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0002 Geant4 - wholenucleardna example
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0004
0005 README file
0006 ----------------------
0007
0008 CORRESPONDING AUTHOR
0009
0010 For any question, please contact:
0011 C. Villagrasa
0012 email: carmen.villagrasa@irsn.fr
0013
0014 This example is provided by the Geant4-DNA collaboration
0015 Any report or published results obtained using the Geant4-DNA software
0016 and the DNA geometry given in the Geom_DNA example
0017 shall cite the following Geant4-DNA collaboration publications:
0018 [1] NIM B 298 (2013) 47-54
0019 [2] Med. Phys. 37 (2010) 4692-4708
0020 [3] Phys. Med. 31 (2015) 861-874
0021
0022 ---->0. INTRODUCTION.
0023
0024 The wholenucleardna example offers the basic tools to simulate the track structure of different charge particles within a
0025 simplified geometrical model of the DNA molecule contained in a cell nucleus.
0026 In this example, the DetectorConstruction file contains the placement of the 6 Gbp (base-pairs) of a human cell respecting five compaction levels in the structure of the DNA molecule: double helix, nucleosome, chromatin fiber, simple chromatin fiber loop and complex chromatin fiber loops.
0027 These complex chromatin fiber loops are then used to fill the chromosome territories using a constant density (~30-31 kbp/µm3.
0028 Even though this geometry defines different volumes for the DNA base, the back-bone region or the histone proteins, the material filling all these volumes in the simulation is liquid water ("G4_WATER")
0029
0030 In order to simulate all the energy transfer points of the track at nanometric level, the Geant4-DNA physics processes and models are used.
0031 These processes and models are further described at:
0032 http://geant4-dna.org
0033
0034 ---->1. GEOMETRY SET-UP.
0035
0036 As indicated in the introduction, the whole DNA molecule contained in a human cell with 5 different compaction levels is described in this geometry. In order to place the complex chromatin loops in each of the 43 chromosome territories, the files called "chromo-number.dat" are needed.
0037 These 43 chromosome territories are then placed in an ellipsoid that has the typical dimensions of a human fibroblast cell nucleus.
0038 All the volumes in the geometry are made of liquid water (G4_WATER material) despite of what they geometrically represent.
0039 Particles are shot from a random (x,y)position covering the main central part of the cell nucleus and at z=2.99 µm from the center of the nucleus. This value allows the primary particle to be either inside the cell nucleus, either not far from the entrance surface so its energy loss before the cell nucleus entrance is negligible.
0040
0041 WARNING: By default, the bases are not built. To build the whole geometry, set the flag fBuildBases in DetectorConstruction to true.
0042
0043 ---->2. SET-UP
0044
0045 Make sure G4LEDATA points to the low energy electromagnetic data files.
0046
0047 The variable G4ANALYSIS_USE must be set to 1.
0048
0049 The code can be compiled with gmake.
0050
0051 ---->3. HOW TO RUN THE EXAMPLE
0052
0053 In normal mode, without interactivity:
0054
0055 > wholeNuclearDNA
0056
0057 In interactive mode, run:
0058
0059 > wholeNuclearDNA -gui -out
0060
0061 The -gui option launches a user interface for interactivity
0062 The -out option create a root file (can be changed for other format). This option may also take argument to set the name of the file (name of the application by default):
0063
0064 > wholeNuclearDNA -gui -out MyFile
0065
0066 The macro wholenucleardna.in is executed by default. A proton of 0.1 MeV is shot. This energy has been chosen because only a few minutes are needed for the proton to lose all its energy and thus the event to finish. Nevertheless, one should keep in mind that for this energy, protons do not traverse the whole cell nucleus width.
0067
0068 Visualization (DAWN) is not activated by default in wholenucleardna.mac. To get visualization, make sure to uncomment the #/control/execute vis.mac.
0069 We would like to warn the users that the time to visualize the whole DNA structure is extremely long.
0070
0071 To build the whole geometry, set the flag fBuildBases in DetectorConstruction to true.
0072
0073 ---->4. PHYSICS
0074
0075 This example uses the Geant4-DNA processes, using the G4EmDNAPhysics constructor as in the dnaphysics example.
0076
0077 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
0078
0079 The output results consist in a wholenucleardna.root file, containing only the information about the energy transfers located in the backbone region of the DNA double helix. Both strands are distinguished with different flags (1 or 2):
0080 - the type of particle for the current step
0081 - the type of process for the current step
0082 - the flag of the strand (1 or 2)
0083 - the track position of the current energy transfer (in nanometers)
0084 - the energy deposit corresponding to the energy transfer (in eV)
0085 - the total energy loss along the current step (in eV)
0086 - the step length (in nm)
0087
0088
0089 This file can be easily analyzed using for example the provided ROOT macro
0090 file plot.C; to do so :
0091 * be sure to have ROOT installed on your machine
0092 * be sure to be in the directory containing the ROOT files created by wholenucleardna
0093 * copy plot.C into this directory
0094 * from there, launch ROOT by typing root
0095 * under your ROOT session, type in : .X plot.C to execute the macro file
0096 * alternatively you can type directly under your session : root plot.C
0097
0098 The naming scheme on the displayed ROOT plots can be seen in the SteppingAction.cc file.
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