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TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.
García García, Omar Rodrigo; Ortiz, Ramon; Moreno-Barbosa, Eduardo; D-Kondo, Naoki; Faddegon, Bruce; Ramos-Méndez, Jose.
Affiliation
  • García García OR; Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico.
  • Ortiz R; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
  • Moreno-Barbosa E; Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico.
  • D-Kondo N; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
  • Faddegon B; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
  • Ramos-Méndez J; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
Int J Mol Sci ; 25(18)2024 Sep 19.
Article in En | MEDLINE | ID: mdl-39337547
ABSTRACT
This work aims to develop and validate a framework for the multiscale simulation of the biological response to ionizing radiation in a population of cells forming a tissue. We present TOPAS-Tissue, a framework to allow coupling two Monte Carlo (MC) codes TOPAS with the TOPAS-nBio extension, capable of handling the track-structure simulation and subsequent chemistry, and CompuCell3D, an agent-based model simulator for biological and environmental behavior of a population of cells. We verified the implementation by simulating the experimental conditions for a clonogenic survival assay of a 2-D PC-3 cell culture model (10 cells in 10,000 µm2) irradiated by MV X-rays at several absorbed dose values from 0-8 Gy. The simulation considered cell growth and division, irradiation, DSB induction, DNA repair, and cellular response. The survival was obtained by counting the number of colonies, defined as a surviving primary (or seeded) cell with progeny, at 2.7 simulated days after irradiation. DNA repair was simulated with an MC implementation of the two-lesion kinetic model and the cell response with a p53 protein-pulse model. The simulated survival curve followed the theoretical linear-quadratic response with dose. The fitted coefficients α = 0.280 ± 0.025/Gy and ß = 0.042 ± 0.006/Gy2 agreed with published experimental data within two standard deviations. TOPAS-Tissue extends previous works by simulating in an end-to-end way the effects of radiation in a cell population, from irradiation and DNA damage leading to the cell fate. In conclusion, TOPAS-Tissue offers an extensible all-in-one simulation framework that successfully couples Compucell3D and TOPAS for multiscale simulation of the biological response to radiation.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Radiation, Ionizing / Monte Carlo Method / DNA Repair Limits: Humans Language: En Journal: Int J Mol Sci Year: 2024 Document type: Article Affiliation country: Mexico Country of publication: Switzerland

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Radiation, Ionizing / Monte Carlo Method / DNA Repair Limits: Humans Language: En Journal: Int J Mol Sci Year: 2024 Document type: Article Affiliation country: Mexico Country of publication: Switzerland