High-precision dosimetry

== <span style="color:#000080"> Introduction </span> ==

This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show three of the examples:

* <span style="color:#ff0000"> dnaphysics </span>: This example shows how to simulate track structures in 100-micron side cube made of liquid water. Different type of particles are shot from the center of the volume. The physics processes are defined using class '''G4EmDNAPhysics'''. You can find more information about the different physics process which are used to build the class '''G4EmDNAPhysics''' [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html here]. [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. The output of this tutorial is the type of particle, type of process, energy deposit and energy loss for every simulation step.  

* <span style="color:#ff0000"> dnageometry </span>: This example simulates the track structure of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. The output is type of particle, type of process, energy deposit and energy loss for every simulation step. 

* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This setup is mainly used to investigate the effects of low dose irradiation on living cells. The realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on the phantom. Calculated is the dose deposited in the cell cytoplasm and in the cell nucleus. 

== <span style="color:#000080"> How to run the tutorial </span> ==

; Connect to the HEP cluster 

<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk 

username@plus1.hep.ucl.ac.uk's password: type your password here

</pre>

; Setup your environment

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 ~]$ source /unix/pbt/software/dev/bin/pbt-dev.sh  
</pre>

; Copy the code to your working directory 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 ~]$ cp -r /unix/pbt/tutorials/advanced/DNAProject .
  
[username@plus1 ~]$ cd DNAProject
</pre>
 
* <span style="color:#ff0000"> dnaphysics </span>:

; Inside /home/username/DNAProject/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ mkdir dnaphysics_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ cd dnaphysics_build 

[username@plus1 dnaphysics_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnaphysics 

[username@plus1 dnaphysics_build]$ make  
</pre>

; Run macro dna.mac. 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 dnaphysics_build]$ ./dnaphysics dna.mac
</pre>

* <span style="color:#ff0000"> dnageometry </span>:

; Inside /home/username/DNAProject/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ mkdir dnageometry_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ cd dnageometry_build 

[username@plus1 dnageometry_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnageometry 

[username@plus1 dnageometry_build]$ make  
</pre>

; Run macro dna.mac. 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 dnageometry_build]$ ./dnageometry dna.mac
</pre>

* <span style="color:#ff0000"> microbeam </span>:

; Inside /home/username/DNAProject/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ mkdir microbeam_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DNAProject]$ cd microbeam_build 

[username@plus1 microbeam_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/microbeam 

[username@plus1 microbeam_build]$ make  
</pre>

; Run macro microbeam.mac. 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 microbeam_build]$ ./microbeam microbeam.mac
</pre>

== <span style="color:#000080"> How to analyze data </span> ==

=== <span style="color:#000080"> dnaphysics </span> ===

==== <span style="color:#000080"> Root file </span> ====

The macro dna.mac produces two root files '''dna_t0.root''' and '''dna_t1.root''' with ntuples containing for every step the following information:

* type of particle
* type of physics process
* x, y and z coordinates of the step 
* total energy deposit [eV]
* step length [nm]
* kinetic energy difference along the step[eV] 

You can analyze the root files using '''plot.C''' macro. 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 dnaphysics_build]$ root -l

root [1] .x plot.C
</pre>

The macro produces two plots. The first plot shows the distribution of the different physics plrocesses when the incident particle interacts with the water cube. The second plot shows the trajectory of the incident particle. [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/flags.txt Here] you can find the codes for '''flagParticle''' and '''flagProcess'''. These are the resulting plots:  

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/plot.png

==== <span style="color:#000080"> Run with different settings </span> ====

You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico: 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 dnaphysics_build]$ pico dna.mac 
</pre>

This is the content of the macro:

<pre style="color: #800000; background-color: #dcdcdc">
#/control/execute vis.mac
/tracking/verbose 0
/run/verbose 2
#/dna/det/setMat G4_WATER_MODIFIED
/dna/det/setMat G4_WATER
/gun/particle e-
#/gun/particle proton
#/gun/particle hydrogen
#/gun/particle alpha
#/gun/particle alpha+
#/gun/particle helium
/gun/energy 1 keV
/run/initialize
/process/em/auger true
/run/beamOn 100
</pre>

==== <span style="color:#000080"> Visualisation </span> ====