| Geant4 Cross Reference |
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2 ---------------------------------------------- << 2 $Id: README,v 1.8 2006/06/23 10:53:39 sincerti Exp $
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4 ========================================= << 4
5 Geant4 - Microbeam example << 5 =========================================================
6 ========================================= << 6 Geant4 - Microbeam example
7 << 7 =========================================================
8 README file << 8
9 -------------------- << 9 README file
10 << 10 ----------------------
11 CORRESPONDING AUTHO << 11
12 << 12 CORRESPONDING AUTHOR
13 S. Incerti (a, *) et al. << 13
14 a. Centre d'Etudes Nucleaires de Bordeaux-Grad << 14 S. Incerti (a, *) et al.
15 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, << 15 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
16 * e-mail:incerti@cenbg.in2p3.fr << 16 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
17 << 17 * e-mail:incerti@cenbg.in2p3.fr
18 ---->0. INTRODUCTION. << 18
19 << 19 Last modified by S. Incerti, 23/06/2006
20 The microbeam example simulates the cellular i << 20
21 installed on the AIFIRA electrostatic accelera << 21 ---->0. INTRODUCTION.
22 CENBG, Bordeaux-Gradignan, France. For more in << 22
23 please visit : << 23 The microbeam example simulates the cellular irradiation beam line
24 http://www.cenbg.in2p3.fr/ << 24 installed on the AIFIRA electrostatic accelerator facility located at
25 << 25 CENBG, Bordeaux-Gradignan, France. For more information on this facility,
26 ---->1. GEOMETRY SET-UP. << 26 please visit :
27 << 27 http://www.cenbg.in2p3.fr/
28 The elements simulated are: << 28
29 << 29
30 1. A switching dipole magnet with fringing fie << 30 ---->1. GEOMETRY SET-UP.
31 beam generated by the electrostatic accelerato << 31
32 oriented at 10 degrees from the main beam dire << 32 The elements simulated are:
33 << 33
34 2. A circular collimator object, defining the << 34 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
35 microbeam line entrance; << 35 beam generated by the electrostatic accelerator into the microbeam line,
36 << 36 oriented at 10 degrees from the main beam direction;
37 3. A quadrupole based magnetic symmetric focus << 37
38 transverse demagnifications of 10. Fringe fiel << 38 2. A circular collimator object, defining the incident beam size at the
39 model. << 39 microbeam line entrance;
40 << 40
41 4. A dedicated cellular irradiation chamber se << 41 3. A quadrupole based magnetic symmetric focusing system allowing equal
42 << 42 transverse demagnifications of 10. Fringe fields are calculated from Enge's
43 5. A set of horizontal and vertical electrosta << 43 model.
44 be turned on or off to deflect the beam on tar << 44
45 << 45 4. A dedicated cellular irradiation chamber setup;
46 6. A realistic human keratinocyte voxellized c << 46
47 microscopy and taking into account realistic n << 47 5. A set of horizontal and vertical electrostatic deflecting plates which can
48 compositions. << 48 be turned on or off to deflect the beam on target;
49 << 49
50 << 50 6. A realistic human keratinocyte voxellized cell observed from confocal
51 ---->2. EXPERIMENTAL SET-UP. << 51 microscopy and taking into account realistic nucleus and cytoplasm chemical
52 << 52 compositions
53 The beam is defined at the microbeam line entr << 53
54 5 micrometer in diameter. The beam is then foc << 54
55 quadruplet of quadrupoles in the so-called Dym << 55 ---->2. EXPERIMENTAL SET-UP.
56 The beam is sent to the irradiation chamber wh << 56
57 isobutane gas detector for counting purpose be << 57 The beam is defined at the microbeam line entrance through a collimator
58 culture foil of the target cell which is immer << 58 5 micrometer in diameter. The beam is then focused onto target using a
59 enclosed within a dish. << 59 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
60 << 60 The beam is sent to the irradiation chamber where it travels through a
61 A cell is placed on the polypropylene foil and << 61 isobutane gas detector for counting purpose before reaching the polypropylene
62 microbeam. The cell is represented through a 3 << 62 culture foil of the target cell which is immersed in the growing medium and
63 obtained from confocal microscopy. In the prov << 63 enclosed within a dish.
64 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) << 64
65 << 65 A cell is placed on the polypropylene foil and is irradiated using the
66 The primary particle beam parameters are gener << 66 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
67 measurements performed on the AIFIRA facility. << 67 obtained from confocal microscopy. In the provided example, the voxels sizes
68 cellular irradiation are 3 MeV alpha particles << 68 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
69 << 69
70 More details on the experimental setup and its << 70 The primary particle beam parameters are generated from experimental
71 be found in the following papers: << 71 measurements performed on the AIFIRA facility. Incident particle used for
72 << 72 cellular irradiation are 3 MeV alpha particles.
73 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO N << 73
74 RADIATION << 74 More details on the experimental setup and its simulation with Geant4 can
75 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. << 75 be found in the following papers :
76 Publsihed in Comp. Math. Meth. Med. (2012) 147 << 76
77 << 77 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
78 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRA << 78 By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec
79 A MICROBEAM FACILITY << 79 To be published in NIMB, 2006
80 By S. Incerti, H. Seznec, M. Simon, Ph. Barber << 80
81 Published in Rad. Prot. Dos. 133, 1 (2009) 2-1 << 81 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
82 << 82 INDIVIDUAL CELLS.
83 - MONTE CARLO SIMULATION OF THE CENBG MICROBEA << 83 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
84 GEANT4 TOOLKIT << 84 Th. Pouthier (CENBG, Gradignan),. Dec 2004. 6pp.
85 By S. Incerti, Q. Zhang, F. Andersson, Ph. Mor << 85 Published in Rev.Sci.Instrum.76:015101, 2005
86 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pout << 86
87 Published in Nucl. Instrum. and Meth. B 260 (2 << 87 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
88 << 88 GEANT4.
89 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQ << 89 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
90 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT << 90 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith
91 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefa << 91 (CENBG, Gradignan),. Oct 2003. 6pp.
92 T. Pouthier, H. Seznec. Dec 2006. 3pp. << 92 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
93 Published in Rad. Prot. Dos. 122, 1-4, (2006) << 93
94 << 94
95 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND << 95 ---->3. SET-UP
96 By S. Incerti, C. Habchi, Ph. Moretto, J. Oliv << 96
97 Published in Nucl.Instrum.Meth.B249:738-742, 2 << 97 - a standard Geant4 example GNUmakefile is provided
98 << 98
99 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE << 99 setup with:
100 SYSTEMS << 100 compiler = gcc-3.2.3
101 By S. Incerti et al., << 101 G4SYSTEM = linux-g++
102 Published in Nucl.Instrum.Meth.B231:76-85, 200 << 102
103 << 103 The following section gives the necessary environment variables.
104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MI << 104
105 INDIVIDUAL CELLS. << 105 ------->>3.1 ENVIRONMENT VARIABLES
106 By Ph. Barberet, A. Balana, S. Incerti, C. Mic << 106
107 Th. Pouthier. Dec 2004. 6pp. << 107 All variables are defined with their default value.
108 Published in Rev.Sci.Instrum.76:015101, 2005 << 108
109 << 109 - G4SYSTEM = Linux-g++
110 - SIMULATION OF CELLULAR IRRADIATION WITH THE << 110
111 GEANT4. << 111 - G4INSTALL points to the installation directory of GEANT4;
112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. << 112
113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, << 113 - G4LIB point to the compiled libraries of GEANT4;
114 Published in IEEE Trans.Nucl.Sci.51:1395-1401, << 114
115 << 115 - G4WORKDIR points to the work directory;
116 - SIMULATION OF ION PROPAGATION IN THE MICROBE << 116
117 GEANT4. << 117 - CLHEP_BASE_DIR points to the installation directory of CHLEP;
118 By S. Incerti, Ph. Barberet, B. Courtois, C. M << 118
119 Ph. Moretto. Sep 2003. << 119 - G4LEDATA points to the low energy electromagnetic libraries;
120 Published in Nucl.Instrum.Meth.B210:92-97, 200 << 120
121 << 121 - LD_LIBRARY_PATH = $CLHEP_BASE_DIR/lib
122 << 122
123 ---->3 VISUALIZATION << 123 - G4LEVELGAMMADATA points to the photoevaporation library;
124 << 124
125 The user can visualize the targeted cell thank << 125 - NeutronHPCrossSections points to the neutron data files;
126 << 126
127 ---->4. HOW TO RUN THE EXAMPLE << 127 - G4RADIOACTIVEDATA points to the libraries for radio-active decay
128 << 128 hadronic processes;
129 The code should be compiled with cmake. << 129
130 << 130 However, the $G4LEVELGAMMADATA, $NeutronHPCrossSections and $G4RADIOACTIVEDATA
131 Run the example from your build directory with << 131 variables do not need to be defined for this example.
132 ./microbeam microbeam.mac << 132
133 << 133 Once these variables have been set, simply type gmake to compile the Microbeam
134 or in interactive mode: << 134 example.
135 ./microbeam << 135
136 << 136 ------->>3.2 VISUALIZATION
137 The example works in MT mode. << 137
138 << 138 The user can visualize the targeted cell with OpenGL, DAWN and vrml,
139 ---->5. PHYSICS << 139 as chosen in the microbeam.mac file. OpenGL is the default viewer. The
140 << 140 cytoplasm in shown in red and the nucleus in green.
141 Livermore physics list is used by default. << 141
142 << 142
143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS << 143 ---->4. HOW TO RUN THE EXAMPLE
144 << 144
145 The output results consist in a microbeam.root << 145 In interactive mode, run:
146 containing several ntuples: << 146
147 << 147 > $G4WORDIR/bin/Linux-g++/Microbeam
148 * total deposited dose in the cell nucleus and << 148
149 cytoplasm by each incident alpha particle; << 149 The macro microbeam.mac is executed by default. To get vizualisation, make
150 << 150 sure to uncomment the /vis/... lines in the microbeam.mac macro.
151 * average on the whole run of the dose deposit << 151 The Microbeam code reads the phantom.dat file containing all the necessary
152 Voxel per incident alpha particle; << 152 information describing the cell phantom. 10 alphas particles are generated.
153 << 153
154 * final stopping (x,y,z) position of the incid << 154
155 alpha particle within the irradiated medium (c << 155 ---->5. PHYSICS
156 << 156
157 * stopping power dE/dx of the incident << 157 Low energy electromagnetic processes (for alphas, electrons, photons) and
158 alpha particle just before penetrating into th << 158 hadronic elastic and inelastic scattering for alphas are activated by default.
159 << 159 Low energy electromagnetic electronic and nuclear stopping power are computed
160 * beam transverse position distribution (X and << 160 from ICRU tables.
161 just before penetrating into the targeted cell << 161
162 << 162
163 These results can be easily analyzed using for << 163 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
164 file plot.C; to do so : << 164
165 * be sure to have ROOT installed on your machi << 165 This example does not need any external analysis package.
166 * be sure to be in the directory where the out << 166 The output results consists in several .txt files:
167 * do: root plot.C << 167
168 * or under your ROOT session, type in : .X plo << 168 * dose.txt : gives the total deposited dose in the cell nucleus and in the cell
169 << 169 cytoplasm by each incident alpha particle;
170 ---------------------------------------------- << 170
171 << 171 * 3DDose.txt : gives the average on the whole run of the dose deposited per
172 Should you have any enquiry, please do not hes << 172 Voxel per incident alpha particle;
173 incerti@cenbg.in2p3.fr << 173
>> 174 * range.txt : indicates the final stopping (x,y,z) position of the incident
>> 175 alpha particle within the irradiated medium (cell or culture medium)
>> 176
>> 177 * stoppingPower.txt : gives the actual stopping power dE/dx of the incident
>> 178 alpha particle just before penetrating into the targeted cell;
>> 179
>> 180 * beamPosition.txt : gives the beam transverse position distribution(X and Y)
>> 181 just before penetrating into the targeted cell;
>> 182
>> 183 These files can be easily analyzed using for example the provided ROOT macro
>> 184 file plot.C; to do so :
>> 185 * be sure to have ROOT installed on your machine
>> 186 * be sure to be in the microbeam directory
>> 187 * launch ROOT by typing root
>> 188 * under your ROOT session, type in : .X plot.C to execute the macro file
>> 189
>> 190 A graphical output obtained with this macro for 40000 incident alpha particles
>> 191 is shown in the file microbeam.gif
>> 192
>> 193 The simulation predicts that 95% of the incident alpha particles detected by the
>> 194 gas detector are located within a circle of 10 um in diameter on the target, in
>> 195 nice agreement with experimental measurements performed on the CENBG setup.
>> 196
>> 197 ---------------------------------------------------------------------------
>> 198
>> 199 Should you have any enquiry, please do not hesitate to contact:
>> 200 incerti@cenbg.in2p3.fr