| Geant4 Cross Reference |
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