| Geant4 Cross Reference |
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>> 2 $Id: README,v 1.12 2010-10-07 14:03:11 sincerti Exp $
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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
>> 19 Last modified by S. Incerti, 07/10/2010
>> 20
18 ---->0. INTRODUCTION. 21 ---->0. INTRODUCTION.
19 22
20 The microbeam example simulates the cellular i 23 The microbeam example simulates the cellular irradiation beam line
21 installed on the AIFIRA electrostatic accelera 24 installed on the AIFIRA electrostatic accelerator facility located at
22 CENBG, Bordeaux-Gradignan, France. For more in 25 CENBG, Bordeaux-Gradignan, France. For more information on this facility,
23 please visit : 26 please visit :
24 http://www.cenbg.in2p3.fr/ 27 http://www.cenbg.in2p3.fr/
25 28
26 ---->1. GEOMETRY SET-UP. 29 ---->1. GEOMETRY SET-UP.
27 30
28 The elements simulated are: 31 The elements simulated are:
29 32
30 1. A switching dipole magnet with fringing fie 33 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
31 beam generated by the electrostatic accelerato 34 beam generated by the electrostatic accelerator into the microbeam line,
32 oriented at 10 degrees from the main beam dire 35 oriented at 10 degrees from the main beam direction;
33 36
34 2. A circular collimator object, defining the 37 2. A circular collimator object, defining the incident beam size at the
35 microbeam line entrance; 38 microbeam line entrance;
36 39
37 3. A quadrupole based magnetic symmetric focus 40 3. A quadrupole based magnetic symmetric focusing system allowing equal
38 transverse demagnifications of 10. Fringe fiel 41 transverse demagnifications of 10. Fringe fields are calculated from Enge's
39 model. 42 model.
40 43
41 4. A dedicated cellular irradiation chamber se 44 4. A dedicated cellular irradiation chamber setup;
42 45
43 5. A set of horizontal and vertical electrosta 46 5. A set of horizontal and vertical electrostatic deflecting plates which can
44 be turned on or off to deflect the beam on tar 47 be turned on or off to deflect the beam on target;
45 48
46 6. A realistic human keratinocyte voxellized c 49 6. A realistic human keratinocyte voxellized cell observed from confocal
47 microscopy and taking into account realistic n 50 microscopy and taking into account realistic nucleus and cytoplasm chemical
48 compositions. << 51 compositions
49 52
50 53
51 ---->2. EXPERIMENTAL SET-UP. 54 ---->2. EXPERIMENTAL SET-UP.
52 55
53 The beam is defined at the microbeam line entr 56 The beam is defined at the microbeam line entrance through a collimator
54 5 micrometer in diameter. The beam is then foc 57 5 micrometer in diameter. The beam is then focused onto target using a
55 quadruplet of quadrupoles in the so-called Dym 58 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
56 The beam is sent to the irradiation chamber wh 59 The beam is sent to the irradiation chamber where it travels through a
57 isobutane gas detector for counting purpose be 60 isobutane gas detector for counting purpose before reaching the polypropylene
58 culture foil of the target cell which is immer 61 culture foil of the target cell which is immersed in the growing medium and
59 enclosed within a dish. 62 enclosed within a dish.
60 63
61 A cell is placed on the polypropylene foil and 64 A cell is placed on the polypropylene foil and is irradiated using the
62 microbeam. The cell is represented through a 3 65 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
63 obtained from confocal microscopy. In the prov 66 obtained from confocal microscopy. In the provided example, the voxels sizes
64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) 67 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
65 68
66 The primary particle beam parameters are gener 69 The primary particle beam parameters are generated from experimental
67 measurements performed on the AIFIRA facility. 70 measurements performed on the AIFIRA facility. Incident particle used for
68 cellular irradiation are 3 MeV alpha particles 71 cellular irradiation are 3 MeV alpha particles.
69 72
70 More details on the experimental setup and its 73 More details on the experimental setup and its simulation with Geant4 can
71 be found in the following papers: << 74 be found in the following papers, which may be found on the SLAC-SPIRES
72 << 75 online database (http://www.slac.stanford.edu/spires/) :
73 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO N <<
74 RADIATION <<
75 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. <<
76 Publsihed in Comp. Math. Meth. Med. (2012) 147 <<
77 76
78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRA 77 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
79 A MICROBEAM FACILITY 78 A MICROBEAM FACILITY
80 By S. Incerti, H. Seznec, M. Simon, Ph. Barber 79 By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 80 Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
82 81
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA 82 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
84 GEANT4 TOOLKIT 83 GEANT4 TOOLKIT
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor 84 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout 85 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
87 Published in Nucl. Instrum. and Meth. B 260 (2 86 Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
88 87
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ 88 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT 89 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa 90 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. 91 T. Pouthier, H. Seznec. Dec 2006. 3pp.
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) 92 Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
94 93
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND 94 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv 95 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 96 Published in Nucl.Instrum.Meth.B249:738-742, 2006
98 97
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE 98 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
100 SYSTEMS 99 SYSTEMS
101 By S. Incerti et al., 100 By S. Incerti et al.,
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 101 Published in Nucl.Instrum.Meth.B231:76-85, 2005
103 102
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI 103 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
105 INDIVIDUAL CELLS. 104 INDIVIDUAL CELLS.
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic 105 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
107 Th. Pouthier. Dec 2004. 6pp. 106 Th. Pouthier. Dec 2004. 6pp.
108 Published in Rev.Sci.Instrum.76:015101, 2005 107 Published in Rev.Sci.Instrum.76:015101, 2005
109 108
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE 109 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
111 GEANT4. 110 GEANT4.
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. 111 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, 112 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, 113 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
115 114
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE 115 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
117 GEANT4. 116 GEANT4.
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M 117 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
119 Ph. Moretto. Sep 2003. 118 Ph. Moretto. Sep 2003.
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 119 Published in Nucl.Instrum.Meth.B210:92-97, 2003
121 120
122 121
123 ---->3 VISUALIZATION << 122 ------->3 VISUALIZATION
124 123
125 The user can visualize the targeted cell thank << 124 The user can visualize the targeted cell by uncommenting the following line in
>> 125 microbeam.mac:
>> 126 #/control/execute vis.mac
126 127
127 ---->4. HOW TO RUN THE EXAMPLE 128 ---->4. HOW TO RUN THE EXAMPLE
>> 129
>> 130 The variable G4ANALYSIS_USE must be set to 1.
>> 131
>> 132 In order to generate histograms, at least one of the AIDA implementations should be
>> 133 available.
128 134
129 The code should be compiled with cmake. << 135 The code should be compiled with gmake and run with :
130 136
131 Run the example from your build directory with << 137 > $G4WORDIR/bin/$G4SYSTEM/microbeam
132 ./microbeam microbeam.mac <<
133 138
134 or in interactive mode: << 139 The macro file microbeam.mac is read by default.
135 ./microbeam <<
136 140
137 The example works in MT mode. <<
138 141
139 ---->5. PHYSICS 142 ---->5. PHYSICS
140 143
141 Livermore physics list is used by default. << 144 Livermore physics list is used by default, see microbeam.mac
142 145
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS 146 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
144 147
145 The output results consist in a microbeam.root << 148 The output results consist in several a microbeam.root file, containing several
146 containing several ntuples: << 149 ntuples:
147 150
148 * total deposited dose in the cell nucleus and 151 * total deposited dose in the cell nucleus and in the cell
149 cytoplasm by each incident alpha particle; 152 cytoplasm by each incident alpha particle;
150 153
151 * average on the whole run of the dose deposit 154 * average on the whole run of the dose deposited per
152 Voxel per incident alpha particle; 155 Voxel per incident alpha particle;
153 156
154 * final stopping (x,y,z) position of the incid 157 * final stopping (x,y,z) position of the incident
155 alpha particle within the irradiated medium (c << 158 alpha particle within the irradiated medium (cell or culture medium)
156 159
157 * stopping power dE/dx of the incident 160 * stopping power dE/dx of the incident
158 alpha particle just before penetrating into th 161 alpha particle just before penetrating into the targeted cell;
159 162
160 * beam transverse position distribution (X and << 163 * beam transverse position distribution(X and Y)
161 just before penetrating into the targeted cell 164 just before penetrating into the targeted cell;
162 165
163 These results can be easily analyzed using for 166 These results can be easily analyzed using for example the provided ROOT macro
164 file plot.C; to do so : 167 file plot.C; to do so :
165 * be sure to have ROOT installed on your machi 168 * be sure to have ROOT installed on your machine
166 * be sure to be in the directory where the out << 169 * be sure to be in the microbeam directory
167 * do: root plot.C << 170 * launch ROOT by typing root
168 * or under your ROOT session, type in : .X plo << 171 * under your ROOT session, type in : .X plot.C to execute the macro file
>> 172
169 173
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171 175
172 Should you have any enquiry, please do not hes 176 Should you have any enquiry, please do not hesitate to contact:
173 incerti@cenbg.in2p3.fr 177 incerti@cenbg.in2p3.fr