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1. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit

Author

K. Murakami, Susanna Guatelli, Vladimir Ivanchenko, Takashi Sasaki, Jeremy M. C. Brown, Ioanna Kyriakou, E. Delage, Mario A. Bernal, H. Payno, Marie-Claude Bordage, Ivan Petrović, Sylvain Meylan, Q.T. Pham, Aleksandra Ristić-Fira, Shirin A. Enger, Yann Perrot, Ziad Francis, Václav Štěpán, Shogo Okada, Z. El Bitar, M. Karamitros, Carmen Villagrasa, Lydia Maigne, Sebastien Incerti, Marie Davídková, H.N. Tran, Instituto de Fisica 'Gleb Wataghin', Universidade Estadual de Campinas (UNICAMP), Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), School of Mathematics and Physics [Belfast], Queen's University [Belfast] (QUB), School of Physics and Astronomy [Clayton], Monash University [Clayton], Department of Radiation Dosimetry, Nuclear Physics Institute of the AS CR, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Medical Physics Unit, Department of Oncology, McGill University = Université McGill [Montréal, Canada], Department of Physics, Faculty of Sciences, Université Saint-Joseph de Beyrouth (USJ), Centre for Medical Radiation Physics, University of Wollongong [Australia], Geant4 Associates International Ltd, Ecoanalytica, Notre Dame Radiation Laboratory, University of Notre Dame [Indiana] (UND), Medical Physics Laboratory, Medical School University of Ioannina, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), KEK (High energy accelerator research organization), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], Division of Nuclear Physics, Tong Duc Thang University, Faculty of Applied Sciences, Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Nuclear Physics Institute of the ASCR, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), McGill University, University of Wollongong, High Energy Accelerator Research Organization (KEK), University of Tsukuba, Universidade Estadual de Campinas = University of Campinas (UNICAMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), University of Ioannina, and Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Chemical process, Ionizing radiation, Chemical Phenomena, Stochastic modelling, Liquid water, Monte Carlo method, Biophysics, General Physics and Astronomy, Track (rail transport), Radiolysis, Humans, Radiology, Nuclear Medicine and imaging, Monte Carlo, Simulation, Physics, Structure (mathematical logic), Physical model, Geant4-DNA, Water, Radiobiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, DNA, General Medicine, Extension (predicate logic), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Systems engineering, Monte Carlo Method
Abstract

International audience; Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of today's radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described.

Published
2015
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2. Diffusion-controlled reactions modeling in Geant4-DNA

Author

Shuang Luan, John Allison, V. Stepan, Sebastien Incerti, Giovanni Santin, Mario A. Bernal, Marie Davídková, G. Baldacchino, M. Karamitros, A. Ivantchenko, H.N. Tran, Werner Friedland, A. Mantero, V. Ivantchenko, P. Nieminem, Ziad Francis, Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut de Neurosciences cognitives et intégratives d'Aquitaine (INCIA), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), UNM Computer Science department [New Mexico], The University of New Mexico [Albuquerque], Instituto de Fisica 'Gleb Wataghin' (INSTITUTO DE FISICA 'GLEB WATAGHIN'), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Geant4 Associates International Ltd, Dynamique et Interactions en phase Condensée (DICO), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Radiation Dosimetry, Nuclear Physics Institute of the AS CR, Department of Physics, Faculty of Sciences, Université Saint-Joseph de Beyrouth (USJ), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Ecoanalytica, SwHaRD S.R.L., European Space Research and Technology Centre (ESTEC), Agence Spatiale Européenne = European Space Agency (ESA), Faculty of Applied Sciences, Tong Duc Thang University, Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas (UNICAMP), Biomolécules Excitées (DICO), and European Space Agency (ESA)

Subjects
k–d tree, Physics and Astronomy (miscellaneous), Smoluchowski diffusion equation, Chemical reaction, symbols.namesake, Brownian dynamics, Radiolysis, Molecule, Statistical physics, Dynamical time steps, Physics, Numerical Analysis, Smoluchowski coagulation equation, Chemical kinetics simulation, Geant4-DNA, Applied Mathematics, Radiobiology, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Computational Mathematics, Chemical species, Cascade, Modeling and Simulation, Brownian bridge, symbols, Fokker–Planck equation, [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], Radiation chemistry, Biological system
Abstract

International audience; 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.

Published
2014
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3. Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study

Author

Incerti, Sebastien, Psaltaki, Maria G., Gillet, Pierre, Barberet, Ph., Bardies, M., Bernal, Mario A., Bordage, Marie Claude, Breton, Vincent, Davídková, Marie, Delage, E., El Bitar, Ziad Ei, Francis, Ziad, Guatelli, Susanna, Ivanchenko, A., Ivanchenko, Vladimir, Karamitros, Mathieu, Lee, Sebyeong, Maigne, Lydia, Meylan, Sylvain, Murakami, Kouichi, Nieminen, Petteri H., Payno, H., Perrot, Yann, Petrović, Ivan M., Pham, Q. T., Ristić-Fira, Aleksandra, Santin, Giovanni, Sasaki, Takashi, Seznec, Herve, Shin, Jae-ik, Stepan, Vaclav, Tran, Ngoc Hoang, Villagrasa, Carmen, Geant4-DNA Collaboration, Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), National Technical University of Athens [Athens] (NTUA), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Instituto de Fisica 'Gleb Wataghin' (INSTITUTO DE FISICA 'GLEB WATAGHIN'), Universidade Estadual de Campinas (UNICAMP), Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Radiation Dosimetry, Nuclear Physics Institute of the AS CR, Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Faculty of Sciences, Université Saint-Joseph de Beyrouth (USJ), Centre for Medical Radiation Physics, University of Wollongong [Australia], Geant4 Associates International (G4AI), Ecoanalytica, Institut de Neurosciences cognitives et intégratives d'Aquitaine (INCIA), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), Proton Therapy Center, National Cancer Center Korea, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), KEK (High energy accelerator research organization), European Space Research and Technology Centre (ESTEC), European Space Agency (ESA), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], Ton Duc Thang University [Hô-Chi-Minh-City], Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), and Agence Spatiale Européenne = European Space Agency (ESA)

Subjects
Nuclear and High Energy Physics, Work (thermodynamics), Radiation transport, Physics::Medical Physics, Reference data (financial markets), Monte Carlo method, Ion, Deposition (phase transition), Statistical physics, Instrumentation, Monte Carlo, Physics, Energy depositions, [PHYS]Physics [physics], Geant4-DNA, Ion track, Geant4 dnas, Monte Carlo methods, Liquids, DNA, Analytical calculation, Monte- carlo simulations, Charged particle, Computational physics, Comparative studies, Liquid water, Dose, Dynamic Monte Carlo method
Abstract

International audience; An accurate modeling of radial energy deposition around ion tracks is a key requirement of radiation transport software used for simulations in radiobiology at the sub-cellular scale. The work presented in this paper is part of the on-going benchmarking of the "Geant4-DNA" physics processes and models, which are available in the Geant4 Monte Carlo simulation toolkit for the low energy transport of particles in liquid water. We present for the first time radial dose distributions of incident ion tracks simulated with "Geant4-DNA". Simulation results are compared to other results available in the literature, obtained from analytical calculations, step-by-step Monte Carlo simulations and measurements. They show a reasonable agreement with reference data. © 2014 Elsevier B.V. All rights reserved.

Published
2014
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4. Dose point kernels in liquid water: An intra-comparison between GEANT4-DNA and a variety of Monte Carlo codes

Author

Vladimir Ivanchenko, Michel Fromm, L. Campos, B. Mascialino, Marie-Claude Bordage, Sebastien Incerti, Christophe Champion, J.-E. Groetz, Yann Perrot, H.N. Tran, R. Delorme, Manuel Bardiès, Mario A. Bernal, Ziad Francis, Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Modélisation et Simulation de Systèmes (LM2S), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, LAboratoire PLasma et Conversion d'Energie (LAPLACE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Saint-Joseph de Beyrouth (USJ), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), ANR-09-BLAN-0135,Geant4-DNA,Modélisation des dommages à l'ADN induits par les rayonnements ionisants avec l'outil Monte Carlo Geant4 et validation expérimentale(2009), Interface Physique et Chimie pour le Vivant ( IPCV ), Centre d'Etudes Nucléaires de Bordeaux Gradignan ( CENBG ), Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique Corpusculaire - Clermont-Ferrand ( LPC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Information, Modèles, Apprentissage [Gif-sur-Yvette], Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire Plasma et Conversion d'Energie [Toulouse] ( LAPLACE ), Institut National Polytechnique [Toulouse] ( INP ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche en Cancérologie de Toulouse ( CRCT ), Université Paul Sabatier - Toulouse 3 ( UPS ) -CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Department of medical radiation physics, Stockholm University, Eco-Analytica Laboratory, North-West University [South Aftrica] ( NWU ), Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas ( UNICAMP ), Université Saint-Joseph de Beyrouth ( USJ ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Departamento de Física, Universidade Federal de Sergipe, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Ecoanalytica, Instituto de Fisica 'Gleb Wataghin' (INSTITUTO DE FISICA 'GLEB WATAGHIN'), Universidade Estadual de Campinas (UNICAMP), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Universidade Federal de Sergipe, Departamento de Física, Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Laboratoire Chrono-environnement (UMR 6249) (LCE), Fromm, Michel, and Blanc - Modélisation des dommages à l'ADN induits par les rayonnements ionisants avec l'outil Monte Carlo Geant4 et validation expérimentale - - Geant4-DNA2009 - ANR-09-BLAN-0135 - Blanc - VALID

Subjects
[PHYS.NUCL]Physics [physics]/Nuclear Theory [nucl-th], [PHYS.NEXP] Physics [physics]/Nuclear Experiment [nucl-ex], Monte Carlo method, Physics::Medical Physics, Elementary particle, Context (language use), Electron, PENELOPE, [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], modelling, particle transport, Dosimetry, Point (geometry), Statistical physics, Monte Carlo, MCNPX, radiotherapy, Physics, energy-matter interaction, Monte Carlo codes, [PHYS.PHYS.PHYS-MED-PH] Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], [STAT.ME] Statistics [stat]/Methodology [stat.ME], Radiation, dosimetry, simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Charged particle, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Liquid water, Dose point kernel, [ CHIM.THEO ] Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], GEANT4-DNA, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, ionizing radiation, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Lepton
Abstract

International audience; Modeling the radio-induced effects in biological medium still requires accurate physics models to describe the interactions induced by all the charged particles present in the irradiated medium in detail. These interactions include inelastic as well as elastic processes. To check the accuracy of the very low energy models recently implemented into the GEANT4 toolkit for modeling the electron slowing-down in liquid water, the simulation of electron dose point kernels remains the preferential test. In this context, we here report normalized radial dose profiles, for mono-energetic point sources, computed in liquid water by using the very low energy "GEANT4-DNA" physics processes available in the GEANT4 toolkit. In the present study, we report an extensive intra-comparison of profiles obtained by a large selection of existing and well-documented Monte-Carlo codes, namely, EGSnrc, PENELOPE, CPA100, FLUKA and MCNPX.

Published
2014
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5. Chlorine Distribution in Soil and Vegetation in Boreal Habitats along a Moisture Gradient from Upland Forest to Lake Margin Wetlands.

Author

Svensson T, Löfgren A, Saetre P, Kautsky U, and Bastviken D

Subjects
Chlorine analysis, Wetlands, Chlorides, Forests, Plants, Ecosystem, Soil
Abstract

The assumed dominance of chloride (Cl - ) in terrestrial ecosystems is challenged by observations of extensive formation of organically bound Cl (Cl org ), resulting in large soil Cl storage and internal cycling. Yet, little is known about the spatial distribution of Cl in ecosystems. We quantified patterns of Cl distribution in different habitats along a boreal hillslope moisture gradient ranging from relatively dry upland coniferous forests to wet discharge areas dominated by alder. We confirmed that dry habitats are important for Cl storage but found that Cl pools tended to be larger in moist and wet habitats. The storage of Cl org was less important in wet habitats, suggesting a shift in the balance between soil chlorination and dechlorination rates. Cl concentrations in the herb layer vegetation were high in wet and moist sites attributed to a shift in plant species composition, indicating plant community-dependent ecosystem Cl cycling. Mass-balance calculations showed that internal Cl cycling increased overall ecosystem Cl residence times at all sites and that plant uptake rates of Cl - were particularly high at wet sites. Our results indicate that habitat characteristics including plant communities and hydrology are key for understanding Cl cycling in the environment.

Published
2023
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6. A carbon mass-balance budget for a periglacial catchment in West Greenland - Linking the terrestrial and aquatic systems.

Author

Lindborg T, Rydberg J, Andersson E, Löfgren A, Lindborg E, Saetre P, Sohlenius G, Berglund S, Kautsky U, and Laudon H

Abstract

Climate change is predicted to have far reaching consequences for the mobility of carbon in arctic landscapes. On a regional scale, carbon cycling is highly dependent on interactions between terrestrial and aquatic parts of a catchment. Despite this, studies that integrate the terrestrial and aquatic systems and study entire catchments using site-specific data are rare. In this work, we use data partly published by Lindborg et al. (2016a) to calculate a whole-catchment carbon mass-balance budget for a periglacial catchment in West Greenland. Our budget shows that terrestrial net primary production is the main input of carbon (99% of input), and that most carbon leaves the system through soil respiration (90% of total export/storage). The largest carbon pools are active layer soils (53% of total carbon stock or 13 kg C m -2 ), permafrost soils (30% of total carbon stock or 7.6 kg C m -2 ) and lake sediments (13% of total carbon stock or 10 kg C m -2 ). Hydrological transport of carbon from the terrestrial to aquatic system is lower than in wetter climates, but the annual input of 4100 kg C yr -1 (or 3.5 g C m -2 yr -1 ) that enters the lake via runoff is still three times larger than the eolian input of terrestrial carbon. Due to the dry conditions, the hydrological export of carbon from the catchment is limited (5% of aquatic export/storage or 0.1% of total export/storage). Instead, CO 2 evasion from the lake surface and sediment burial accounts for 57% and 38% of aquatic export/storage, respectively (or 0.8% and 0.5% of total export/storage), and Two-Boat Lake acts as a net source of carbon to the atmosphere. The limited export of carbon to downstream water bodies make our study system different from wetter arctic environments, where hydrological transport is an important export pathway for carbon., (Copyright © 2019 The Author(s). Published by Elsevier B.V. All rights reserved.)

Published
2020
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7. Environmental DNA (eDNA) detects the pool frog (Pelophylax lessonae) at times when traditional monitoring methods are insensitive.

Author

Eiler A, Löfgren A, Hjerne O, Nordén S, and Saetre P

Subjects
Animals, Endangered Species, Probability, DNA analysis, Environmental Monitoring methods, Ranidae genetics
Abstract

Detection of endangered species is invaluable for conservation efforts, yet many traditional sampling techniques are ineffective at low population abundances or during certain periods of the year. Here, we compared results from a newly developed eDNA approach and the traditional observational method for the endangered pool frog (Pelophylax lessonae). Analysis using an occupancy-modeling framework indicated that the probability of pools being occupied using eDNA (0.93) was higher than for the traditional method of counting calling males and silent observed individuals (0.72). Detailed analysis revealed complementarity among the methods. That is, the traditional method gave a high rate of observation in June, whereas eDNA gave at least as many or more observations during other parts of the year. Discrepancies among the methods depended on the dominant lifecycle stage, and eDNA concentrations were higher when juveniles were present than at times when spawning occurred. eDNA concentrations were also positively related to P. lessonae observations. Our study demonstrates that an eDNA protocol for monitoring of endangered amphibian species can be particularly valuable during periods when individuals are hard to detect by observational methods, and provides guidance to sampling efforts for research and monitoring programs in other regions and systems.

Published
2018
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8. Local dose enhancement of proton therapy by ceramic oxide nanoparticles investigated with Geant4 simulations.

Author

McKinnon S, Guatelli S, Incerti S, Ivanchenko V, Konstantinov K, Corde S, Lerch M, Tehei M, and Rosenfeld A

Subjects
Cerium chemistry, Cerium pharmacology, Gold chemistry, Humans, Male, Metal Nanoparticles chemistry, Prostatic Neoplasms radiotherapy, Radiotherapy Dosage, Tantalum chemistry, Tantalum pharmacology, Monte Carlo Method, Nanoparticles, Oxides chemistry, Oxides pharmacology, Proton Therapy methods, Radiation Dosage
Abstract

Nanoparticles (NPs) have been shown to enhance X-ray radiotherapy and proton therapy of cancer. The effectiveness of radiation damage is enhanced in the presence of high atomic number (high-Z) NPs due to increased production of low energy, higher linear energy transfer (LET) secondary electrons when NPs are selectively internalized by tumour cells. This work quantifies the local dose enhancement produced by the high-Z ceramic oxide NPs Ta 2 O 5 and CeO 2 , in the target tumour, for the first time in proton therapy, by means of Geant4 simulations. The dose enhancement produced by the ceramic oxides is compared against gold NPs. The energy deposition on a nanoscale around a single nanoparticle of 100nm diameter is investigated using the Geant4-DNA extension to model particle interactions in the water medium. Enhancement of energy deposition in nano-sized shells of water, local to the NP boundary, ranging between 14% and 27% was observed for proton energies of 5MeV and 50MeV, depending on the NP material. Enhancement of electron production and energy deposition can be correlated to the direct DNA damage mechanism if the NP is in close proximity to the nucleus., (Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.)

Published
2016
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9. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit.

Author

Bernal MA, Bordage MC, Brown JMC, Davídková M, Delage E, El Bitar Z, Enger SA, Francis Z, Guatelli S, Ivanchenko VN, Karamitros M, Kyriakou I, Maigne L, Meylan S, Murakami K, Okada S, Payno H, Perrot Y, Petrovic I, Pham QT, Ristic-Fira A, Sasaki T, Štěpán V, Tran HN, Villagrasa C, and Incerti S

Subjects
Chemical Phenomena, Humans, DNA chemistry, Models, Molecular, Monte Carlo Method, Water chemistry
Abstract

Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of today's radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described., (Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.)

Published
2015
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10. The Influence of DNA Configuration on the Direct Strand Break Yield.

Author

Bernal MA, deAlmeida CE, Incerti S, Champion C, Ivanchenko V, and Francis Z

Subjects
Algorithms, Computational Biology, Computer Simulation, DNA, A-Form radiation effects, DNA, B-Form radiation effects, DNA, Z-Form radiation effects, Humans, Linear Energy Transfer, Models, Theoretical, Nucleic Acid Conformation, Probability, Software, DNA Breaks, Double-Stranded radiation effects, DNA, A-Form chemistry, DNA, B-Form chemistry, DNA, Z-Form chemistry
Abstract

Purpose: To study the influence of DNA configuration on the direct damage yield. No indirect effect has been accounted for., Methods: The GEANT4-DNA code was used to simulate the interactions of protons and alpha particles with geometrical models of the A-, B-, and Z-DNA configurations. The direct total, single, and double strand break yields and site-hit probabilities were determined. Certain features of the energy deposition process were also studied., Results: A slight increase of the site-hit probability as a function of the incident particle linear energy transfer was found for each DNA configuration. Each DNA form presents a well-defined site-hit probability, independently of the particle linear energy transfer. Approximately 70% of the inelastic collisions and ~60% of the absorbed dose are due to secondary electrons. These fractions are slightly higher for protons than for alpha particles at the same incident energy., Conclusions: The total direct strand break yield for a given DNA form depends weakly on DNA conformation topology. This yield is practically determined by the target volume of the DNA configuration. However, the double strand break yield increases with the packing ratio of the DNA double helix; thus, it depends on the DNA conformation.

Published
2015
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