| Geant4 Cross Reference |
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>> 2 $Id: README,v 1.10 2007/02/27 12:02:09 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, 27/02/2007
>> 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, T. Pouthier, H. Seznec, Ph. Moretto, O. Boissonnade,
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 << 83 T. M. H. Ha, F. Andersson, Ph. Barberet, C. Habchi and D. T. Nguyen
>> 84 In preparation (2007)
82 85
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA 86 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
84 GEANT4 TOOLKIT 87 GEANT4 TOOLKIT
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor 88 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout 89 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
87 Published in Nucl. Instrum. and Meth. B 260 (2 << 90 In press in Nucl.Instrum.Meth.B, 2007
88 91
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ 92 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT 93 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa 94 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. 95 T. Pouthier, H. Seznec. Dec 2006. 3pp.
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) << 96 Published in Rad.Prot.Dos.,1-3,2006 (Micros 2005 special issue).
94 97
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND 98 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv 99 By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp.
97 Published in Nucl.Instrum.Meth.B249:738-742, 2 100 Published in Nucl.Instrum.Meth.B249:738-742, 2006
98 101
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE 102 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
100 SYSTEMS 103 SYSTEMS
101 By S. Incerti et al., 104 By S. Incerti et al.,
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 105 Published in Nucl.Instrum.Meth.B231:76-85, 2005
103 106
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI 107 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
105 INDIVIDUAL CELLS. 108 INDIVIDUAL CELLS.
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic 109 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
107 Th. Pouthier. Dec 2004. 6pp. 110 Th. Pouthier. Dec 2004. 6pp.
108 Published in Rev.Sci.Instrum.76:015101, 2005 111 Published in Rev.Sci.Instrum.76:015101, 2005
109 112
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE 113 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
111 GEANT4. 114 GEANT4.
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. 115 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, 116 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, 117 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
115 118
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE 119 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
117 GEANT4. 120 GEANT4.
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M 121 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
119 Ph. Moretto. Sep 2003. 122 Ph. Moretto. Sep 2003.
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 123 Published in Nucl.Instrum.Meth.B210:92-97, 2003
121 124
122 125
123 ---->3 VISUALIZATION << 126 ---->3. SET-UP
>> 127
>> 128 - a standard Geant4 example GNUmakefile is provided
>> 129
>> 130 setup with:
>> 131 compiler = gcc-3.2.3
>> 132 G4SYSTEM = linux-g++
>> 133
>> 134 The following section gives the necessary environment variables.
>> 135
>> 136 ------->>3.1 ENVIRONMENT VARIABLES
>> 137
>> 138 All variables are defined with their default value.
>> 139
>> 140 - G4SYSTEM = Linux-g++
>> 141
>> 142 - G4INSTALL points to the installation directory of GEANT4;
>> 143
>> 144 - G4LIB point to the compiled libraries of GEANT4;
>> 145
>> 146 - G4WORKDIR points to the work directory;
>> 147
>> 148 - CLHEP_BASE_DIR points to the installation directory of CHLEP;
>> 149
>> 150 - G4LEDATA points to the low energy electromagnetic libraries;
>> 151
>> 152 - LD_LIBRARY_PATH = $CLHEP_BASE_DIR/lib
>> 153
>> 154 - G4LEVELGAMMADATA points to the photoevaporation library;
>> 155
>> 156 - NeutronHPCrossSections points to the neutron data files;
>> 157
>> 158 - G4RADIOACTIVEDATA points to the libraries for radio-active decay
>> 159 hadronic processes;
>> 160
>> 161 However, the $G4LEVELGAMMADATA, $NeutronHPCrossSections and $G4RADIOACTIVEDATA
>> 162 variables do not need to be defined for this example.
>> 163
>> 164 Once these variables have been set, simply type gmake to compile the Microbeam
>> 165 example.
>> 166
>> 167 ------->>3.2 VISUALIZATION
>> 168
>> 169 The user can visualize the targeted cell with OpenGL, DAWN and vrml,
>> 170 as chosen in the microbeam.mac file. OpenGL is the default viewer. The
>> 171 cytoplasm in shown in red and the nucleus in green.
124 172
125 The user can visualize the targeted cell thank <<
126 173
127 ---->4. HOW TO RUN THE EXAMPLE 174 ---->4. HOW TO RUN THE EXAMPLE
128 <<
129 The code should be compiled with cmake. <<
130 175
131 Run the example from your build directory with << 176 In interactive mode, run:
132 ./microbeam microbeam.mac << 177
>> 178 > $G4WORDIR/bin/Linux-g++/Microbeam
133 179
134 or in interactive mode: << 180 The macro microbeam.mac is executed by default. To get vizualisation, make
135 ./microbeam << 181 sure to uncomment the /vis/... lines in the microbeam.mac macro.
>> 182 The Microbeam code reads the phantom.dat file containing all the necessary
>> 183 information describing the cell phantom. 10 alphas particles are generated.
136 184
137 The example works in MT mode. <<
138 185
139 ---->5. PHYSICS 186 ---->5. PHYSICS
140 187
141 Livermore physics list is used by default. << 188 Low energy electromagnetic processes (for alphas, electrons, photons) and
>> 189 hadronic elastic and inelastic scattering for alphas are activated by default.
>> 190 Low energy electromagnetic electronic and nuclear stopping power are computed
>> 191 from ICRU tables.
>> 192
142 193
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS 194 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
144 195
145 The output results consist in a microbeam.root << 196 This example does not need any external analysis package.
146 containing several ntuples: << 197 The output results consists in several .txt files:
147 198
148 * total deposited dose in the cell nucleus and << 199 * dose.txt : gives the total deposited dose in the cell nucleus and in the cell
149 cytoplasm by each incident alpha particle; 200 cytoplasm by each incident alpha particle;
150 201
151 * average on the whole run of the dose deposit << 202 * 3DDose.txt : gives the average on the whole run of the dose deposited per
152 Voxel per incident alpha particle; 203 Voxel per incident alpha particle;
153 204
154 * final stopping (x,y,z) position of the incid << 205 * range.txt : indicates the final stopping (x,y,z) position of the incident
155 alpha particle within the irradiated medium (c << 206 alpha particle within the irradiated medium (cell or culture medium)
156 207
157 * stopping power dE/dx of the incident << 208 * stoppingPower.txt : gives the actual stopping power dE/dx of the incident
158 alpha particle just before penetrating into th 209 alpha particle just before penetrating into the targeted cell;
159 210
160 * beam transverse position distribution (X and << 211 * beamPosition.txt : gives the beam transverse position distribution(X and Y)
161 just before penetrating into the targeted cell 212 just before penetrating into the targeted cell;
162 213
163 These results can be easily analyzed using for << 214 These files can be easily analyzed using for example the provided ROOT macro
164 file plot.C; to do so : 215 file plot.C; to do so :
165 * be sure to have ROOT installed on your machi 216 * be sure to have ROOT installed on your machine
166 * be sure to be in the directory where the out << 217 * be sure to be in the microbeam directory
167 * do: root plot.C << 218 * launch ROOT by typing root
168 * or under your ROOT session, type in : .X plo << 219 * under your ROOT session, type in : .X plot.C to execute the macro file
>> 220
>> 221 A graphical output obtained with this macro for 40000 incident alpha particles
>> 222 is shown in the file microbeam.gif
>> 223
>> 224 The simulation predicts that 95% of the incident alpha particles detected by the
>> 225 gas detector are located within a circle of 10 um in diameter on the target, in
>> 226 nice agreement with experimental measurements performed on the CENBG setup.
169 227
170 ---------------------------------------------- 228 ---------------------------------------------------------------------------
171 229
172 Should you have any enquiry, please do not hes 230 Should you have any enquiry, please do not hesitate to contact:
173 incerti@cenbg.in2p3.fr 231 incerti@cenbg.in2p3.fr