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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Diffusion-controlled reactions modeling in Geant4-DNA

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Author(s):
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Karamitros, M. [1, 2] ; Luan, S. [3] ; Bernal, M. A. [4] ; Allison, J. [5] ; Baldacchino, G. [6, 7] ; Davidkova, M. [8] ; Francis, Z. [9] ; Friedland, W. [10] ; Ivantchenko, V. [5, 11] ; Ivantchenko, A. [5] ; Mantero, A. [12] ; Nieminem, P. [13] ; Santin, G. [13] ; Tran, H. N. [14, 15] ; Stepan, V. [1] ; Incerti, S. [1]
Total Authors: 16
Affiliation:
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[1] CNRS, CENBG, UMR 5797, IN2P3, F-33170 Gradignan - France
[2] CNRS, INCIA, UMR 5287, F-33400 Talence - France
[3] Univ New Mexico, Dept Comp Sci, Albuquerque, NM 87131 - USA
[4] Univ Estadual Campinas, Inst Fis Gleb Wataghin, BR-13081970 Campinas, SP - Brazil
[5] Geant4 Associates Int Ltd, Manchester, Lancs - England
[6] CEA Saclay, IRAMIS, LIDYL, Radiat Phys Chem Grp, F-91191 Gif Sur Yvette - France
[7] CNRS, UMR3299, SIS2M, F-91191 Gif Sur Yvette - France
[8] Acad Sci Czech Republic, Inst Nucl Phys, Prague - Czech Republic
[9] St Joseph Univ, Fac Sci, Dept Phys, Beirut - Lebanon
[10] Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Radiat Protect, D-85764 Neuherberg - Germany
[11] Ecoanalytica, Moscow 119899 - Russia
[12] SwHaRD Srl, I-16153 Genoa - Italy
[13] European Space Agcy, Estec, NL-2200 AG Noordwijk - Netherlands
[14] Ton Duc Thang Univ, Div Nucl Phys, Ho Chi Minh City - Vietnam
[15] Ton Duc Thang Univ, Fac Sci Appl, Ho Chi Minh City - Vietnam
Total Affiliations: 15
Document type: Journal article
Source: Journal of Computational Physics; v. 274, p. 841-882, OCT 1 2014.
Web of Science Citations: 52
Abstract

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: (I) 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 key). 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. (C) 2014 Elsevier Inc. All rights reserved. (AU)

FAPESP's process: 11/51594-2 - Development of a computational system for the simulation of the interaction of ionizing radiations with the human genetic material
Grantee:Mario Antonio Bernal Rodriguez
Support Opportunities: Research Grants - Young Investigators Grants