Features Of TOPAS-NBio - Release 1.0
Schuemann, J. McNamara, A. Ramos-Mendez, J. Dominguez-Kondo, N. Perl, J. Yoo, D. Henthorn, Nicholas Warmenhoven, John Ingram, Samuel Merchant, Michael J
Schuemann, J.
McNamara, A.
Ramos-Mendez, J.
Dominguez-Kondo, N.
Perl, J.
Yoo, D.
Henthorn, Nicholas
Warmenhoven, John
Ingram, Samuel
Merchant, Michael J
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Abstract
Purpose: The goal of the TOPAS-nBio project is to provide intuitive nanometer scale Monte Carlo (MC) simulations for radiobiology experiments that do not require
programming expertise. Here we present new functionalities of the TOPAS-nBio system available in the first full release (v1.0). Methods: Since the open-source
beta-release of TOPAS-nBio in 2019, the framework offers to connect energy deposition within irradiated cells (physics) via molecular reactions (chemistry) to cell
kill/repair (biology) at the level of sub-cellular targets such as DNA. To facilitate the setup of simulations we further developed a Graphical User (GUI) Interface.
TOPAS-nBio is an extension to TOPAS and layered on top of the Geant4/Geant4-DNA MC toolkit. The new release was built for TOPAS release 3.6 (based on
Geant4.10.6.p3) and will be compatible with all future releases of TOPAS. Results: New geometries that were developed include two new methods to fill the cell
nucleus: a whole nucleus DNA model using chromatin fibers and a fractal walk filling pattern, as well as a filling of the nucleus using spheres to represent topologically
associated domains (TADs) of DNA based on the Hi-C technique. New scoring options offer direct scoring of single and double strand breaks (SSB and DSB) as
well as output the DNA damage in the SDD (Standard for DNA Damage) scoring format. Chemistry was improved to provide better agreement with experimental
data of G-values, both for step-by-step chemistry and a newly included independent reaction time method, which offers faster chemistry simulations. Biological
outcome can now be simulated directly within TOPAS-nBio using the DaMaRiS biological effect model, or via the SDD which offers a convenient interface to other
models such as MEDRAS. Conclusion: The new features of TOPAS-nBio v1.0, offer improved modeling from initial DNA damage to cell outcome, or from energy
depositions to G-value propagation over time is possible
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Date
2021
Publisher
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Citation
Schuemann J, McNamara A, Ramos-Mendez J, Dominguez-Kondo N, Perl J, Yoo D, et al. Features Of TOPAS-NBio - Release 1.0. Medical Physics. 2021;48(6).