Diffusion-controlled reactions modeling in Geant4-DNA

0433589 - ÚJF 2015 RIV US eng J - Článek v odborném periodiku
Karamitros, M. - Luan, S. - Bernal, M. A. - Allison, J. - Baldacchino, G. - Davídková, Marie - Francis, Z. - Friedland, W. - Ivanchenko, A. - Ivanchenko, V. - Mantero, A. - Nieminen, P. - Santin, G. - Tran, H. N. - Stepan, V. - Incerti, S.
Diffusion-controlled reactions modeling in Geant4-DNA.
Journal of Computational Physics. Roč. 274, OCT (2014), s. 841-882. ISSN 0021-9991. E-ISSN 1090-2716
Institucionální podpora: RVO:61389005
Klíčová slova: chemical kinetics simulation * radiation chemistry * Fokker-Planck equation * Smoluchowski diffusion equation * Brownian bridge * dynamical time steps * k-d tree * radiolysis * radiobiology * Geant4-DNA * Brownian dynamics
Kód oboru RIV: BO - Biofyzika
Impakt faktor: 2.434, rok: 2014

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.
Trvalý link: http://hdl.handle.net/11104/0237815