[en] Simulation of biological effects of ionizing radiation at the DNA scale requires not only the modeling of direct damages induced on DNA by the incident radiation and by secondary particles but also the modeling of indirect effects of radiolytic products resulting from water radiolysis. They can provoke single and double strand breaks by reacting with DNA. The Geant4 Monte Carlo toolkit is currently being extended for the simulation of biological damages of ionizing radiation at the DNA scale in the framework of the 'Geant4-DNA' project. Physics models for the modeling of direct effects are already available in Geant4. In the present paper, an approach for the modeling of radiation chemistry in pure liquid water within Geant4 is presented. In particular, this modeling includes Brownian motion and chemical reactions between molecules following water radiolysis. First results on time-dependent radiochemical yields from 1 picosecond up to 1 microsecond after irradiation are compared to published data and discussed. (author)

[en] This work presents a Monte Carlo study of energy depositions due to protons, alpha particles and carbon ions of the same linear-energy-transfer (LET) in liquid water. The corresponding track structures were generated using the Geant4-DNA toolkit, and the energy deposition spatial distributions were analyzed using an adapted version of the DBSCAN clustering algorithm. Combining the Geant4 simulations and the clustering algorithm it was possible to compare the quality of the different radiation types. The ratios of clustered and single energy depositions are shown versus particle LET and frequency-mean lineal energies. The estimated effect of these types of radiation on biological tissues is then discussed by comparing the results obtained for different particles with the same LET. (paper)

[en] This paper presents stopping power and ranges of electrons, protons, and alpha particles in liquid water, calculated using the latest Geant4-DNA processes implemented in the Geant4 Monte Carlo simulation toolkit. Inelastic cross sections are obtained using the first Born approximation and semi-empirical formulas like Rudd's model for ionisation and the Miller and Green formula for excitation. Elastic collisions and vibrational excitations are considered for tracking electrons until complete thermalisation (0.025 eV). A speed scaling procedure with an effective charge screening term was used to compute alpha particle and heavy ion cross sections. Geant4-DNA simulations were carried out using thin liquid water volumes to determine the linear energy loss (dE/dX), while larger volumes were used to obtain the particle range. While results converge for highly energetic particles, differences are observed for low energies when the applied theoretical models begin to diverge from each other. Results show a good agreement between the analytical calculations obtained from the models, the Geant4-DNA Monte Carlo simulation predictions and the data published in the ICRU reports. Geant4-DNA processes apply to the following energy ranges: 0.025 eV-1 MeV for electrons, 100 eV-100 MeV for protons and 1 keV-400 MeV for alpha particles in liquid water, however since experimental data for very low energies is scarce and very difficult to obtain these processes could not be thoroughly validated so they are recommended for energies above 1 eV for electrons, 1 keV for protons and 10 keV for alpha particles. Relativistic, highly charged ions were implemented in our own 'house' version of the code and will be available in future releases of Geant4.

[en] We have recently developed an atomistic model of the B-DNA configuration, up to the 30-nm chromatin fiber. This model is intended to be used in Monte Carlo simulations of the DNA-radiation interaction, specifically in conjunction with the Geant4-DNA extension of the Geant4 Monte Carlo toolkit. In this work, 11449 parallel chromatin fibers have been arranged within a cube mimicking a cell nucleus containing about 6.5×10⁹ base pairs. Each atom in the model is represented by a sphere with the corresponding van der Waals radius. Direct single, double and total DNA strand break yields due to the impact of protons and alpha particles with LET ranging from 4.57 to 207.1 keV/μm have been determined. Also, the corresponding site-hit probabilities have been calculated

[en] In the perspective of building an open source simulation platform dedicated to the modelling of early biological molecular damages due to ionising radiation at the DNA scale, the general-purpose Geant4 Monte Carlo simulation toolkit has been recently extended with specific very low energy electromagnetic physics processes for liquid water medium. These processes – also called “Geant4-DNA” processes – simulate the physical interactions induced by electrons, hydrogen and helium atoms of different charge states. The present work reports on the energy deposit distributions obtained for incident electrons, protons and alpha particles in nanometre-size volumes comparable to those present in the genetic material of mammalian cells. The frequency distributions of the energy deposition obtained for three typical geometries of nanometre-size cylindrical targets placed in a spherical phantom are found to be in reasonable agreement with prior works. Furthermore, we present a combination of the Geant4-DNA processes with a simplified geometrical model of a cellular nucleus allowing the evaluation of energy deposits in volumes of biological interest

[en] In this study, fragmentation yields of carbon therapy beams are estimated using the Geant4 simulation toolkit version 9.5. Simulations are carried out in a step-by-step mode using the Geant4-DNA processes for each of the major contributing fragments. The energy of the initial beam is taken 400 MeV amu"−"1 as this is the highest energy, which is used for medical accelerators and this would show the integral role of secondary contributions in radiotherapy irradiations. The obtained results showed that 64% of the global dose deposition is initiated by carbon ions, while up to 36% is initiated by the produced fragments including all their isotopes. The energy deposition clustering yields of each of the simulated fragments are then estimated using the DBSCAN clustering algorithm and they are compared to the yields of the incident primary beam. (paper)

[en] Accurate modeling of DNA damages resulting from ionizing radiation remains a challenge of today’s radiobiology research. An original set of physics processes has been recently developed for modeling the detailed transport of protons and neutral hydrogen atoms in liquid water and in DNA nucleobases using the Geant4-DNA extension of the open source Geant4 Monte Carlo simulation toolkit. The theoretical cross sections as well as the mean energy transfers during the different ionizing processes were taken from recent works based on classical as well as quantum mechanical predictions. Furthermore, in order to compare energy deposition patterns in liquid water and DNA material, we here propose a simplified cellular nucleus model made of spherical voxels, each containing randomly oriented nanometer-size cylindrical targets filled with either liquid water or DNA material (DNA nucleobases) both with a density of 1 g/cm³. These cylindrical volumes have dimensions comparable to genetic material units of mammalian cells, namely, 25 nm (diameter) × 25 nm (height) for chromatin fiber segments, 10 nm (d) × 5 nm (h) for nucleosomes and 2 nm (d) × 2 nm (h) for DNA segments. Frequencies of energy deposition in the cylindrical targets are presented and discussed

[en] The full text of the publication follows. The precise modeling of interactions of ionizing radiation with biological matter remains one of the current radiobiology challenges. Simulation work through the Monte Carlo technique can provide unique and valuable solutions allowing, for example the prediction of biological DNA damages, such as DNA single and double-strand breaks. The Geant4 Monte Carlo simulation tool-kit, an open source set of libraries developed for understanding the passage of particles through matter, covers a large variety of application domains, ranging from high energy physics to space and medical applications. The Geant4-DNA project, initiated by the European Space Agency and sponsored by the French Research National Agency, aims at providing Geant4 with new capabilities specific for radiobiology applications, including: -) Elementary physical interactions down to the sub-eV scale; -) Water radiolysis, diffusion and interactions between molecules and DNA; -) a detailed geometry of biological cells at the DNA scale. Applications are foreseen for long duration manned space exploration programs as well as for the use of radiation in the medical sector (e.g., particle therapy and imaging) where radiation effects at the cellular level are of concern. An overview of the Geant4-DNA project, its recent developments and current status will be presented. We will focus on the modeling of chemical reactions into Geant4 and its preliminary results. (authors)

[en] The Geant4 Monte Carlo simulation toolkit provides a set of electromagnetic physics processes adapted to the detailed simulation of particle interactions in liquid water for microdosimetry applications, such as single-cell irradiation with light ion beams. These processes, developed within the framework of the Geant4-DNA project, adopt a software design allowing their combination with other electromagnetic physics processes available in the Geant4 toolkit. This work describes the combination of Geant4-DNA electron processes with Geant4 photon processes.

[en] We report on the recent progress within the Geant4 electromagnetic physics subpackages. Several new interfaces and models recently introduced are already used in LHC applications and may be useful for any type of simulation. Significant developments were carried out to improve the user interface, develop models of single and multiple scattering, and validate high energy models. Part of these developments are included in the Geant4 10.2 release and the full set are available in the new version 10.3 of December, 2016. (paper)