A convenient (and computationally efficient) way to benchmark Monte Carlo is by modeling DNA damage induced by radiation using DNA plasmid supercoiled models.
In our group, the Monte Carlo Track-Structure tool TOPAS-nBio is validated by reproducing the experimental conditions of dissolved DNA plasmid in solutes irradiated by low LET particles (electrons, photons). These conditions include absorbed dose, temperature, the scavenging capacity of solutes, and DNA supercoiling degree, among others. By using low LET particles, the indirect damage produced by radiolytic species is substantial thus, the physical-chemical stages of water radiolysis can be accurately benchmarked.
Relevant Publications
- D-Kondo N, Masilela T A M, Shin W-G, Faddegon B, LaVerne J, Schuemann J and Ramos-Mendez J 2024 Modeling the oxygen effect in DNA strand break induced by gamma-rays with TOPAS-nBio Phys. Med. Biol. 69 215028
- Sakata D, et al., 2023 Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA Physica Medica 105 102508
- Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne J A, Schuemann J, Moreno-Barbosa E and Faddegon B 2022 TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields Phys. Med. Biol. 67 145007
- Ramos-Mendez J A, LaVerne J A, Domínguez-Kondo J N, Milligan J, Stepan V, Stefanová K, Perrot Y, Villagrasa C, Shin W-G, Incerti S, McNamara A L, Paganetti H, Perl J, Schuemann J and Faddegon B A 2021 TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation Phys. Med. Biol. Online: https://iopscience.iop.org/article/10.1088/1361-6560/ac1f39
- D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B and Ramos-Méndez J 2021 DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions Phys. Med. Biol. 66 245017