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molecularDNA

Results and analysis

Table of contents

  1. Implementation overview
    1. Histograms
    2. Tuples
  2. Analysis files
  3. Reference

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
    1. Primary
    2. Energy
    3. PosX in um
    4. PosY in um
    5. PosZ in um
    6. Momentum X
    7. Momentum Y
    8. Momentum Ζ
  • Source (Break Source Frequency)
    1. Primary
    2. Energy
    3. None
    4. SSBd
    5. SSBi
    6. SSBm
    7. DSBd
    8. DSBi
    9. DSBm
    10. DSBh
  • Damage (DNA damage locations)
    1. Event
    2. Primary
    3. Energy
    4. TypeClassification
    5. SourceClassification
    6. Position_x_um
    7. Position_y_um
    8. Position_z_um
    9. Size_nm
    10. FragmentLength
    11. BaseDamage
    12. StrandDamage
    13. DirectBreaks
    14. IndirectBreaks
    15. EaqBaseHits
    16. EaqStrandHits
    17. OHBaseHits
    18. OHStrandHits
    19. HBaseHits
    20. HStrandHits
    21. EnergyDeposited_eV
    22. InducedBreaks
    23. Chain
    24. Strand
    25. BasePair
    26. 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 : to plot damage and fragments distribution from human_cell geometry
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.

Reference

  1. Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events, H. Nikjoo et al.,International Journal of Radiation Biology, 1997, 71, 467
  2. A new standard DNA damage (SDD) data format, J. Schuemann et al., Rad. Res. 191 (2019) 76-92