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The Development of Advanced Biological Geometries for the Monte Carlo Toolkit TOPAS-NBio

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A McNamara

A McNamara1*, J Ramos-Mendez2 , J Perl3 , K Held1 , B Faddegon2 , H Paganetti1 , J Schuemann1 , (1) Massachusetts General Hospital & Harvard Med. Sch., Boston, MA, (2) University of California San Francisco, San Francisco, CA, (3) Stanford Linear Accelerator Center, Menlo Park, CA


MO-DE-605-9 (Monday, July 31, 2017) 1:45 PM - 3:45 PM Room: 605

Purpose: Computational simulations, such as Monte Carlo (MC) track structure simulations, offer a powerful tool for quantitatively investigating radiation interactions within the cell. To date, modeled cells have generally been simplistic e.g., spheres. The TOPAS-nBio toolkit, an extension to TOPAS, aims to provide users with a comprehensive framework for radiobiology simulations, including an extensive library of advanced, realistic biological geometries.

Methods: TOPAS-nBio utilizes the physics processes of Geant4-DNA to model particles and their secondary electrons down to vibrational energies (~ 2eV), an energy range significant for damage on the cellular scale. Specialized cell, organelle and molecular geometries have been designed for the toolkit. These geometries range from the micron-scale (e.g., cells and organelles) to complex nano-scale geometries (e.g., DNA and proteins).

Results: Users interact with TOPAS-nBio through easy-to-use input parameter files and can design complex radiobiology experiments without advanced programming skills. Realistic cell geometries are included in the toolkit, such as irregularly shaped cells (e.g., fibroblasts) and neurons. TOPAS-nBio has the ability to read in geometry files from the extensive NeuroMorpho.org database, giving users the capability of simulating over 50000 different types of neuron cell geometries. Most simulation studies assume that nuclear DNA is the only radiation target, however, experimental evidence strongly suggests that non-nuclear targets could exist and contribute to the biological responses. For this reason, extra-nuclear target geometries have also been included in TOPAS-nBio, including circular mitochondria DNA and neuron dendritic spines. Since DNA is undoubtedly the primary target in radiobiology, TOPAS-nBio also includes realistic nuclear DNA geometry, with chromatin fiber folding based on fractal folding.

Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, allowing users without advanced programming skills to design and run complex simulations.

Funding Support, Disclosures, and Conflict of Interest: This work was supported by the National Institutes of Health (NIH)/National Cancer Institute (NCI) grant R01 CA187003

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