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$Id: README 70524 2013-05-31 16:36:26Z gcosmo $
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 		  Geant4 - Microbeam example
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                                README file
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                           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

---->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/

---->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:

- IN SILICO NANODOSIMETRY: NEW INSIGHTS INTO NON-TARGETED BIOLOGICAL RESPONSES TO 
RADIATION
By Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti
Publsihed in Comp. Math. Meth. Med. (2012) 147252 

- 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 code should be compiled with cmake.

Put the 'phantom.dat' file into your build directory.

Run the example from your build directory with:
./microbeam

The macro file microbeam.mac is read by default. 

The works in MT mode.

---->5. PHYSICS

Livermore physics list is used by default.

---->6. SIMULATION OUTPUT AND RESULT ANALYZIS                                    

The output results consist in a microbeam.root file per thread, 
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 directory where the output ROOT files have been created
* copy plot.C into this directory
* launch ROOT by typing root
* under your ROOT session, type in : .X plot.C to execute the macro file


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Should you have any enquiry, please do not hesitate to contact: 
incerti@cenbg.in2p3.fr
