Influence of the chromatin density on the number of direct clustered damages calculated for proton and alpha irradiations using a Monte Carlo code

Santos, M. Dos; Villagrasa, C.; Clairand, I.; Incerti, S.

doi:10.15669/pnst.4.449

Cited by 12 publications

(9 citation statements)

References 14 publications

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“…The Geant4-DNA model represents the whole genome (∼ 6 × 10 9 bps) within an ellipsoid nucleus for a cell in the G0/G1 phase and is further described in Dos Santos et al (2014). The DNA structure is divided into 5 organisation levels: chromosome territories, chromatin fibre loops, chromatin fibres, nucleosomes and the DNA double helix.…”

Section: Resultsmentioning

confidence: 99%

Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit

McNamara¹,

Ramos-Méndez²,

Perl³

et al. 2018

Phys. Med. Biol.

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Computational simulations, such as Monte Carlo track structure simulations, offer a powerful tool for quantitatively investigating radiation interactions within cells. The modelling of the spatial distribution of energy deposition events as well as diffusion of chemical free radical species, within realistic biological geometries, can help provide a comprehensive understanding of the effects of radiation on cells. Track structure simulations, however, generally require advanced computing skills to implement. The TOPAS-nBio toolkit, an extension to TOPAS (TOol for PArticle Simulation), aims to provide users with a comprehensive framework for radiobiology simulations, without the need for advanced computing skills. This includes providing users with an extensive library of advanced, realistic, biological geometries ranging from the micrometer scale (e.g. cells and organelles) down to the nanometer scale (e.g. DNA molecules and proteins). Here we present the geometries available in TOPAS-nBio.

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Section: Resultsmentioning

confidence: 99%

Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit

McNamara¹,

Ramos-Méndez²,

Perl³

et al. 2018

Phys. Med. Biol.

Self Cite

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“…With this study, the authors could underline the dependence of the quantity and complexity of clusters with increasing DNA density, as in endothelium cells. They extended this work to alpha particles (5 -50 MeV range) [70] and confirmed that the quantity and the complexity of the potential direct damages in the endothelium cell nucleus are always higher than in the fibroblast cell nucleus. In addition, both studies showed that for a given LET, a proton irradiation induces more direct complex clustered damages than an alpha particle irradiation.…”

Section: The Mixed Approachmentioning

confidence: 56%

“…In parallel to the previously described applications, a mixed approach has been proposed by Dos Santos and colleagues from 2013 using Geant4-DNA [67][68][69][70][71].…”

Section: The Mixed Approachmentioning

confidence: 99%

“…Using a similar approach, they also investigated the influence of chromatin condensation on direct DSBs induced by incident protons and alpha particles by comparing two types of chromosome territories corresponding to euchromatin (decondensed) or heterochromatin (condensed) regions [69,70]. They reported that condensed chromatin could be the location of more severe radiation-induced lesions than decondensed chromatin.…”

Section: The Mixed Approachmentioning

confidence: 99%

See 1 more Smart Citation

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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“…For example, the comparison of dose point kernels [114], S-values [115], radial doses [116], cluster patterns for ions with the same LET [117], the effect of a magnetic field on electron track structures [118], and the modeling of direct DNA damage [119][120][121][122] have so far been explored utilizing these tools. They even provide a framework for the future study of non-targeted biological effects [123], extending further the first applications of GEANT4 electromagnetic physics at the physics-biology frontier [124][125][126][127][128][129][130].…”

Section: Geant4-dna Physics Modelsmentioning

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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Influence of the chromatin density on the number of direct clustered damages calculated for proton and alpha irradiations using a Monte Carlo code

Cited by 12 publications

References 14 publications

Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit

Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit

Review of Geant4-DNA applications for micro and nanoscale simulations

Recent Developments in Geant4

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