Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.
Zhu, Hongyu, et al. "A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio." Physics in Medicine and Biology (Online), vol. 65, no. 8, Apr. 2020. https://doi.org/10.1088/1361-6560/ab7a6b
Zhu, Hongyu, McNamara, Aimee L., Ramos-Mendez, Jose, McMahon, Stephen J., Henthorn, Nicholas T., Faddegon, Bruce, Held, Kathryn D., Perl, Joseph, Li, Junli, Paganetti, Harald, & Schuemann, Jan (2020). A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Physics in Medicine and Biology (Online), 65(8). https://doi.org/10.1088/1361-6560/ab7a6b
Zhu, Hongyu, McNamara, Aimee L., Ramos-Mendez, Jose, et al., "A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio," Physics in Medicine and Biology (Online) 65, no. 8 (2020), https://doi.org/10.1088/1361-6560/ab7a6b
@article{osti_1633446,
author = {Zhu, Hongyu and McNamara, Aimee L. and Ramos-Mendez, Jose and McMahon, Stephen J. and Henthorn, Nicholas T. and Faddegon, Bruce and Held, Kathryn D. and Perl, Joseph and Li, Junli and Paganetti, Harald and others},
title = {A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio},
annote = {Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.},
doi = {10.1088/1361-6560/ab7a6b},
url = {https://www.osti.gov/biblio/1633446},
journal = {Physics in Medicine and Biology (Online)},
issn = {ISSN 1361-6560},
number = {8},
volume = {65},
place = {United States},
publisher = {IOP Publishing},
year = {2020},
month = {04}}
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 506, Issue 3https://doi.org/10.1016/S0168-9002(03)01368-8
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 835https://doi.org/10.1016/j.nima.2016.06.125