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0005 Geant4 - Microbeam example
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0007
0008 README file
0009 ----------------------
0010
0011 CORRESPONDING AUTHOR
0012
0013 S. Incerti (a, *) et al.
0014 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
0015 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
0016 * e-mail:incerti@cenbg.in2p3.fr
0017
0018 ---->0. INTRODUCTION.
0019
0020 The microbeam example simulates the cellular irradiation beam line
0021 installed on the AIFIRA electrostatic accelerator facility located at
0022 CENBG, Bordeaux-Gradignan, France. For more information on this facility,
0023 please visit :
0024 http://www.cenbg.in2p3.fr/
0025
0026 ---->1. GEOMETRY SET-UP.
0027
0028 The elements simulated are:
0029
0030 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
0031 beam generated by the electrostatic accelerator into the microbeam line,
0032 oriented at 10 degrees from the main beam direction;
0033
0034 2. A circular collimator object, defining the incident beam size at the
0035 microbeam line entrance;
0036
0037 3. A quadrupole based magnetic symmetric focusing system allowing equal
0038 transverse demagnifications of 10. Fringe fields are calculated from Enge's
0039 model.
0040
0041 4. A dedicated cellular irradiation chamber setup;
0042
0043 5. A set of horizontal and vertical electrostatic deflecting plates which can
0044 be turned on or off to deflect the beam on target;
0045
0046 6. A realistic human keratinocyte voxellized cell observed from confocal
0047 microscopy and taking into account realistic nucleus and cytoplasm chemical
0048 compositions.
0049
0050
0051 ---->2. EXPERIMENTAL SET-UP.
0052
0053 The beam is defined at the microbeam line entrance through a collimator
0054 5 micrometer in diameter. The beam is then focused onto target using a
0055 quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
0056 The beam is sent to the irradiation chamber where it travels through a
0057 isobutane gas detector for counting purpose before reaching the polypropylene
0058 culture foil of the target cell which is immersed in the growing medium and
0059 enclosed within a dish.
0060
0061 A cell is placed on the polypropylene foil and is irradiated using the
0062 microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
0063 obtained from confocal microscopy. In the provided example, the voxels sizes
0064 are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
0065
0066 The primary particle beam parameters are generated from experimental
0067 measurements performed on the AIFIRA facility. Incident particle used for
0068 cellular irradiation are 3 MeV alpha particles.
0069
0070 More details on the experimental setup and its simulation with Geant4 can
0071 be found in the following papers:
0072
0073 - IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO NON-TARGETED BIOLOGICAL RESPONSES TO
0074 RADIATION
0075 By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti
0076 Publsihed in Comp. Math. Meth. Med. (2012) 147252
0077
0078 - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
0079 A MICROBEAM FACILITY
0080 By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
0081 Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
0082
0083 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
0084 GEANT4 TOOLKIT
0085 By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
0086 M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
0087 Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
0088
0089 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
0090 THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
0091 By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
0092 T. Pouthier, H. Seznec. Dec 2006. 3pp.
0093 Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
0094
0095 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
0096 By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp.
0097 Published in Nucl.Instrum.Meth.B249:738-742, 2006
0098
0099 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
0100 SYSTEMS
0101 By S. Incerti et al.,
0102 Published in Nucl.Instrum.Meth.B231:76-85, 2005
0103
0104 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
0105 INDIVIDUAL CELLS.
0106 By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
0107 Th. Pouthier. Dec 2004. 6pp.
0108 Published in Rev.Sci.Instrum.76:015101, 2005
0109
0110 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
0111 GEANT4.
0112 By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
0113 C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp.
0114 Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
0115
0116 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
0117 GEANT4.
0118 By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
0119 Ph. Moretto. Sep 2003.
0120 Published in Nucl.Instrum.Meth.B210:92-97, 2003
0121
0122
0123 ---->3 VISUALIZATION
0124
0125 The user can visualize the targeted cell thanks to the Qt interface.
0126
0127 ---->4. HOW TO RUN THE EXAMPLE
0128
0129 The code should be compiled with cmake.
0130
0131 Run the example from your build directory with:
0132 ./microbeam microbeam.mac
0133
0134 or in interactive mode:
0135 ./microbeam
0136
0137 The example works in MT mode.
0138
0139 ---->5. PHYSICS
0140
0141 Livermore physics list is used by default.
0142
0143 ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
0144
0145 The output results consist in a microbeam.root file per thread,
0146 containing several ntuples:
0147
0148 * total deposited dose in the cell nucleus and in the cell
0149 cytoplasm by each incident alpha particle;
0150
0151 * average on the whole run of the dose deposited per
0152 Voxel per incident alpha particle;
0153
0154 * final stopping (x,y,z) position of the incident
0155 alpha particle within the irradiated medium (cell or culture medium);
0156
0157 * stopping power dE/dx of the incident
0158 alpha particle just before penetrating into the targeted cell;
0159
0160 * beam transverse position distribution (X and Y)
0161 just before penetrating into the targeted cell;
0162
0163 These results can be easily analyzed using for example the provided ROOT macro
0164 file plot.C; to do so :
0165 * be sure to have ROOT installed on your machine
0166 * be sure to be in the directory where the output ROOT files have been created
0167 * do: root plot.C
0168 * or under your ROOT session, type in : .X plot.C to execute the macro file
0169
0170 ---------------------------------------------------------------------------
0171
0172 Should you have any enquiry, please do not hesitate to contact:
0173 incerti@cenbg.in2p3.fr
