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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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