Gabriele Cosmo
174 lines
6.6 KiB
Plaintext
174 lines
6.6 KiB
Plaintext
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Geant4 - Microbeam example
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README file
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----------------------
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CORRESPONDING AUTHOR
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S. Incerti (a, *) et al.
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a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
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(CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
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* e-mail:incerti@cenbg.in2p3.fr
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---->0. INTRODUCTION.
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The microbeam example simulates the cellular irradiation beam line
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installed on the AIFIRA electrostatic accelerator facility located at
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CENBG, Bordeaux-Gradignan, France. For more information on this facility,
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please visit :
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http://www.cenbg.in2p3.fr/
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---->1. GEOMETRY SET-UP.
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The elements simulated are:
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1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
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beam generated by the electrostatic accelerator into the microbeam line,
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oriented at 10 degrees from the main beam direction;
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2. A circular collimator object, defining the incident beam size at the
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microbeam line entrance;
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3. A quadrupole based magnetic symmetric focusing system allowing equal
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transverse demagnifications of 10. Fringe fields are calculated from Enge's
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model.
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4. A dedicated cellular irradiation chamber setup;
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5. A set of horizontal and vertical electrostatic deflecting plates which can
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be turned on or off to deflect the beam on target;
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6. A realistic human keratinocyte voxellized cell observed from confocal
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microscopy and taking into account realistic nucleus and cytoplasm chemical
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compositions.
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---->2. EXPERIMENTAL SET-UP.
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The beam is defined at the microbeam line entrance through a collimator
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5 micrometer in diameter. The beam is then focused onto target using a
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quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
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The beam is sent to the irradiation chamber where it travels through a
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isobutane gas detector for counting purpose before reaching the polypropylene
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culture foil of the target cell which is immersed in the growing medium and
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enclosed within a dish.
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A cell is placed on the polypropylene foil and is irradiated using the
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microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
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obtained from confocal microscopy. In the provided example, the voxels sizes
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are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
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The primary particle beam parameters are generated from experimental
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measurements performed on the AIFIRA facility. Incident particle used for
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cellular irradiation are 3 MeV alpha particles.
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More details on the experimental setup and its simulation with Geant4 can
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be found in the following papers:
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- IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO NON-TARGETED BIOLOGICAL RESPONSES TO
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RADIATION
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By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti
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Publsihed in Comp. Math. Meth. Med. (2012) 147252
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- MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
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A MICROBEAM FACILITY
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By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto
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Published in Rad. Prot. Dos. 133, 1 (2009) 2-11
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- MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
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GEANT4 TOOLKIT
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By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
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M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
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Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27
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- A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
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THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
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By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
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T. Pouthier, H. Seznec. Dec 2006. 3pp.
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Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329
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- GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
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By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp.
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Published in Nucl.Instrum.Meth.B249:738-742, 2006
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- A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
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SYSTEMS
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By S. Incerti et al.,
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Published in Nucl.Instrum.Meth.B231:76-85, 2005
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- DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
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INDIVIDUAL CELLS.
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By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
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Th. Pouthier. Dec 2004. 6pp.
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Published in Rev.Sci.Instrum.76:015101, 2005
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- SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
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GEANT4.
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By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
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C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp.
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Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
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- SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
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GEANT4.
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By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
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Ph. Moretto. Sep 2003.
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Published in Nucl.Instrum.Meth.B210:92-97, 2003
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---->3 VISUALIZATION
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The user can visualize the targeted cell thanks to the Qt interface.
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---->4. HOW TO RUN THE EXAMPLE
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The code should be compiled with cmake.
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Run the example from your build directory with:
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./microbeam microbeam.mac
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or in interactive mode:
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./microbeam
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The example works in MT mode.
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---->5. PHYSICS
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Livermore physics list is used by default.
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---->6. SIMULATION OUTPUT AND RESULT ANALYZIS
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The output results consist in a microbeam.root file per thread,
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containing several ntuples:
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* total deposited dose in the cell nucleus and in the cell
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cytoplasm by each incident alpha particle;
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* average on the whole run of the dose deposited per
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Voxel per incident alpha particle;
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* final stopping (x,y,z) position of the incident
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alpha particle within the irradiated medium (cell or culture medium);
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* stopping power dE/dx of the incident
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alpha particle just before penetrating into the targeted cell;
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* beam transverse position distribution (X and Y)
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just before penetrating into the targeted cell;
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These results can be easily analyzed using for example the provided ROOT macro
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file plot.C; to do so :
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* be sure to have ROOT installed on your machine
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* be sure to be in the directory where the output ROOT files have been created
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* do: root plot.C
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* or under your ROOT session, type in : .X plot.C to execute the macro file
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---------------------------------------------------------------------------
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Should you have any enquiry, please do not hesitate to contact:
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incerti@cenbg.in2p3.fr
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