Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit

Abstract

Computational simulations, such as Monte Carlo track structure simulations, offer a powerful tool for quantitatively investigating radiation interactions within cells. The modelling of the spatial distribution of energy deposition events as well as diffusion of chemical free radical species, within realistic biological geometries, can help provide a comprehensive understanding of the effects of radiation on cells. Track structure simulations, however, generally require advanced computing skills to implement. The TOPAS-nBio toolkit, an extension to TOPAS (TOol for PArticle Simulation), aims to provide users with a comprehensive framework for radiobiology simulations, without the need for advanced computing skills. This includes providing users with an extensive library of advanced, realistic, biological geometries ranging from the micrometer scale (e.g. cells and organelles) down to the nanometer scale (e.g. DNA molecules and proteins). Here we present the geometries available in TOPAS-nBio.

Analysis in the generation of reactive oxygen species through the interaction between the secondary radiation of the compound system (cisplatin and silica nanoparticle) and intracellular water

“…5, it is shown the production of the hydroxyl radical, OH * , which has an inverse behavior to that of hydrogen peroxide. Where it is observed that its production decay of this radical is approximately 80% in a time of nanoseconds, which is consistent with its half-life [9,11]. This last result shows that the hydroxyl radical "existence" time is around a few nanoseconds, which is in agreement with its half-life, as previously expressed.…”

“…In the case that free radicals have been generated in the cell nucleus, these propagate inside it, see chemical reactions (9) and (10), having the ability to attack DNA strands.…”

“…This work simulates the production of reactive oxygen species generated when Auger electrons react with intracellular water. To do this, the TOPAS-nBio [8][9][10] code was used, which was efficient in quantifying the amount of ROS as a function of time and the energy spectrum of the Auger electrons. The reactive species e aq¯s olvated electron, OH * hydroxyl radical, H Hydrogen,…”

Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio

“…The TOPAS-nBio extension is an advanced, yet userfriendly, Monte Carlo track structure simulation tool based on Geant4-DNA (9,10). It offers an extensive library of advanced biological geometries ranging from the micrometer scale (e.g., cells and organelles) down to the nanometer scale (e.g., DNA molecules and proteins) (38) to support simulation studies at the cellular and subcellular levels with the goal of furthering our understanding of radiobiological effects at the DNA (nanometer) scale (38)(39)(40). A full nucleus model was developed based on folding chromatin fibers in a fractal as indicated by Lieberman-Aiden et al (41); the chromatin conformation is consistent with a knot-free fractal globule at the megabase scale.…”

“…Each fiber consists of 51 nucleosomes and contains 15,150 base pairs (bp) of DNA. Chromatin fibers were folded according to a continuous 3D Hilbert space-filling curve (38) to form chromatin fiber loops and fill a voxel (Fig. 1D).…”