dna/icsd/README.md

0001 \page Exampleicsd Example icsd
0002
0003 \author Sylvain Meylan , Yann Perrot, Marcin Pietrzak, Carmen Villagrasa (a)       \n
0004 (a) carmen.villagrasa _irsn _ fr             \n
0005
0006 This example is provided by the Geant4-DNA collaboration \n
0007 Any report or published results obtained using the Geant4-DNA software
0008 shall cite the following Geant4-DNA collaboration publications: \n
0009 [1] Med. Phys. 37 (2010) 4692-4708 \n
0010 [2] Phys. Med. 31 (2015) 861-874 \n
0011 In addition, for this example using DNA-materials cross-sections, please cite: \n
0012 [3] Rad. Phys and Chem. 130 (2017) 459-479 \n
0013 For this example using N2 cross-sections, please cite:\n
0014 [4] Phys. Med. 102 (2022) 103-109\n
0015
0016 ## INTRODUCTION
0017
0018 The icsd name of this example stands for: Ionisation Cluster Size Distribution.
0019 This example allows the calculation of the distribution concerning the number of ionisations per event in an small cylinder of 2.3 nanometers diameter and 3.4 nanometers heigh, typical dimensions of a 10 base pairs piece of chromatin.
0020
0021 It constitutes the first use of new DNA-like material's cross-sections that were experimentally obtained at PTB (Rad. Phys and Chem. 130 (2017) 459-479) for electrons and calculated for protons on THF, TMP, PY and PU materials.
0022
0023 The new physical models corresponding to the DNA materials have recently been implemented in Geant4-DNA thaks to new classes, that allow the use of other materials different from liquid water: G4VDNAModel, G4DNAModelInterface,G4DNADummyModel and other associated classes.
0024
0025 These new models are further described at:
0026 http://geant4-dna.org
0027
0028 ## GEOMETRY SET-UP AND PRIMARY PARTICLES
0029
0030 As indicated in the introduction, the geometry used in this exercise is a cylinder.
0031 Two options are proposed: one nanometric cylinder made of DNA or a macroscopic volume with low nitrogen density.
0032 The selection of the geometry is performed in the macro file:
0033
0034 --> `/icsd/setGeom dna`: a cylinder of 2.3 nanometers diameter and 3.4 nanometers height, typical dimensions of a 10 base pairs piece of chromatin that is centered in a cubic world of 10 nanometers side length filled with liquid water.
0035 This cylinder is filled with THF material. The definition of the THF material must be done using the G4String="THF". Currently, other materials are available than also use the G4Strings to be recognized by the model classes "TMP", "PY" or "PU" for the DNA-like materials and "deoxyribose","adenine", "guanine", "thymine" or "cytosine" for the derived DNA materials.
0036
0037 --> `/icsd/setGeom nanodosimeter`: a cylinder of 10 mm nanometers diameter and 10 nanometers height filled with low pressure nitrogen (0.34 µg/cm3)  mimicking the size of a short of segment od DNA of 2.3 nm in both diameter and height
0038 The obtained results can be compared to experimental data from Jet Counter nanodosimeter as shown in Pietrazk et al.
0039 Phys. Med. 102 (2022) 103-109
0040
0041 Primary particles are electrons starting at the cylinder's edge) and initial momentum (1,0,0)
0042
0043 ## PHYSICS LIST
0044
0045 The PhysicsList used in this example show how to use the new classes that allow Geant4-DNA to use other materials than liquid water :
0046 -# Models are built: classical Geant4-DNA models for liquid water material and PTB models for DNA-like materials
0047 -# G4DNAModelInterface object is built for each type of interaction (elastic, ionisation, excitation)
0048 -# G4DNAModels are registered within the corresponding  G4DNAModelInterface. For liquid water models, the particle name must be added to the RegisterModel function. For DNA-like material models and Vacuum no other parameter is needed.
0049 -# G4DNAProcesses objects are built and the corresponding G4DNAModelInterface is registered within. G4DNAModelInterface acts like a classical G4VEmModel
0050
0051 Remember that new DNA-like material classes are available for:
0052 ```
0053 electrons from 12 eV-1 keV, including elastic, ionisation and excitation processes
0054 protons from 70 keV to 10 MeV, only for ionisation processes following a modified HKS formalism
0055 ```
0056
0057 ## SET UP
0058
0059 Make sure G4LEDATA points to the low energy electromagnetic data files.
0060
0061 ## HOW TO RUN THE EXAMPLE
0062
0063  ./icsd  will run in multi-threaded mode with 2 threads by default.
0064  Two ntuples will be filled in the output file:
0065  - Ntuple 1 contains the information for calculating the ionisation cluster size distribution per event
0066  - Ntuple 2 contains interaction information at the step level
0067
0068 ```
0069 Please, do not forget to make "hadd ICSD.root ICSD_t0.root ICSD_t1.root" before using plot.C
0070 ```