| 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
>> 29 An overall description of this example is also available in this directory:
>> 30 to access it, simply open the microbeam.htm file with your internet browser.
>> 31
26 ---->1. GEOMETRY SET-UP. 32 ---->1. GEOMETRY SET-UP.
27 33
28 The elements simulated are: 34 The elements simulated are:
29 35
30 1. A switching dipole magnet with fringing fie 36 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
31 beam generated by the electrostatic accelerato 37 beam generated by the electrostatic accelerator into the microbeam line,
32 oriented at 10 degrees from the main beam dire 38 oriented at 10 degrees from the main beam direction;
33 39
34 2. A circular collimator object, defining the 40 2. A circular collimator object, defining the incident beam size at the
35 microbeam line entrance; 41 microbeam line entrance;
36 42
37 3. A quadrupole based magnetic symmetric focus 43 3. A quadrupole based magnetic symmetric focusing system allowing equal
38 transverse demagnifications of 10. Fringe fiel 44 transverse demagnifications of 10. Fringe fields are calculated from Enge's
39 model. 45 model.
40 46
41 4. A dedicated cellular irradiation chamber se 47 4. A dedicated cellular irradiation chamber setup;
42 48
43 5. A set of horizontal and vertical electrosta 49 5. A set of horizontal and vertical electrostatic deflecting plates which can
44 be turned on or off to deflect the beam on tar 50 be turned on or off to deflect the beam on target;
45 51
46 6. A realistic human keratinocyte voxellized c 52 6. A realistic human keratinocyte voxellized cell observed from confocal
47 microscopy and taking into account realistic n 53 microscopy and taking into account realistic nucleus and cytoplasm chemical
48 compositions. << 54 compositions
49 55
50 56
51 ---->2. EXPERIMENTAL SET-UP. 57 ---->2. EXPERIMENTAL SET-UP.
52 58
53 The beam is defined at the microbeam line entr 59 The beam is defined at the microbeam line entrance through a collimator
54 5 micrometer in diameter. The beam is then foc 60 5 micrometer in diameter. The beam is then focused onto target using a
55 quadruplet of quadrupoles in the so-called Dym 61 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
56 The beam is sent to the irradiation chamber wh 62 The beam is sent to the irradiation chamber where it travels through a
57 isobutane gas detector for counting purpose be 63 isobutane gas detector for counting purpose before reaching the polypropylene
58 culture foil of the target cell which is immer 64 culture foil of the target cell which is immersed in the growing medium and
59 enclosed within a dish. 65 enclosed within a dish.
60 66
61 A cell is placed on the polypropylene foil and 67 A cell is placed on the polypropylene foil and is irradiated using the
62 microbeam. The cell is represented through a 3 68 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
63 obtained from confocal microscopy. In the prov 69 obtained from confocal microscopy. In the provided example, the voxels sizes
64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) 70 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
65 71
66 The primary particle beam parameters are gener 72 The primary particle beam parameters are generated from experimental
67 measurements performed on the AIFIRA facility. 73 measurements performed on the AIFIRA facility. Incident particle used for
68 cellular irradiation are 3 MeV alpha particles 74 cellular irradiation are 3 MeV alpha particles.
69 75
70 More details on the experimental setup and its 76 More details on the experimental setup and its simulation with Geant4 can
71 be found in the following papers: << 77 be found in the following papers, which may be found on the SLAC-SPIRES
72 << 78 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 79
78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRA 80 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
79 A MICROBEAM FACILITY 81 A MICROBEAM FACILITY
80 By S. Incerti, H. Seznec, M. Simon, Ph. Barber 82 By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 83 Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
82 84
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA 85 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
84 GEANT4 TOOLKIT 86 GEANT4 TOOLKIT
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor 87 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout 88 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
87 Published in Nucl. Instrum. and Meth. B 260 (2 89 Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
88 90
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ 91 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT 92 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa 93 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. 94 T. Pouthier, H. Seznec. Dec 2006. 3pp.
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) 95 Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
94 96
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND 97 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv 98 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 99 Published in Nucl.Instrum.Meth.B249:738-742, 2006
98 100
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE 101 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
100 SYSTEMS 102 SYSTEMS
101 By S. Incerti et al., 103 By S. Incerti et al.,
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 104 Published in Nucl.Instrum.Meth.B231:76-85, 2005
103 105
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI 106 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
105 INDIVIDUAL CELLS. 107 INDIVIDUAL CELLS.
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic 108 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
107 Th. Pouthier. Dec 2004. 6pp. 109 Th. Pouthier. Dec 2004. 6pp.
108 Published in Rev.Sci.Instrum.76:015101, 2005 110 Published in Rev.Sci.Instrum.76:015101, 2005
109 111
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE 112 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
111 GEANT4. 113 GEANT4.
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. 114 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, 115 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, 116 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
115 117
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE 118 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
117 GEANT4. 119 GEANT4.
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M 120 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
119 Ph. Moretto. Sep 2003. 121 Ph. Moretto. Sep 2003.
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 122 Published in Nucl.Instrum.Meth.B210:92-97, 2003
121 123
122 124
123 ---->3 VISUALIZATION << 125 ------->3 VISUALIZATION
124 126
125 The user can visualize the targeted cell thank << 127 The user can visualize the targeted cell by uncommenting the following line in
>> 128 microbeam.mac:
>> 129 #/control/execute vis.mac
126 130
127 ---->4. HOW TO RUN THE EXAMPLE 131 ---->4. HOW TO RUN THE EXAMPLE
>> 132
>> 133 The variable G4ANALYSIS_USE must be set to 1.
>> 134
>> 135 In order to generate histograms, at least one of the AIDA implementations should be
>> 136 available.
128 137
129 The code should be compiled with cmake. << 138 The code should be compiled with gmake and run with :
130 139
131 Run the example from your build directory with << 140 > $G4WORDIR/bin/$G4SYSTEM/Microbeam
132 ./microbeam microbeam.mac <<
133 141
134 or in interactive mode: << 142 The macro file microbeam.mac is read by default.
135 ./microbeam <<
136 143
137 The example works in MT mode. <<
138 144
139 ---->5. PHYSICS 145 ---->5. PHYSICS
140 146
141 Livermore physics list is used by default. << 147 Livermore, Binary and Binary_ion physics lists are used by default,
>> 148 see microbeam.mac
142 149
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS 150 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
144 151
145 The output results consist in a microbeam.root << 152 The output results consist in several a microbeam.root file, containing several
146 containing several ntuples: << 153 ntuples:
147 154
148 * total deposited dose in the cell nucleus and 155 * total deposited dose in the cell nucleus and in the cell
149 cytoplasm by each incident alpha particle; 156 cytoplasm by each incident alpha particle;
150 157
151 * average on the whole run of the dose deposit 158 * average on the whole run of the dose deposited per
152 Voxel per incident alpha particle; 159 Voxel per incident alpha particle;
153 160
154 * final stopping (x,y,z) position of the incid 161 * final stopping (x,y,z) position of the incident
155 alpha particle within the irradiated medium (c << 162 alpha particle within the irradiated medium (cell or culture medium)
156 163
157 * stopping power dE/dx of the incident 164 * stopping power dE/dx of the incident
158 alpha particle just before penetrating into th 165 alpha particle just before penetrating into the targeted cell;
159 166
160 * beam transverse position distribution (X and << 167 * beam transverse position distribution(X and Y)
161 just before penetrating into the targeted cell 168 just before penetrating into the targeted cell;
162 169
163 These results can be easily analyzed using for 170 These results can be easily analyzed using for example the provided ROOT macro
164 file plot.C; to do so : 171 file plot.C; to do so :
165 * be sure to have ROOT installed on your machi 172 * be sure to have ROOT installed on your machine
166 * be sure to be in the directory where the out << 173 * be sure to be in the microbeam directory
167 * do: root plot.C << 174 * launch ROOT by typing root
168 * or under your ROOT session, type in : .X plo << 175 * under your ROOT session, type in : .X plot.C to execute the macro file
>> 176
169 177
170 ---------------------------------------------- 178 ---------------------------------------------------------------------------
171 179
172 Should you have any enquiry, please do not hes 180 Should you have any enquiry, please do not hesitate to contact:
173 incerti@cenbg.in2p3.fr 181 incerti@cenbg.in2p3.fr