------------------------------------------------------------------- $Id: README,v 1.12 2010/10/07 14:03:11 sincerti Exp $ ------------------------------------------------------------------- ========================================================= Geant4 - Microbeam example ========================================================= README file ---------------------- CORRESPONDING AUTHOR S. Incerti (a, *) et al. a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France * e-mail:incerti@cenbg.in2p3.fr Last modified by S. Incerti, 07/10/2010 ---->0. INTRODUCTION. The microbeam example simulates the cellular irradiation beam line installed on the AIFIRA electrostatic accelerator facility located at CENBG, Bordeaux-Gradignan, France. For more information on this facility, please visit : http://www.cenbg.in2p3.fr/ An overall description of this example is also available in this directory: to access it, simply open the microbeam.htm file with your internet browser. ---->1. GEOMETRY SET-UP. The elements simulated are: 1. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha beam generated by the electrostatic accelerator into the microbeam line, oriented at 10 degrees from the main beam direction; 2. A circular collimator object, defining the incident beam size at the microbeam line entrance; 3. A quadrupole based magnetic symmetric focusing system allowing equal transverse demagnifications of 10. Fringe fields are calculated from Enge's model. 4. A dedicated cellular irradiation chamber setup; 5. A set of horizontal and vertical electrostatic deflecting plates which can be turned on or off to deflect the beam on target; 6. A realistic human keratinocyte voxellized cell observed from confocal microscopy and taking into account realistic nucleus and cytoplasm chemical compositions ---->2. EXPERIMENTAL SET-UP. The beam is defined at the microbeam line entrance through a collimator 5 micrometer in diameter. The beam is then focused onto target using a quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration. The beam is sent to the irradiation chamber where it travels through a isobutane gas detector for counting purpose before reaching the polypropylene culture foil of the target cell which is immersed in the growing medium and enclosed within a dish. A cell is placed on the polypropylene foil and is irradiated using the microbeam. The cell is represented through a 3D phantom (G4PVParameterization) obtained from confocal microscopy. In the provided example, the voxels sizes are : 359 nm (X) x 359 nm (Y) x 163 nm (Z) The primary particle beam parameters are generated from experimental measurements performed on the AIFIRA facility. Incident particle used for cellular irradiation are 3 MeV alpha particles. More details on the experimental setup and its simulation with Geant4 can be found in the following papers, which may be found on the SLAC-SPIRES online database (http://www.slac.stanford.edu/spires/) : - MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING A MICROBEAM FACILITY By S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto Published in Rad. Prot. Dos. 133, 1 (2009) 2-11 - MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE GEANT4 TOOLKIT By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime, M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec Published in Nucl. Instrum. and Meth. B 260 (2007) 20-27 - A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING THE GEANT4 MONTE CARLO SIMULATION TOOLKIT By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy, T. Pouthier, H. Seznec. Dec 2006. 3pp. Published in Rad. Prot. Dos. 122, 1-4, (2006) 327-329 - GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp. Published in Nucl.Instrum.Meth.B249:738-742, 2006 - A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM SYSTEMS By S. Incerti et al., Published in Nucl.Instrum.Meth.B231:76-85, 2005 - DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF INDIVIDUAL CELLS. By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto, Th. Pouthier. Dec 2004. 6pp. Published in Rev.Sci.Instrum.76:015101, 2005 - SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING GEANT4. By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier, C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp. Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004 - SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING GEANT4. By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi, Ph. Moretto. Sep 2003. Published in Nucl.Instrum.Meth.B210:92-97, 2003 ------->3 VISUALIZATION The user can visualize the targeted cell by uncommenting the following line in microbeam.mac: #/control/execute vis.mac ---->4. HOW TO RUN THE EXAMPLE The variable G4ANALYSIS_USE must be set to 1. In order to generate histograms, at least one of the AIDA implementations should be available. The code should be compiled with gmake and run with : > $G4WORDIR/bin/$G4SYSTEM/Microbeam The macro file microbeam.mac is read by default. ---->5. PHYSICS Livermore, Binary and Binary_ion physics lists are used by default, see microbeam.mac ---->6. SIMULATION OUTPUT AND RESULT ANALYZIS The output results consist in several a microbeam.root file, containing several ntuples: * total deposited dose in the cell nucleus and in the cell cytoplasm by each incident alpha particle; * average on the whole run of the dose deposited per Voxel per incident alpha particle; * final stopping (x,y,z) position of the incident alpha particle within the irradiated medium (cell or culture medium) * stopping power dE/dx of the incident alpha particle just before penetrating into the targeted cell; * beam transverse position distribution(X and Y) just before penetrating into the targeted cell; These results can be easily analyzed using for example the provided ROOT macro file plot.C; to do so : * be sure to have ROOT installed on your machine * be sure to be in the microbeam directory * launch ROOT by typing root * under your ROOT session, type in : .X plot.C to execute the macro file --------------------------------------------------------------------------- Should you have any enquiry, please do not hesitate to contact: incerti@cenbg.in2p3.fr