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| 2 | $Id: README,v 1.12 2010/10/07 14:03:11 sincerti Exp $ |
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| 3 | ------------------------------------------------------------------- |
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| 4 | |
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| 5 | ========================================================= |
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| 6 | Geant4 - Microbeam example |
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| 7 | ========================================================= |
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| 8 | |
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| 9 | README file |
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| 10 | ---------------------- |
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| 11 | |
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| 12 | CORRESPONDING AUTHOR |
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| 13 | |
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| 14 | S. Incerti (a, *) et al. |
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| 15 | a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan |
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| 16 | (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France |
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| 17 | * e-mail:incerti@cenbg.in2p3.fr |
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| 18 | |
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| 19 | Last modified by S. Incerti, 07/10/2010 |
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| 20 | |
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| 21 | ---->0. INTRODUCTION. |
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| 22 | |
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| 23 | The microbeam example simulates the cellular irradiation beam line |
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| 24 | installed on the AIFIRA electrostatic accelerator facility located at |
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| 25 | CENBG, Bordeaux-Gradignan, France. For more information on this facility, |
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| 26 | please visit : |
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| 27 | http://www.cenbg.in2p3.fr/ |
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| 28 | |
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| 29 | An overall description of this example is also available in this directory: |
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| 30 | to access it, simply open the microbeam.htm file with your internet browser. |
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| 31 | |
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| 32 | ---->1. GEOMETRY SET-UP. |
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| 33 | |
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| 34 | The elements simulated are: |
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| 35 | |
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| 36 | 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha |
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| 37 | beam generated by the electrostatic accelerator into the microbeam line, |
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| 38 | oriented at 10 degrees from the main beam direction; |
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| 39 | |
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| 40 | 2. A circular collimator object, defining the incident beam size at the |
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| 41 | microbeam line entrance; |
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| 42 | |
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| 43 | 3. A quadrupole based magnetic symmetric focusing system allowing equal |
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| 44 | transverse demagnifications of 10. Fringe fields are calculated from Enge's |
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| 45 | model. |
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| 46 | |
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| 47 | 4. A dedicated cellular irradiation chamber setup; |
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| 48 | |
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| 49 | 5. A set of horizontal and vertical electrostatic deflecting plates which can |
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| 50 | be turned on or off to deflect the beam on target; |
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| 51 | |
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| 52 | 6. A realistic human keratinocyte voxellized cell observed from confocal |
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| 53 | microscopy and taking into account realistic nucleus and cytoplasm chemical |
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| 54 | compositions |
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| 55 | |
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| 56 | |
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| 57 | ---->2. EXPERIMENTAL SET-UP. |
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| 58 | |
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| 59 | The beam is defined at the microbeam line entrance through a collimator |
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| 60 | 5 micrometer in diameter. The beam is then focused onto target using a |
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| 61 | quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration. |
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| 62 | The beam is sent to the irradiation chamber where it travels through a |
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| 63 | isobutane gas detector for counting purpose before reaching the polypropylene |
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| 64 | culture foil of the target cell which is immersed in the growing medium and |
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| 65 | enclosed within a dish. |
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| 66 | |
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| 67 | A cell is placed on the polypropylene foil and is irradiated using the |
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| 68 | microbeam. The cell is represented through a 3D phantom (G4PVParameterization) |
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| 69 | obtained from confocal microscopy. In the provided example, the voxels sizes |
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| 70 | are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) |
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| 71 | |
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| 72 | The primary particle beam parameters are generated from experimental |
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| 73 | measurements performed on the AIFIRA facility. Incident particle used for |
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| 74 | cellular irradiation are 3 MeV alpha particles. |
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| 75 | |
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| 76 | More details on the experimental setup and its simulation with Geant4 can |
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| 77 | be found in the following papers, which may be found on the SLAC-SPIRES |
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| 78 | online database (http://www.slac.stanford.edu/spires/) : |
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| 79 | |
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| 80 | - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING |
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| 81 | A MICROBEAM FACILITY |
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| 82 | By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto |
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| 83 | Published in Rad. Prot. Dos. 133, 1 (2009) 2-11 |
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| 84 | |
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| 85 | - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE |
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| 86 | GEANT4 TOOLKIT |
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| 87 | By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime, |
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| 88 | M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec |
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| 89 | Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27 |
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| 90 | |
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| 91 | - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING |
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| 92 | THE GEANT4 MONTE CARLO SIMULATION TOOLKIT |
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| 93 | By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy, |
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| 94 | T. Pouthier, H. Seznec. Dec 2006. 3pp. |
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| 95 | Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329 |
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| 96 | |
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| 97 | - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY |
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| 98 | By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp. |
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| 99 | Published in Nucl.Instrum.Meth.B249:738-742, 2006 |
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| 100 | |
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| 101 | - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM |
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| 102 | SYSTEMS |
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| 103 | By S. Incerti et al., |
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| 104 | Published in Nucl.Instrum.Meth.B231:76-85, 2005 |
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| 105 | |
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| 106 | - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF |
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| 107 | INDIVIDUAL CELLS. |
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| 108 | By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto, |
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| 109 | Th. Pouthier. Dec 2004. 6pp. |
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| 110 | Published in Rev.Sci.Instrum.76:015101, 2005 |
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| 111 | |
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| 112 | - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING |
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| 113 | GEANT4. |
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| 114 | By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier, |
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| 115 | C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp. |
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| 116 | Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004 |
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| 117 | |
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| 118 | - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING |
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| 119 | GEANT4. |
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| 120 | By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi, |
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| 121 | Ph. Moretto. Sep 2003. |
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| 122 | Published in Nucl.Instrum.Meth.B210:92-97, 2003 |
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| 123 | |
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| 124 | |
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| 125 | ------->3 VISUALIZATION |
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| 126 | |
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| 127 | The user can visualize the targeted cell by uncommenting the following line in |
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| 128 | microbeam.mac: |
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| 129 | #/control/execute vis.mac |
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| 130 | |
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| 131 | ---->4. HOW TO RUN THE EXAMPLE |
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| 132 | |
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| 133 | The variable G4ANALYSIS_USE must be set to 1. |
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| 134 | |
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| 135 | In order to generate histograms, at least one of the AIDA implementations should be |
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| 136 | available. |
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| 137 | |
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| 138 | The code should be compiled with gmake and run with : |
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| 139 | |
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| 140 | > $G4WORDIR/bin/$G4SYSTEM/Microbeam |
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| 141 | |
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| 142 | The macro file microbeam.mac is read by default. |
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| 143 | |
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| 144 | |
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| 145 | ---->5. PHYSICS |
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| 146 | |
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| 147 | Livermore, Binary and Binary_ion physics lists are used by default, |
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| 148 | see microbeam.mac |
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| 149 | |
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| 150 | ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS |
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| 151 | |
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| 152 | The output results consist in several a microbeam.root file, containing several |
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| 153 | ntuples: |
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| 154 | |
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| 155 | * total deposited dose in the cell nucleus and in the cell |
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| 156 | cytoplasm by each incident alpha particle; |
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| 157 | |
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| 158 | * average on the whole run of the dose deposited per |
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| 159 | Voxel per incident alpha particle; |
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| 160 | |
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| 161 | * final stopping (x,y,z) position of the incident |
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| 162 | alpha particle within the irradiated medium (cell or culture medium) |
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| 163 | |
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| 164 | * stopping power dE/dx of the incident |
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| 165 | alpha particle just before penetrating into the targeted cell; |
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| 166 | |
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| 167 | * beam transverse position distribution(X and Y) |
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| 168 | just before penetrating into the targeted cell; |
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| 169 | |
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| 170 | These results can be easily analyzed using for example the provided ROOT macro |
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| 171 | file plot.C; to do so : |
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| 172 | * be sure to have ROOT installed on your machine |
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| 173 | * be sure to be in the microbeam directory |
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| 174 | * launch ROOT by typing root |
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| 175 | * under your ROOT session, type in : .X plot.C to execute the macro file |
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| 176 | |
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| 177 | |
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| 178 | --------------------------------------------------------------------------- |
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| 179 | |
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| 180 | Should you have any enquiry, please do not hesitate to contact: |
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| 181 | incerti@cenbg.in2p3.fr |
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