Diffusion-controlled reactions modeling in Geant4-DNA
- University of New Mexico, Department of Computer Science, Albuquerque, NM (United States)
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, SP (Brazil)
- Geant4 Associates International Ltd (United Kingdom)
- CEA Saclay, IRAMIS, LIDYL, Radiation Physical Chemistry Group, F-91191 Gif sur Yvette Cedex (France)
- Nuclear Physics Institute of the ASCR, Prague (Czech Republic)
- Saint Joseph University, Faculty of Sciences, Department of Physics, Mkalles, Beirut (Lebanon)
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Radiation Protection, Ingolstädter Landstr. 1, 85764 Neuherberg (Germany)
- Ecoanalytica, 119899 Moscow (Russian Federation)
- SwHaRD s.r.l., via Buccari 9, 16153 Genova (Italy)
- ESA-ESTEC, 2200 AG Noordwijk (Netherlands)
- Division of Nuclear Physics and Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam)
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France)
Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.
- OSTI ID:
- 22382124
- Journal Information:
- Journal of Computational Physics, Vol. 274; Other Information: Copyright (c) 2014 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9991
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
GENERAL PHYSICS
60 APPLIED LIFE SCIENCES
ALGORITHMS
BIOLOGICAL MATERIALS
COMPARATIVE EVALUATIONS
COMPUTERIZED SIMULATION
DIFFUSION EQUATIONS
DNA
FLUIDS
G CODES
HYDROXIDES
IRRADIATION
MOLECULES
MONTE CARLO METHOD
PROTONS
RADIATION CHEMISTRY
RADIOBIOLOGY
RADIOLYSIS
SOLVATED ELECTRONS
STEADY-STATE CONDITIONS
TIME DEPENDENCE