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Geant4/examples/advanced/microbeam/

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File README 6748 bytes       2024-12-05 15:16:16
C++ file microbeam.cc 3558 bytes       2024-12-05 15:16:16
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File vis.mac 1976 bytes       2024-12-05 15:16:16

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