TOPAS-nBio is an extension to the TOPAS toolkit that is being developed as part of an ongoing NCI-R01. The goal is to follow the approach of the TOPAS software package, making Monte Carlo simulations easy-to-use with focus on radiation biology at sub-cellular scales. 

TOPAS-nBio is based on the Geant4-DNA extension to Geant4, including track structure simulations in cell and sub-cellular geometries, first physicochemical and chemical reactions. The aim is to provide biologically relevant properties such as single and double strand breaks of nuclear DNA about 1 microsecond post-irradiation, i.e. before the onset of repair processes.

TOPAS-nBio is described in mode detail here. This page includes a class documentation and the license. The TOPAS-nBio package was described in Schuemann et al., Radiation Research, 2019, 191(2), p.125. This reference should be cited for all work using the TOPAS-nBio package.

TOPAS-nBio is an extension of TOPAS (TOol for PArticle Simulations), which can be obtained here. The TOPAS documentation can be found here.

The extension source code of the extension can be found here


Key MGH personnel involved

  • Jan Schuemann, PhD (PI)
  • Kathryn Held, PhD
  • Harald Paganetti, PhD 
  • Kathryn Held, PhD
  • Aimee McNamara, PhD


  • Joseph Perl (SLAC)
  • Bruce Faddegon (UCSF)
  • Jose Ramos Mendez (UCSF)
  • Dudley Goodhead (Medical Research Council, UK)



  • Wonmo Sung, PhD
  • Hongyu Zhu, PhD student