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bioRxiv · 10.1101/2020.04.09.034926

Development of a Coupled Simulation Toolkit for Computational Radiation Biology Based on Geant4 and CompuCell3D

Liu, R.·Higley, K. A.·Swat, M. J.·Chaplain, M. A.·Powathil, G.·Glazier, J. A.
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Abstract

Understanding and designing clinical radiation therapy is one of the most important areas of state-of-the-art oncological treatment regimens. Decades of research have gone into developing sophisticated treatment devices and optimization protocols for schedules and dosages. In this paper, we presented a comprehensive computational platform that facilitates building of the sophisticated multi-cell-based model of how radiation affects the biology of living tissue. We designed and implemented a coupled simulation method, including a radiation transport model, and a cell biology model, to simulate the tumor response after irradiation. The radiation transport simulation was implemented through Geant4 which is an open-source Monte Carlo simulation platform that provides many flexibilities for users, as well as low energy DNA damage simulation physics, Geant4-DNA. The cell biology simulation was implemented using CompuCell3D (CC3D) which is a cell biology simulation platform. In order to couple Geant4 solver with CC3D, we developed a "bridging" module that extracts tumor cellular geometry of the CC3D simulation (including specification of the individual cells) and ported it to the Geant4 for radiation transport simulation. The cell dose and cell DNA damage distribution in multicellular system were obtained using Geant4. The tumor response was simulated using cell-based tissue models based on CC3D. By merging two powerful and widely used modeling platforms, CC3D and Geant4, we delivered a novel tool that can give us the ability to simulate the dynamics of biological tissue in the presence of ionizing radiation, which provides a powerful framework for quantifying the biological consequences of radiation therapy. The developed tool has an advantage on that it has strong extensibility due to the exploitability of two modeling platforms. In this introductory methods paper, we described our modeling platform in detail and showed how it can be applied to study the application of radiotherapy to a vascularized tumor.

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Liu, R., Higley, K. A., Swat, M. J., Chaplain, M. A., Powathil, G., Glazier, J. A.. 2020-04-10. Development of a Coupled Simulation Toolkit for Computational Radiation Biology Based on Geant4 and CompuCell3D. https://doi.org/10.1101/2020.04.09.034926

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