Results and analysis
Table of contents
Implementation overview
As the simulation runs, it keeps track of three main elements in relation to DNA damage.
- Energy depositions in each chromosome
- Energy depositions and track length in the cell
- DNA damage in the DNA geometry
At the end of each event, the DNA damage events are collected and analysed, reconstructing the damage pattern in the DNA and assigning it a complexity.
In the damage model, a probability is assigned that certain events cause strand breaks (i.e. \(Pr(\ce{e^{-}_{aq}} + \mathrm{Sugar} \rightarrow \mathrm{SSB})\)). These conditions are tested at the end of each event when the analysis runs to determine the damage that occurs.
At the completion of the run, the following outputs in a ROOT file are saved:
Histograms
- SSB counter (ssb_counts)
- Deposit energy in SSBs (ssb_energies_ev)
- DNA fragment size
- Strand interaction positions
Tuples
- Primary Source
- Primary
- Energy
- PosX in um
- PosY in um
- PosZ in um
- Momentum X
- Momentum Y
- Momentum Ζ
- Source (Break Source Frequency)
- Primary
- Energy
- None
- SSBd
- SSBi
- SSBm
- DSBd
- DSBi
- DSBm
- DSBh
- Damage (DNA damage locations)
- Event
- Primary
- Energy
- TypeClassification
- SourceClassification
- Position_x_um
- Position_y_um
- Position_z_um
- Size_nm
- FragmentLength
- BaseDamage
- StrandDamage
- DirectBreaks
- IndirectBreaks
- EaqBaseHits
- EaqStrandHits
- OHBaseHits
- OHStrandHits
- HBaseHits
- HStrandHits
- EnergyDeposited_eV
- InducedBreaks
- Chain
- Strand
- BasePair
- Name
Analysis files
In multithreading mode, ROOT data files (molecular-dna_t*.root) associated with the threads are created. ROOT6.x should be installed to analyse these ROOT data files.
Several ROOT macro files are provided to join the ROOT data files into an unique ROOT data file (molecular-dna.root) and analyse the results:
- cylinders.C : to plot damage from cylinders geometry
- ecoli.C : to plot damage from E.coli geometry
- human_cell.C and human_cell_alphas.C: to plot damage and fragments distribution from human cell geometries (as in [3] for human_cell_alphas.C)
root cylinders.C
User can also join the ROOT files (molecular-dna_t*.root) using the following command :
hadd -O -f molecular-dna.root molecular-dna_t*.root
A python macro file is provided to modify ROOT output in SDD [2] file format:
- createSDD.py : to use it, insert the command “python3 createSDD.py”. If error with ROOT, simply source /path/to/root/bin/thisroot.(c)sh, do “pip install pyroot” and try again.
References
[1] Computational modelling of lowenergy electron-induced DNA damage by early physical and chemical events, H. Nikjoo et al., Int. J. Radiat. Biol. 71 (1997) 467–483 - link
[2] A new standard DNA damage (SDD) data format, J. Schuemann et al., Rad. Res. 191 (2019) 76-92 - link
[3] Geant4-DNA simulation of human cancer cells irradiation with helium ion beams, K. Chatzipapas et al., Phys. Med. 112 (2023) 102613 - link