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.

• Klíčová slova
• Geant4-DNA, Ionizing radiation, Monte Carlo, Radiobiology, Radiolysis,
• MeSH
• chemické jevy MeSH
• DNA chemie   MeSH
• lidé MeSH
• metoda Monte Carlo * MeSH
• molekulární modely * MeSH
• voda chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• DNA MeSH
• voda MeSH

The preservation of cultural heritage is very important. Ionizing radiation is widely used for this purpose and use of gamma irradiation has become common practice in cultural heritage preservation. The number of available electron accelerators is two orders of magnitude greater than for gamma facilities, and many countries do not have gamma facilities. In this work we demonstrate the possibility of using an electron accelerator and X-rays generated from accelerated electrons for radiation treatment of wooden cultural heritage. The GEANT4 toolkit was used for the simulation of the passage of particles through matter. The accuracy of radiation treatment numerical simulation in comparison with experiment was in range of 1.5-11.8%.

• Klíčová slova
• Cultural heritage, Dose mapping, Electron beam accelerator, GEANT4, Radiation treatment, X-rays,
• Publikační typ
• časopisecké články MeSH

PURPOSE: The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy. METHODS: The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for • OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented. RESULTS: The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, • OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for • OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities. CONCLUSION: The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.

• Klíčová slova
• Geant4-DNA, LET, Monte Carlo, independent reaction times, radiolysis, track-structure,
• MeSH
• chemické modely * MeSH
• DNA MeSH
• lineární přenos energie * MeSH
• metoda Monte Carlo MeSH
• počítačová simulace MeSH
• reakční čas MeSH
• voda MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH
• voda MeSH

PURPOSE: The Geant4 Monte Carlo simulation toolkit was used to reproduce radiobiological parameters measured by irradiating three different cancerous cell lines with monochromatic and clinical proton beams. METHODS: The experimental set-up adopted for irradiations was fully simulated with a dedicated open-source Geant4 application. Cells survival fractions was calculated coupling the Geant4 simulations with two analytical radiobiological models: one based on the LEM (Local Effect Model) approach and the other on a semi-empirical parameterisation. Results was evaluated and compared with experimental data. RESULTS AND CONCLUSIONS: The results demonstrated the Geant4 ability to reproduce radiobiological quantities for different cell lines.

• Klíčová slova
• Geant4, Monte Carlo, Proton, RBE, Radiobiological model, Radiotherapy, Survival fraction,
• MeSH
• celková dávka radioterapie MeSH
• lidé MeSH
• metoda Monte Carlo * MeSH
• nádorové buněčné linie MeSH
• protonová terapie * MeSH
• radiobiologie MeSH
• reprodukovatelnost výsledků MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.

• Klíčová slova
• DNA damage, geant4-DNA, plasmid, radiation chemistry, simulation, track-structure,
• MeSH
• dimethylsulfoxid * MeSH
• DNA chemie   MeSH
• konformace nukleové kyseliny MeSH
• metoda Monte Carlo MeSH
• plazmidy MeSH
• počítačová simulace MeSH
• poškození DNA * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• dimethylsulfoxid * MeSH
• DNA MeSH

PURPOSE: Geant4-DNA is used to calculate S-values for different subcellular distributions of low-energy electron sources in various cell geometries. METHOD: Calculations of cellular S-values for monoenergetic electron sources with energy from 1 to 100 keV and the Auger-electron emitting radionuclides Tc-99m, In-111, and I-125 have been made using the Geant4 Monte Carlo toolkit. The Geant4-DNA low-energy extension is employed for simulating collision-by-collision the complete slowing-down of electron tracks (down to 8 eV) in liquid water, used as a surrogate of human cells. The effect of cell geometry on S-values is examined by simulating electron tracks within different cell geometries, namely, a spherical, two ellipsoidal, and an irregular shape, all having equal cellular and nuclear volumes. Algorithms for randomly sampling the volume of the nucleus, cytoplasm, surface, and whole cell for each cell phantom are presented. RESULTS: Differences between Geant4-DNA and MIRD database up to 50% were found, although, for the present radionuclides, they mostly remain below 10%. For most source-target combinations the S-values for the spherical cell geometry were found to be within 20% of those for the ellipsoidal cell geometries, with a maximum deviation of 32%. Differences between the spherical and irregular geometries are generally larger reaching 100-300%. Most sensitive to the cell geometry is the absorbed dose to the nucleus when the source is localized on the cell surface. Interestingly, two published AAPM spectra for I-125 yield noticeable differences (up to 19%) in cellular S-values. CONCLUSION: Monte Carlo simulations of cellular S-values with Geant4-DNA reveal that, for the examined radionuclides, the widely used approximation of spherical cells is reasonably accurate (within 20-30%) even for ellipsoidal geometries. For irregular cell geometries the spherical approximation should be used with caution because, as in the present example, it may lead to erroneous results for the nuclear dose for the commonly encountered situation where the source is localized to the cell surface.

• Klíčová slova
• Cellular dosimetry, Geant4-DNA, Monte Carlo, Radionuclide dosimetry, S-values,
• MeSH
• absorpce radiace * MeSH
• biologické modely * MeSH
• dávka záření MeSH
• elektrony MeSH
• lidé MeSH
• metoda Monte Carlo MeSH
• počítačová simulace MeSH
• radiometrie metody   MeSH
• statistické modely * MeSH
• velikost buňky * MeSH
• viabilita buněk účinky léků   fyziologie   MeSH
• vztah dávky záření a odpovědi MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The main purpose of this paper is to quantitatively study the possibility of delivering dose distributions of clinical relevance with laser-driven proton beams. A Monte Carlo application has been developed with the Geant4 toolkit, simulating the ELIMED (MEDical and multidisciplinary application at ELI-Beamlines) transport and dosimetry beam line which is being currently installed at the ELI-Beamlines in Prague (CZ). The beam line will be used to perform irradiations for multidisciplinary studies, with the purpose of demonstrating the possible use of optically accelerated ion beams for therapeutic purposes. The ELIMED Geant4-based application, already validated against reference transport codes, accurately simulates each single element of the beam line, necessary to collect the accelerated beams and to select them in energy. Transversal dose distributions at the irradiation point have been studied and optimized to try to quantitatively answer the question if such kind of beam lines, and specifically the systems developed for ELIMED in Prague, will be actually able to transport ion beams not only for multidisciplinary applications, such as pitcher-catcher nuclear reactions (e.g. neutrons), PIXE analysis for cultural heritage and space radiation, but also for delivering dose patterns of clinical relevance in a future perspective of possible medical applications.

• Klíčová slova
• ELIMED beam line, Geant4, Laser-driven ions, Medical applications, Transversal dose distributions,
• MeSH
• částice - urychlovače * MeSH
• celková dávka radioterapie MeSH
• dávka záření * MeSH
• lasery * MeSH
• metoda Monte Carlo * MeSH
• protonová terapie přístrojové vybavení   MeSH
• radiometrie MeSH
• Publikační typ
• časopisecké články MeSH

PURPOSE: Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4-DNA. METHODS: This new approach has been designed to respect the current Geant4-DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4-DNA were compared for the dynamic time step approach of the step-by-step (SBS) method, currently used in Geant4-DNA, and this newly implemented IRT. RESULTS: Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4-DNA. CONCLUSION: Offering in Geant4-DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.

• Klíčová slova
• DNA damage, Geant4-DNA, IRT, diffusion-controlled reaction,
• MeSH
• chromatin genetika   MeSH
• DNA * genetika   MeSH
• metoda Monte Carlo MeSH
• poškození DNA * MeSH
• reakční čas MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chromatin MeSH
• DNA * MeSH

This work presents a Monte Carlo model of Leksell Gamma Knife Perfexion as well as the main parameters of the dose distribution in the standard phantom obtained using this model. The model is developed in the Geant4 simulation toolkit in a modular way which enables its reuse in other Perfexion studies. Large phase space files were created, containing particles that are entering the inner machine cavity after being transported through the collimation system. All 14 output factors of the machine and effective output factors for both the 4 mm (0.830 ± 0.009) and 8 mm (0.921 ± 0.004) collimators were calculated. Dose profiles along the main axes are also included for each collimator size. All results are compared to the values obtained from the treatment planning system, from experiments, and from other Monte Carlo models.

• MeSH
• fantomy radiodiagnostické * MeSH
• lidé MeSH
• metoda Monte Carlo * MeSH
• nádory chirurgie   MeSH
• plánování radioterapie pomocí počítače MeSH
• počítačová simulace * MeSH
• radiochirurgie metody   MeSH
• statistické modely * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Diffuse and specular characteristics of the Tyvek 1025-BL material are reported with respect to their implementation in the Geant4 Monte Carlo simulation toolkit. This toolkit incorporates the UNIFIED model. Coefficients defined by the UNIFIED model were calculated from the bidirectional reflectance distribution function (BRDF) profiles measured with a scatterometer for several angles of incidence. Results were amended with profile measurements made by a profilometer.

• MeSH
• chemické modely * MeSH
• počítačová simulace MeSH
• polymery chemie   MeSH
• programovací jazyk * MeSH
• radiační rozptyl MeSH
• refraktometrie MeSH
• software * MeSH
• světlo MeSH
• testování materiálů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• polymery MeSH
• tyvek MeSH Prohlížeč