MyTOPASProject

The pipeline couples track-structure Monte Carlo simulation in realistic ellipsoidal cell/nucleus geometries with mechanistic DNA repair/misrepair modeling, enabling dose–response analysis before and after repair under low-dose-rate internal irradiation.

This repository supports low-dose-rate internal irradiation studies by coupling track-structure Monte Carlo simulation (OpenTOPAS / TOPAS-nBio / TOPAS-CellModels) with downstream DNA damage analysis (and optionally repair/misrepair modeling), enabling dose–response characterization in realistic ellipsoidal cell/nucleus geometries.

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Key custom features (implemented in this project)

Compared with stock components, this project includes custom implementations for:

• Regular multi-cell arrangement on the bottom of the culture medium
• Ellipsoidal phase-space scoring surface on/around the target nucleus
  (used to collect particles reaching the target ellipsoidal surface)
• Ellipsoidal cell membrane/cytoplasm
• Ellipsoidal nucleus

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Repository layout

• OpenTOPAS/
  OpenTOPAS source code (included for reproducibility)

• TOPAS-nBio/
  TOPAS-nBio extension (sub-cellular radiobiology framework)

• TOPAS-CellModels/
  Cell model extension (cell/nucleus/membrane geometries)

• geant4/
  Geant4 source code (included for reproducibility)

• Project Python scripts (workflow entry points)

  • process_phsp.py
    Data collection & summarization.
    This script is used to:

    1. collect particle information reaching the target ellipsoidal phase-space surface, and
    2. collect information related to nuclear DNA damage induced by irradiation,
       then export structured tables for convenient statistics and plotting.

  • beta_medium_topasfile.py
    Scenario: β electrons emitted by radionuclides in the culture medium → scored on the target nucleus surface phase space.

  • IC_medium_topasfile.py
    Scenario: IC (internal conversion) electrons emitted by radionuclides in the culture medium → scored on the target nucleus surface phase space.

  • beta_cell_topasfile.py
    Scenario: β electrons emitted by radionuclides in the target cell and surrounding cells (typically cytoplasm, and can also represent membrane depending on configuration)
    → scored on the target nucleus surface phase space.

  • IC_cell_topasfile.py
    Scenario: IC electrons emitted by radionuclides in the target cell and surrounding cells (typically cytoplasm, and can also represent membrane depending on configuration)
    → scored on the target nucleus surface phase space.

Note: With appropriate parameter settings, beta_cell_topasfile.py and IC_cell_topasfile.py can also represent radionuclide distributions in the cell membrane (instead of cytoplasm).

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Typical pipeline

1. Generate TOPAS input using one of:

   • beta_medium_topasfile.py
   • IC_medium_topasfile.py
   • beta_cell_topasfile.py
   • IC_cell_topasfile.py

2. Run OpenTOPAS with the generated parameter file(s) to produce:

   • phase-space outputs on the target ellipsoidal surface
   • DNA damage outputs (depending on your scoring configuration)

3. Post-process / summarize using process_phsp.py to obtain structured tables for statistics and plotting.

Note

The exact output paths / naming conventions depend on how you set parameters inside each script and which TOPAS scoring blocks you enable. If you change output directories or file name prefixes, keep the post-processing script consistent.

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Quick start

• For Debian/Ubuntu, follow:
  • OpenTOPAS_quickStart_Debian.md

If you already have your own OpenTOPAS build workflow, make sure the build/runtime configuration properly enables the TOPAS-nBio and TOPAS-CellModels extensions.

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Reproducibility tips (recommended)

To make results easier to reproduce, consider recording the following in your notes / issues / supplementary material:

• OS / compiler / CMake versions
• Geant4 / OpenTOPAS / TOPAS-nBio versions (or commit IDs)
• key physics list + cuts/steps + scoring configuration summary
• random seed strategy and number of histories
• output directory structure (phase space vs. damage outputs)

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References & acknowledgements

• OpenTOPAS documentation: https://opentopas.readthedocs.io/
• TOPAS-nBio documentation: https://topas-nbio.readthedocs.io/
• Geant4: https://geant4.org/

If you use TOPAS-nBio in publications, please cite the TOPAS-nBio reference listed in the TOPAS-nBio repository documentation.

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Bugs / contact

If you encounter issues, please open a GitHub Issue with:

• your OS + compiler + CMake version
• build log snippet (or runtime error log)
• minimal input needed to reproduce the issue (minimal parameter file + relevant scripts/data)