wholeNuclearDNA
Extended example located in $G4INSTALL/examples/extended/medical/dna
Contact : Carmen Villagrasa ([email protected])
Overview
The wholeNuclearDNA example offers the possibility of simulating the energy deposition of ionizing radiation
at nanometric scale within a geometrical representation of the whole DNA molecule contained in a
eukaryotic cell nucleus. For this purpose, the transport of particles is made using the Geant4-DNA physics
processes and models. The volume-definition for the different DNA components and its compaction levels
are given in the DetectorContruction class. Output data are stored in a ROOT ntuple
See details about the Geant4-DNA project at http://geant4-dna.org.
Description
The DetectorConstruction class of this example represents a typical fibroblast cell nucleus by an ellipsoid with
semi-axes of sizes: 11.82, 8.52 and 3 µm. The cell nucleus contains the 6.109 base pairs of eukaryotic cells
divided in five organization levels:
• DNA double helix: containing the amino basis as spheres of 0.17 nm and the backbone region
• the nucleosome: formed by an histone protein core (cylinder) wrapped by two turns of the DNA
double helix
• chromatin fibers : composed of 90 nucleosomes placed on an helix
• chromatin fiber loops: “flower” loops composed of 28 chromatin fibers
• Chromosome territories: with volumes proportional to the number of base pairs composing the
chromosome. The position of the flower loops for each chromosome territories are given in the
chromosome+number.dat files
The placement of the chromatin fiber loops is parameterized and the positions are contained in the
chromosome(nn).dat files.
All the volumes in the geometry are made of liquid water (G4_WATER material) despite of what they
geometrically represent.
WARNING: By default, the bases are not built. If users want the whole geometry to be built, the flag
fBuildBases in DetectorConstruction must be set to true.
The PhysicsList class uses the recommended G4EmDNAPhysics physics constructor.
In the SteppingAction class, only energy deposits located in the backbone region of the DNA molecule are
stored into an ntuple, together with their strand flag. The ntuple information is defined in the RunAction class
wholeNuclearDNA
How to run the example
The example can be compiled with cmake and make. The use multithreading mode is facultative. It can be
launched in normal mode (> wholeNuclearDNA) or in interactive mode (>wholeNuclearDNA –gui –out).
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. Proton projectiles 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.
Visualization (DAWN) is not activated by default in wholenucleardna.mac. To get visualization, make sure to
uncomment the #/control/execute vis.mac.
We would like to warn the users that the time to visualize the whole DNA structure is extremely long.
Results and future developments
The output results consists in ROOT files (http://root.cern.ch), containing an ntuple with:
•
the type of particle at the origin of the energy deposition in the backbone.
•
the type of process leading to the energy deposition
•
The strand information
•
The corresponding coordinate position of the post step (in nanometers)
•
the amount of energy deposited (in eV)
The output file can be easily analyzed using the provided ROOT macro file plot.C.
This example provides a realistic volume description of the backbone region in B-DNA molecule that can be
used in order to evaluate direct energy deposition for DNA damages calculations. The strand flag
information allows recognizing double strand breaks, for example. The description of the 5 different
chromatin levels is also an interesting tool for studying the complexity of these damages or the distance
distribution between them that is a parameter needed in DNA repair models.
The geometry DNA description in this example is currently under development in order to include the
definition of the molecular components of DNA (sugar, phosphate, bases) and to be compatible with the
chemical stage simulation in the future.
References
Refer to Geant4-DNA publications (http://geant4-dna.org) and in particular to:
•
Influence of the chromatin density on the number of direct clustered damages calculated for proton
and alpha irradiations using a Monte Carlo code, M. Dos Santos, C. Villagrasa, I. Clairand and S.
Incerti , Prog. Nucl. Sci. Tech. 4, (2014) 449-453
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wholeNuclearDNA
•
Comparison of Geant4 very low energy cross section models with experimental data in water, S.
Incerti, A. Ivanchenko, M. Karamitros, A. Mantero, P. Moretto, H. N. Tran, B. Mascialino, C. Champion,
V. N. Ivanchenko, M. A. Bernal, Z. Francis, C. Villagrasa, G. Baldacchino, P. Guèye, R. Capra, P.
Nieminen, C. Zacharatou, Med. Phys. 37 (2010) 4692-4708
Note that any report or published results obtained using the Geant4-DNA software shall cite the following
Geant4-DNA collaboration publication: Med. Phys. 37 (2010) 4692-4708
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