OpenTOPAS-nBio is an extension to the OpenTOPAS toolkit that is being developed as part of an ongoing NCI-R01. The goal is to follow the approach of the OpenTOPAS software package, making Monte Carlo simulations easy-to-use with focus on radiation biology at sub-cellular scales.
OpenTOPAS-nBio (also called TOPAS-nBio or just 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.
OpenTOPAS-nBio is described in mode detail here. This page includes a class documentation and the license. The OpenTOPAS-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 OpenTOPAS-nBio package.
OpenTOPAS-nBio is an extension of OpenTOPAS (TOol for PArticle Simulations), which can be obtained here. The OpenTOPAS 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
- Wook-Geun Shin, PhD
- Isaac Meyer, PhD
- Victor V. Onecha, PhD
Collaborators
- Jose Ramos Mendez, PhD (UCSF)
- Bruce Faddegon, PhD (UCSF)
- Naoki Dominguez Kondo, PhD (UCSF)
- Ramon Ortiz, PhD (UCSF)
- Thongchai Masilela, PhD (UCSF)
- John Warmenhoven (U Manchester)
- Nick Henthorn, PhD (U Manchester)
- Sam Ingram, PhD (U Manchester)
- Charlotte Heaven, PhD (U Manchester)
- Stephen McMahon, PhD (QUB)
- Jay LaVerne, PhD (Notre Dame)
- Dudley Goodhead, PhD (Medical Research Council, UK)
Alumni
- Aimee McNamara, PhD
- Wonmo Sung, PhD
- Hongyu Zhu, PhD
- Jungwook Shin, PhD
