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Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach

In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based (“on-lattice”) model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volu...

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Autores principales: Tran, Hoang Ngoc, Chappuis, Flore, Incerti, Sébastien, Bochud, Francois, Desorgher, Laurent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8199710/
https://www.ncbi.nlm.nih.gov/pubmed/34199598
http://dx.doi.org/10.3390/ijms22116023
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author Tran, Hoang Ngoc
Chappuis, Flore
Incerti, Sébastien
Bochud, Francois
Desorgher, Laurent
author_facet Tran, Hoang Ngoc
Chappuis, Flore
Incerti, Sébastien
Bochud, Francois
Desorgher, Laurent
author_sort Tran, Hoang Ngoc
collection PubMed
description In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based (“on-lattice”) model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume (“mesh”), which is divided into sub-volumes (or “voxels”). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME (“hRDME”). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step (“SBS”) Brownian dynamics model and the compartment-based model (“SBS-RDME model”) for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy.
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spelling pubmed-81997102021-06-14 Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach Tran, Hoang Ngoc Chappuis, Flore Incerti, Sébastien Bochud, Francois Desorgher, Laurent Int J Mol Sci Article In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based (“on-lattice”) model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume (“mesh”), which is divided into sub-volumes (or “voxels”). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME (“hRDME”). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step (“SBS”) Brownian dynamics model and the compartment-based model (“SBS-RDME model”) for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy. MDPI 2021-06-02 /pmc/articles/PMC8199710/ /pubmed/34199598 http://dx.doi.org/10.3390/ijms22116023 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tran, Hoang Ngoc
Chappuis, Flore
Incerti, Sébastien
Bochud, Francois
Desorgher, Laurent
Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title_full Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title_fullStr Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title_full_unstemmed Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title_short Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach
title_sort geant4-dna modeling of water radiolysis beyond the microsecond: an on-lattice stochastic approach
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8199710/
https://www.ncbi.nlm.nih.gov/pubmed/34199598
http://dx.doi.org/10.3390/ijms22116023
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