Diffusion-controlled reactions modeling in Geant4-DNA

Karamitros, Mathieu; Luan, Shuang; Bernal, Mario A.; Allison, J.; Baldacchino, Gérard; Davídková, Marie; Francis, Z.; Friedland, W.; Ivantchenko, Vladimir; Ivantchenko, Anton; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H.N.; Štěpán, Václav; Incerti, S.

doi:10.1016/j.jcp.2014.06.011

Cited by 134 publications

(189 citation statements)

References 51 publications

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“…The simulation of the radicals created after the ionisation or excitation of the water molecules around the DNA target was performed using the processes implemented in Geant4-DNA since December 2014 [8,11]. The simulation takes into account the creation of 7 different radical species, their diffusion in liquid water and their chemical reactions.…”

Section: Chemical Interactions In the Dna Targetmentioning

confidence: 99%

Geant4-DNA simulation of DNA damage caused by direct and indirect radiation effects and comparison with biological data.

et al. 2017

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Abstract. In this work we present results obtained in the frame of the BioQuaRT project. The objective of the study was the correlation between the number of radiation-induced double strand breaks (DSB) of the DNA molecule and the probability of detecting nuclear foci after targeted microbeam irradiation of cells with protons and alpha particles of different LET. The former were obtained by simulation with new methods integrated into Geant4-DNA that permit calculating the number of DSB in a DNA target model induced by direct and indirect radiation effects. A particular focus was laid in this work on evaluating the influence of different criteria applied to the simulated results for predicting the formation of a direct SSB. Indeed, these criteria have an important impact on the predicted number of DSB per particle track and its dependence with LET. Among the criteria tested in this work, the case that a direct radiation interaction leads to a strand break if the cumulative energy deposited in the backbone part of one nucleotide exceeds a threshold of 17.5 eV leads to the best agreement with the relative LET dependence of number of radiation induced foci. Further calculations and experimental data are nevertheless needed in order to fix the simulation parameters and to help interpreting the biological experimental data observed by immunofluorescence in terms of the DSB complexity.

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Section: Chemical Interactions In the Dna Targetmentioning

confidence: 99%

Geant4-DNA simulation of DNA damage caused by direct and indirect radiation effects and comparison with biological data.

et al. 2017

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“…Such functionalities allow the simulation of water radiolysis up to one microsecond after irradiation. These developments are described in detail in the recent papers by Karamitros et al [41,42], which include comparisons of Geant4-DNA simulated radiochemical yields to simulation and experimental literature data. They will be required for the simulation of indirect effects of ionising radiation to DNA.…”

Section: Water Radiolysis Modellingmentioning

confidence: 99%

“…Key parameters are based on PARTRAC as further explained in [41,42]. In particular, the dissociation scheme is presented in Table 1 and reaction and reactions rates are given in Table 2.…”

Section: Water Radiolysis Modellingmentioning

confidence: 99%

Review of Geant4-DNA applications for micro and nanoscale simulations

et al. 2016

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Emerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-byevent electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis. Since its release, Geant4-DNA has been adopted as an investigational tool in kV and MV external beam radiotherapy, hadron therapies using protons and heavy ions, targeted therapies and radiobiology studies. It has been benchmarked with respect to other track structure Monte Carlo codes and, where available, against reference experimental measurements. While Geant4-DNA physics models and radiolysis modelling functionalities have already been described in detail in the literature, this review paper summarises and discusses a selection of representative papers with the aim of providing an overview of a) geometrical descriptions of biological targets down to the DNA size, and b) the full spectrum of current micro-and nano-scale applications of Geant4-DNA. Disciplines Engineering | Science and Technology Studies Publication DetailsIncerti, S., Douglass, M., Penfold, S., Guatelli, S. & Bezak, E. (2016). Review of Geant4-DNA applications for micro and nanoscale simulations. Physica Medica: an international journal devoted to the applications of physics to medicine and biology, 32 (10), 1187-1200. AbstractEmerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-by-event electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis.

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“…In addition to models for low and high energy EM physics for simulation of radiation effects in media, a sub-library of very low energy models was developed within the framework of the GEANT4-DNA project, with the goal of simulating radiation effects involving physics and chemistry at the sub-cellular level [33].…”

Section: Electromagnetic Physicsmentioning

confidence: 99%

“…In the context of the GEANT4-DNA project, a prototype for simulating radiation chemistry was developed [33,111] …”

Section: Geant4-dna Physico-chemistry Modulementioning

confidence: 99%

Recent Developments in Geant4

2014

SNA + MC 2013 - Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo

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During the last two to three years extensive development of the Geant4 simulation toolkit has occurred, which will culminate in a major release at the end of 2013. This development includes the adoption of multi-threading, the extension and improvement of physics models, improvements to the geometry modeler with a revised implementation of most geometrical primitives, advances in visualization and graphical user interfaces (GUI), the move from GNU make to CMake and the extension and automation of the Geant4 testing suite. The reasons for and implementation of multi-threading will be discussed. Certain electromagnetic and hadronic model extensions will also be discussed along with their effects on calorimeter results. Finally, visualization and GUI improvements will be highlighted along with the new configuration, build and testing systems.

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Diffusion-controlled reactions modeling in Geant4-DNA

Cited by 134 publications

References 51 publications

Geant4-DNA simulation of DNA damage caused by direct and indirect radiation effects and comparison with biological data.

Geant4-DNA simulation of DNA damage caused by direct and indirect radiation effects and comparison with biological data.

Review of Geant4-DNA applications for micro and nanoscale simulations

Recent Developments in Geant4

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