Warning, /geant4/examples/extended/medical/dna/icsd/README is written in an unsupported language. File is not indexed.
0001 -------------------------------------------------------------------
0002
0003 =========================================================
0004 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
0005 =========================================================
0006
0007 icsd
0008 -------
0009
0010 Authors: Sylvain Meylan, Yann Perrot and Carmen Villagrasa (IRSN, France)
0011 Marcin Pietrzak (NCBJ, Poland)
0012 For any question, please contact:
0013 carmen.villagrasa@irsn.fr
0014
0015 This example is provided by the Geant4-DNA collaboration
0016 Any report or published results obtained using the Geant4-DNA software
0017 shall cite the following Geant4-DNA collaboration publications:
0018 [1] Med. Phys. 37 (2010) 4692-4708
0019 [2] Phys. Med. 31 (2015) 861-874
0020 In addition, for this example using DNA-materials cross-sections, please cite:
0021 [3] Rad. Phys and Chem. 130 (2017) 459-479
0022 For this example using N2 cross-sections, please cite:
0023 [4] Phys. Med. 102 (2022) 103-109
0024
0025 ---->0. INTRODUCTION.
0026
0027 The icsd name of this example stands for: Ionisation Cluster Size Distribution.
0028 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.
0029 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.
0030 The new physical models corresponding to the DNA materials a,d nitrogen 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.
0031
0032 These new models are further described at:
0033 http://geant4-dna.org
0034
0035 ---->1. GEOMETRY SET-UP AND PRIMARY PARTICLES
0036
0037 As indicated in the introduction, the geometry used in this exercise is a cylinder.
0038 Two options are proposed: one nanometric cylinder made of DNA or a macroscopic volume with low nitrogen density.
0039 The selection of the geometry is performed in the macro file:
0040
0041 --> /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.
0042 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.
0043
0044 --> /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
0045 The obtained results can be compared to experimental data from Jet Counter nanodosimeter as shown in Pietrazk et al.
0046 Phys. Med. 102 (2022) 103-109
0047
0048 Primary particles are electrons starting at the cylinder's edge) and initial momentum (1,0,0)
0049
0050 ---->2. PHYSICS LIST
0051
0052 The PhysicsList used in this example show how to use the new classes that allow Geant4-DNA to use other materials than liquid water :
0053 1/ Models are built: classical Geant4-DNA models for liquid water material and PTB models for DNA-like materials
0054 2/ G4DNAModelInterface object is built for each type of interaction (elastic, ionisation, excitation)
0055 3/ 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.
0056 4/ G4DNAProcesses objects are built and the corresponding G4DNAModelInterface is registered within. G4DNAModelInterface acts like a classical G4VEmModel
0057
0058 Remember that new DNA-like material classes are available for:
0059
0060 electrons from 12 eV-1 keV, including elastic, ionisation and excitation processes
0061 protons from 70 keV to 10 MeV, only for ionisation processes following a modified HKS formalism
0062
0063 ---->3. SET UP
0064
0065 Make sure G4LEDATA points to the low energy electromagnetic data files.
0066
0067 ---->4. HOW TO RUN THE EXAMPLE
0068
0069 ./icsd will run in multi-threaded mode with 2 threads by default.
0070 Two ntuples will be filled in the output file:
0071 - Ntuple 1 contains the information for calculating the ionisation cluster size distribution per event
0072 - Ntuple 2 contains interaction information at the step level
0073
