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Diffusion-controlled reactions modeling in Geant4-DNA

hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
hal.structure.identifierInstitut de Neurosciences cognitives et intégratives d'Aquitaine [INCIA]
dc.contributor.authorKARAMITROS, M.
hal.structure.identifierUNM Computer Science department [New Mexico]
dc.contributor.authorLUAN, S.
hal.structure.identifierInstituto de Fisica "Gleb Wataghin" [INSTITUTO DE FISICA "GLEB WATAGHIN"]
dc.contributor.authorBERNAL, M.A.
hal.structure.identifierGeant4 Associates International Ltd
dc.contributor.authorALLISON, J.
hal.structure.identifierDynamique et Interactions en phase Condensée [DICO]
hal.structure.identifierLaboratoire Interactions, Dynamiques et Lasers (ex SPAM) [LIDYL]
dc.contributor.authorBALDACCHINO, G.
hal.structure.identifierDepartment of Radiation Dosimetry
dc.contributor.authorDAVIDKOVA, M.
hal.structure.identifierDepartment of Physics, Faculty of Sciences
dc.contributor.authorFRANCIS, Z.
hal.structure.identifierHelmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research [UFZ]
dc.contributor.authorFRIEDLAND, W.
hal.structure.identifierGeant4 Associates International Ltd
hal.structure.identifierEcoanalytica
dc.contributor.authorIVANTCHENKO, V.
hal.structure.identifierGeant4 Associates International Ltd
dc.contributor.authorIVANTCHENKO, A.
hal.structure.identifierSwHaRD S.R.L.
dc.contributor.authorMANTERO, A.
hal.structure.identifierEuropean Space Research and Technology Centre [ESTEC]
dc.contributor.authorNIEMINEM, P.
hal.structure.identifierEuropean Space Research and Technology Centre [ESTEC]
dc.contributor.authorSANTIN, G.
hal.structure.identifierFaculty of Applied Sciences
dc.contributor.authorTRAN, H.N.
hal.structure.identifierDepartment of Radiation Dosimetry
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorSTEPAN, V.
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorINCERTI, S.
dc.date.issued2014-10-01
dc.identifier.issn0021-9991
dc.description.abstractEnContext 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.
dc.language.isoen
dc.publisherElsevier
dc.subject.enDynamical time steps
dc.subject.enk–d tree
dc.subject.enChemical kinetics simulation
dc.subject.enRadiation chemistry
dc.subject.enFokker–Planck equation
dc.subject.enSmoluchowski diffusion equation
dc.subject.enBrownian bridge
dc.subject.enRadiolysis
dc.subject.enBrownian dynamics
dc.subject.enRadiobiology
dc.subject.enGeant4-DNA
dc.title.enDiffusion-controlled reactions modeling in Geant4-DNA
dc.typeArticle de revue
dc.identifier.doi10.1016/j.jcp.2014.06.011
dc.subject.halPhysique [physics]/Physique [physics]/Physique Médicale [physics.med-ph]
dc.subject.halChimie/Chimie théorique et/ou physique
bordeaux.journalJournal of Computational Physics
bordeaux.page841–882
bordeaux.volume274
bordeaux.peerReviewedoui
hal.identifiercea-01296702
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//cea-01296702v1
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