source: trunk/examples/advanced/microbeam/README @ 1337

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2$Id: README,v 1.11 2010/06/09 18:13:46 sincerti Exp $
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4
5     =========================================================
6                  Geant4 - Microbeam example
7     =========================================================
8
9                                README file
10                          ----------------------
11
12                           CORRESPONDING AUTHOR
13
14S. Incerti (a, *) et al.
15a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
16(CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
17* e-mail:incerti@cenbg.in2p3.fr
18
19Last modified by S. Incerti, 09/06/2010
20
21---->0. INTRODUCTION.                                                   
22                                                                       
23The microbeam example simulates the cellular irradiation beam line
24installed on the AIFIRA electrostatic accelerator facility located at
25CENBG, Bordeaux-Gradignan, France. For more information on this facility,
26please visit :
27http://www.cenbg.in2p3.fr/
28
29An overall description of this example is also available in this directory:
30to access it, simply open the microbeam.htm file with your internet browser.
31
32---->1. GEOMETRY SET-UP.
33 
34The elements simulated are:
35
361. A switching dipole magnet with fringing field, to deflect the 3 MeV alpha
37beam generated by the electrostatic accelerator into the microbeam line,
38oriented at 10 degrees from the main beam direction;
39
402. A circular collimator object, defining the incident beam size at the
41microbeam line entrance;
42
433. A quadrupole based magnetic symmetric focusing system allowing equal
44transverse demagnifications of 10. Fringe fields are calculated from Enge's
45model.
46
474. A dedicated cellular irradiation chamber setup;
48
495. A set of horizontal and vertical electrostatic deflecting plates which can
50be turned on or off to deflect the beam on target;
51
526. A realistic human keratinocyte voxellized cell observed from confocal
53microscopy and taking into account realistic nucleus and cytoplasm chemical
54compositions
55
56
57---->2. EXPERIMENTAL SET-UP.     
58                                 
59The beam is defined at the microbeam line entrance through a collimator
605 micrometer in diameter. The beam is then focused onto target using a
61quadruplet of quadrupoles in the so-called Dymnikov magnetic configuration.
62The beam is sent to the irradiation chamber where it travels through a
63isobutane gas detector for counting purpose before reaching the polypropylene
64culture foil of the target cell which is immersed in the growing medium and
65enclosed within a dish. 
66
67A cell is placed on the polypropylene foil and is irradiated using the
68microbeam. The cell is represented through a 3D phantom (G4PVParameterization)
69obtained from confocal microscopy. In the provided example, the voxels sizes
70are : 359 nm (X) x 359 nm (Y) x 163 nm (Z)
71
72The primary particle beam parameters are generated from experimental
73measurements performed on the AIFIRA facility. Incident particle used for
74cellular irradiation are 3 MeV alpha particles.
75
76More details on the experimental setup and its simulation with Geant4 can
77be found in the following papers, which may be found on the SLAC-SPIRES
78online database (http://www.slac.stanford.edu/spires/) :
79
80- MONTE CARLO MICRODOSIMETRY FOR TARGETED IRRADIATION OF INDIVIDUAL CELLS USING
81A MICROBEAM FACILITY
82By S. Incerti, T. Pouthier, H. Seznec, Ph. Moretto, O. Boissonnade,
83T. M. H. Ha, F. Andersson, Ph. Barberet, C. Habchi and D. T. Nguyen
84In preparation (2007)
85
86- MONTE CARLO SIMULATION OF THE CENBG MICROBEAM AND NANOBEAM LINES WITH THE
87GEANT4 TOOLKIT
88By S. Incerti, Q. Zhang, F. Andersson, Ph. Moretto, G.W. Grime,
89M.J. Merchant, D.T. Nguyen, C. Habchi, T. Pouthier and H. Seznec
90In press in Nucl.Instrum.Meth.B, 2007
91
92- A COMPARISON OF CELLULAR IRRADIATION TECHNIQUES WITH ALPHA PARTICLES USING
93THE GEANT4 MONTE CARLO SIMULATION TOOLKIT
94By S. Incerti, N. Gault, C. Habchi, J.L.. Lefaix, Ph. Moretto, J.L.. Poncy,
95T. Pouthier, H. Seznec. Dec 2006. 3pp.
96Published in Rad.Prot.Dos.,1-3,2006 (Micros 2005 special issue).
97
98- GEANT4 SIMULATION OF THE NEW CENBG MICRO AND NANO PROBES FACILITY
99By S. Incerti, C. Habchi, Ph. Moretto, J. Olivier and H. Seznec. May 2006. 5pp.
100Published in Nucl.Instrum.Meth.B249:738-742, 2006
101
102- A COMPARISON OF RAY-TRACING SOFTWARE FOR THE DESIGN OF QUADRUPOLE MICROBEAM
103SYSTEMS
104By S. Incerti et al.,
105Published in Nucl.Instrum.Meth.B231:76-85, 2005
106
107- DEVELOPMENT OF A FOCUSED CHARGED PARTICLE MICROBEAM FOR THE IRRADIATION OF
108INDIVIDUAL CELLS.
109By Ph. Barberet, A. Balana, S. Incerti, C. Michelet-Habchi, Ph. Moretto,
110Th. Pouthier. Dec 2004. 6pp.
111Published in Rev.Sci.Instrum.76:015101, 2005
112
113- SIMULATION OF CELLULAR IRRADIATION WITH THE CENBG MICROBEAM LINE USING
114GEANT4.
115By S. Incerti, Ph. Barberet, R. Villeneuve, P. Aguer, E. Gontier,
116C. Michelet-Habchi, Ph. Moretto, D.T. Nguyen, T. Pouthier, R.W. Smith. Oct 2003. 6pp.
117Published in IEEE Trans.Nucl.Sci.51:1395-1401, 2004
118
119- SIMULATION OF ION PROPAGATION IN THE MICROBEAM LINE OF CENBG USING
120GEANT4.
121By S. Incerti, Ph. Barberet, B. Courtois, C. Michelet-Habchi,
122Ph. Moretto. Sep 2003.
123Published in Nucl.Instrum.Meth.B210:92-97, 2003
124
125
126---->3. SET-UP
127                                                                       
128- a standard Geant4 example GNUmakefile is provided                     
129
130The following section gives the necessary environment variables.                     
131
132------->>3.1  ENVIRONMENT VARIABLES
133
134All variables are defined with their default value.
135
136 - G4SYSTEM = Linux-g++
137
138 - G4INSTALL              points to the installation directory of GEANT4;
139
140 - G4LIB                  point to the compiled libraries of GEANT4;
141
142 - G4WORKDIR              points to the work directory;
143
144 - CLHEP_BASE_DIR         points to the installation directory of CHLEP;
145
146 - G4LEDATA               points to the low energy electromagnetic libraries;
147
148 - LD_LIBRARY_PATH = $CLHEP_BASE_DIR/lib
149
150 - G4LEVELGAMMADATA       points to the photoevaporation library;
151
152 - NeutronHPCrossSections points to the neutron data files;
153
154 - G4RADIOACTIVEDATA      points to the libraries for radio-active decay
155                          hadronic processes;
156 
157However, the $G4LEVELGAMMADATA, $NeutronHPCrossSections and $G4RADIOACTIVEDATA
158variables do not need to be defined for this example.
159
160Once these variables have been set, simply type gmake to compile the Microbeam
161example.
162
163------->>3.2  VISUALIZATION
164
165The user can visualize the targeted cell with OpenGL, DAWN and vrml,
166as chosen in the microbeam.mac file. OpenGL is the default viewer. The
167cytoplasm in shown in red and the nucleus in green.
168
169
170---->4. HOW TO RUN THE EXAMPLE                                         
171
172In interactive mode, run:
173
174> $G4WORDIR/bin/Linux-g++/Microbeam
175
176The macro microbeam.mac is executed by default.
177All visualisation commands are in the vis.mac macro file.
178
179
180---->5. PHYSICS
181
182Livermore, Binary and Binary_ion physics lists are used by default,
183see microbeam.mac
184
185---->6. SIMULATION OUTPUT AND RESULT ANALYZIS                                   
186
187This example does not need any external analysis package.
188The output results consists in several .txt files:
189
190* dose.txt : gives the total deposited dose in the cell nucleus and in the cell
191cytoplasm by each incident alpha particle;
192
193* 3DDose.txt : gives the average on the whole run of the dose deposited per
194Voxel per incident alpha particle;
195
196* range.txt : indicates the final stopping (x,y,z) position of the incident
197alpha particle within the irradiated medium (cell or culture medium)
198
199* stoppingPower.txt : gives the actual stopping power dE/dx of the incident
200alpha particle just before penetrating into the targeted cell;
201
202* beamPosition.txt : gives the beam transverse position distribution(X and Y)
203just before penetrating into the targeted cell;
204
205These files can be easily analyzed using for example the provided ROOT macro
206file plot.C; to do so :
207* be sure to have ROOT installed on your machine
208* be sure to be in the microbeam directory
209* launch ROOT by typing root
210* under your ROOT session, type in : .X plot.C to execute the macro file
211
212A graphical output obtained with this macro for 40000 incident alpha particles
213is shown in the file microbeam.gif
214
215The simulation predicts that 95% of the incident alpha particles detected by the
216gas detector are located within a circle of 10 um in diameter on the target, in
217nice agreement with experimental measurements performed on the CENBG setup.
218
219---------------------------------------------------------------------------
220
221Should you have any enquiry, please do not hesitate to contact:
222incerti@cenbg.in2p3.fr
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