 RADIATION 75 RADIATION
75 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. 76 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti
76 Publsihed in Comp. Math. Meth. Med. (2012) 147 77 Publsihed in Comp. Math. Meth. Med. (2012) 147252
77 78
78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRA 79 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
79 A MICROBEAM FACILITY 80 A MICROBEAM FACILITY
80 By S. Incerti, H. Seznec, M. Simon, Ph. Barber 81 By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 82 Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
82 83
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA 84 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
84 GEANT4 TOOLKIT 85 GEANT4 TOOLKIT
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor 86 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout 87 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
87 Published in Nucl. Instrum. and Meth. B 260 (2 88 Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
88 89
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ 90 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT 91 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa 92 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. 93 T. Pouthier, H. Seznec. Dec 2006. 3pp.
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) 94 Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
94 95
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND 96 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv 97 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 98 Published in Nucl.Instrum.Meth.B249:738-742, 2006
98 99
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE 100 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
100 SYSTEMS 101 SYSTEMS
101 By S. Incerti et al., 102 By S. Incerti et al.,
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 103 Published in Nucl.Instrum.Meth.B231:76-85, 2005
103 104
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI 105 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
105 INDIVIDUAL CELLS. 106 INDIVIDUAL CELLS.
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic 107 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
107 Th. Pouthier. Dec 2004. 6pp. 108 Th. Pouthier. Dec 2004. 6pp.
108 Published in Rev.Sci.Instrum.76:015101, 2005 109 Published in Rev.Sci.Instrum.76:015101, 2005
109 110
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE 111 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
111 GEANT4. 112 GEANT4.
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. 113 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, 114 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, 115 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
115 116
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE 117 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
117 GEANT4. 118 GEANT4.
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M 119 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
119 Ph. Moretto. Sep 2003. 120 Ph. Moretto. Sep 2003.
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 121 Published in Nucl.Instrum.Meth.B210:92-97, 2003
121 122
122 123
123 ---->3 VISUALIZATION << 124 ------->3 VISUALIZATION
124 125
125 The user can visualize the targeted cell thank << 126 The user can visualize the targeted cell by uncommenting the following line in
>> 127 microbeam.mac:
>> 128
>> 129 #/control/execute vis.mac
126 130
127 ---->4. HOW TO RUN THE EXAMPLE 131 ---->4. HOW TO RUN THE EXAMPLE
128 132
129 The code should be compiled with cmake. 133 The code should be compiled with cmake.
130 134
131 Run the example from your build directory with << 135 Put the 'phantom.dat' file into your build directory.
132 ./microbeam microbeam.mac <<
133 136
134 or in interactive mode: << 137 Run the example from your build directory with:
135 ./microbeam 138 ./microbeam
136 139
137 The example works in MT mode. << 140 The macro file microbeam.mac is read by default.
>> 141
>> 142 The works in MT mode.
138 143
139 ---->5. PHYSICS 144 ---->5. PHYSICS
140 145
141 Livermore physics list is used by default. 146 Livermore physics list is used by default.
142 147
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS 148 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
144 149
145 The output results consist in a microbeam.root 150 The output results consist in a microbeam.root file per thread,
146 containing several ntuples: 151 containing several ntuples:
147 152
148 * total deposited dose in the cell nucleus and 153 * total deposited dose in the cell nucleus and in the cell
149 cytoplasm by each incident alpha particle; 154 cytoplasm by each incident alpha particle;
150 155
151 * average on the whole run of the dose deposit 156 * average on the whole run of the dose deposited per
152 Voxel per incident alpha particle; 157 Voxel per incident alpha particle;
153 158
154 * final stopping (x,y,z) position of the incid 159 * final stopping (x,y,z) position of the incident
155 alpha particle within the irradiated medium (c << 160 alpha particle within the irradiated medium (cell or culture medium)
156 161
157 * stopping power dE/dx of the incident 162 * stopping power dE/dx of the incident
158 alpha particle just before penetrating into th 163 alpha particle just before penetrating into the targeted cell;
159 164
160 * beam transverse position distribution (X and 165 * beam transverse position distribution (X and Y)
161 just before penetrating into the targeted cell 166 just before penetrating into the targeted cell;
162 167
163 These results can be easily analyzed using for 168 These results can be easily analyzed using for example the provided ROOT macro
164 file plot.C; to do so : 169 file plot.C; to do so :
165 * be sure to have ROOT installed on your machi 170 * be sure to have ROOT installed on your machine
166 * be sure to be in the directory where the out 171 * be sure to be in the directory where the output ROOT files have been created
167 * do: root plot.C << 172 * copy plot.C into this directory
168 * or under your ROOT session, type in : .X plo << 173 * launch ROOT by typing root
>> 174 * under your ROOT session, type in : .X plot.C to execute the macro file
>> 175
169 176
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171 178
172 Should you have any enquiry, please do not hes 179 Should you have any enquiry, please do not hesitate to contact:
173 incerti@cenbg.in2p3.fr 180 incerti@cenbg.in2p3.fr