High-precision dosimetry

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This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show three of the examples:
This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show three of the examples:
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* <span style="color:#ff0000"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. The incident particles are generated using G4ParticleGun class and are shot from the center of the cube. The output of this tutorial is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.   
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* <span style="color:#ff0000"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. The incident particles are generated using class '''G4ParticleGun''' and are shot from the center of the cube. The output of this tutorial is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.   
* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. The output is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.  
* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. The output is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.  

Revision as of 14:00, 1 September 2014

Contents

Introduction

This tutorial is based on the Geant4-DNA project tutorials. We chose to show three of the examples:

  • dnaphysics : This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class G4EmDNAPhysics. Here you can find more information about the different physics process that are used to build class G4EmDNAPhysics . Here you can find how to build your own G4EmDNAPhysics class. The incident particles are generated using class G4ParticleGun and are shot from the center of the cube. The output of this tutorial is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.
  • dnageometry : This example simulates track structures of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. The output is ntuple with type of particle, type of process, energy deposit and energy loss for every simulation step.
  • microbeam : This example simulates the cellular irradiation beam line installed on the AIFIRA electrostatic accelerator facility located at CENBG, Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output is dose deposited in the cell cytoplasm and in the cell nucleus.

How to run the tutorial

Connect to the HEP cluster
ssh -X username@plus1.hep.ucl.ac.uk 

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

Setup your environment
[username@plus1 ~]$ source /unix/pbt/software/dev/bin/pbt-dev.sh  
Copy the code to your working directory
[username@plus1 ~]$ cp -r /unix/pbt/tutorials/advanced/DNAProject .
  
[username@plus1 ~]$ cd DNAProject
  • dnaphysics :
Inside /home/username/DNAProject/ create a directory
[username@plus1 DNAProject]$ mkdir dnaphysics_build  
To compile the code enter this directory and run cmake and make
[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  
Run macro dna.mac.
[username@plus1 dnaphysics_build]$ ./dnaphysics dna.mac
  • dnageometry :
Inside /home/username/DNAProject/ create a directory
[username@plus1 DNAProject]$ mkdir dnageometry_build  
To compile the code enter this directory and run cmake and make
[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  
Run macro dna.mac.
[username@plus1 dnageometry_build]$ ./dnageometry dna.mac
  • microbeam :
Inside /home/username/DNAProject/ create a directory
[username@plus1 DNAProject]$ mkdir microbeam_build  
To compile the code enter this directory and run cmake and make
[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  
Run macro microbeam.mac.
[username@plus1 microbeam_build]$ ./microbeam microbeam.mac

How to analyze data

dnaphysics

Root file

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

  • 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.

[username@plus1 dnaphysics_build]$ root -l

root [1] .x plot.C

The macro produces two plots. The first plot shows the distribution of the different physics plrocesses. The second plot shows the trajectory of the incident particle. Here you can find the codes for flagParticle and flagProcess. These are the resulting plots:

plot.png

Run with different settings

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

[username@plus1 dnaphysics_build]$ pico dna.mac 

This is the content of the macro:

#/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

Visualisation

There is an option to run dna.mac with visualisation (in dna.mac uncomment line /control/execute vis.mac). However, runing with visualisation is very slow and it is not recommended.

dnageometry

Root file

Run with different settings

microbeam

Root file

Run with different settings

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