Monte Carlo track-structure and Agent-based algorithms.

Monte Carlo track-structure (MCTS) has proven high accuracy in modeling radiation-induced biological damage. However, there exist limitations in terms of scalability and accountability of biological cell behavior. Agent-based software allows scalability and accounts for cell behavior but lacks sufficient resolution to determine radiation-induced damage from first principles. Our group develops a framework for coupling two powerful modeling tools: 1) TOPAS-nBio [1] for simulating the ionizing radiation transport and radiobiology, and 2) CompuCell3D [2] for simulation of celluar behavior and microenvironment.

Coupled TOPAS-nBio/Compucell3D simulation of a cell colony growth, irradiation, and cell fate.

Relevant Publications.

  • Ortiz R and Ramos-Méndez J 2024 Tumor growth and vascular redistribution contributes to the dosimetric preferential effect of microbeam radiotherapy: a Monte Carlo study Sci Rep 14 26585 https://www.nature.com/articles/s41598-024-77415-5
  • García O R G, Ortiz R, Moreno-Barbosa E, D-Kondo N, Faddegon B and Ramos-Méndez J 2024 TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level. Int. J. Mol. Sci. 2024, 25, 10061. https://doi.org/10.3390/ijms251810061
  • Ortiz R and Ramos-Mendez J 2024 A clustering tool for generating biological geometries for computational modeling in radiobiology. Phys. Med. Biol., https://doi.org/10.1088/1361-6560/ad7f1d

 

References

[1] Schuemann J, McNamara A L, Ramos-Méndez J, Perl J, Held K D, Paganetti H, Incerti S and Faddegon B 2018 TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology Radiation Research 191 125. http://www.rrjournal.org/doi/10.1667/RR15226.1

[2] Shirinifard A, Gens J S, Zaitlen B L, Popławski N J, Swat M and Glazier J A 2009 3D Multi-Cell Simulation of Tumor Growth and Angiogenesis ed N A Hotchin PLoS ONE 4 e7190. https://doi.org/10.1371/journal.pone.0007190