Overview
Version 2 release of our custom TOPAS MC application, Clustered DNA Damage, which incorporates the simulation of indirect action with our DNA model and features updated scoring functionality that categorizes damage resulting from direct and indirect action. Patch notes provided below.
Date: 2022-08-07
The software is provided open source under the MIT license.
Patch notes
Nuclear DNA model:
- Added unique identification of histone volumes via their composing material was added.
Clustered DNA damage scorer:
- Simulation of indirect action events and indirect damage scoring using the model described in:
- Zhu H et al. (2020). Cellular response to proton irradiation: a simulation study with TOPAS-nBio. Radiation Research 194; 9-21.
- Constraints simulated by default during the chemical stage:
- All radical tracks generated inside DNA and histone volumes are immediately terminated.
- ·OH radical tracks are terminated after an indirect action event (whether or not DNA damage was inflicted).
- Radical tracks (·OH, e-aq, and H· specifically) are terminated immediately upon diffusion into a histone volume.
- By default, only ·OH radicals can damage DNA volumes with a damage probability of 40%.
- The damage probabilities of other radiolytic species with backbone or nitrogenous base volumes can be modified via the parameter file.
- Other user-modifiable simulation parameters:
- Toggle to score direct damage.
- Toggle to score indirect damage.
- Toggle for histone scavenging.
- Molecule species scavenged by the DNA volumes.
- Molecule species scavenged by the histone volumes.
- The DNA damage clustering algorithm was updated to account for indirect and hybrid lesions.
- Multithreading support for indirect action simulations to decrease simulation time.