Status and Extension of the Geant4-DNA Dielectric Models for Application to Electron Transport

Kyriakou, Ioanna; Emfietzoglou, Dimitris; Incerti, S.

doi:10.3389/fphy.2021.711317

Cited by 7 publications

(4 citation statements)

References 39 publications

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“…Option4 physics models provide a more consistent treatment of the energy loss function for liquid water, compared with option2, which was used in earlier studies. 37 Electrons and protons were simulated as primary particles, irradiating the "cylinders" and the "human cell" geometries, respec. with each other or with the DNA targets to produce indirect damage.…”

Section: Physical Stagementioning

confidence: 99%

Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application

Chatzipapas

Tran

Dordevic³

et al. 2023

Precision Radiation Oncology

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Purpose:The scientific community shows great interest in the study of DNA damage induction, DNA damage repair, and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in silico methods have been proposed so far to study these mechanisms using Monte Carlo simulations. This study outlines a Geant4-DNA example application, named "molecularDNA", publicly released in the 11.1 version of Geant4 (December 2022).Methods: It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. The example includes two different DNA-scale geometries of biological targets, namely "cylinders" and "human cell". This public version is based on a previous prototype and includes new features, such as: the adoption of a new approach for the modeling of the chemical stage, the use of the standard DNA damage format to describe radiation-induced DNA damage, and upgraded computational tools to estimate DNA damage response.Results: Simulation data in terms of single-strand break and double-strand break yields were produced using each of the available geometries. The results were compared with the literature, to validate the example, producing less than 5% difference in all cases.Conclusion: "molecularDNA" is a prototype tool that can be applied in a wide variety of radiobiology studies, providing the scientific community with an open-access base for DNA damage quantification calculations. New DNA and cell geometries for the "molecularDNA" example will be included in future versions of Geant4-DNA.

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Section: Physical Stagementioning

confidence: 99%

Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application

Chatzipapas

Tran

Dordevic³

et al. 2023

Precision Radiation Oncology

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“…To study these processes by MCS it is necessary to include appropriate electron scattering cross for the nucleobases (adenine, thymine, guanine and cytosine). These were implemented recently for high energy processes such as ionization in Geant4-DNA within a specialized physics constructor (option6) providing good agreement with experimental work in the high energy range, while still deviating in the low-energy region, where attachment processes come into play [169,170]. To improve this situation combined effort of theoreticians and experimentalist is undertaken in evaluating scattering behaviour of model systems such as THF and isolated DNA constituents [87,[169][170][171][172][173][174].…”

Section: Dnamentioning

confidence: 99%

Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations

Hahn

2023

J. Phys. Commun.

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Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells an their organelles, the study of linear-energy-transfer (LET), the relative-biological-effectiveness (RBE), ion-beam cancer-therapy, microbeam-radiation-therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.

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“…Only one code used a newly developed cross section dataset for electron interactions in gold at energies down to the ionization threshold, derived from theoretical models [22]. In the meantime, cross sections for low-energy electron transport in gold have also become publicly available in the Geant4-DNA code system [23][24][25][26][27][28][29].…”

Section: Receivedmentioning

confidence: 99%

“…The use of Penelope and Geant4 for this study was motivated by the fact that the results initially obtained with the two codes showed the largest differences in a recent code comparison for gold nanoparticles [20]. In addition, Geant4 was the first general radiation-transport toolkit with a low-energy extension that allows for track structure simulations [23][24][25][26], with cross sections for low-energy electron transport in gold recently added [27][28][29]. Penelope has also been shown to have the capability to simulate track structures [37].…”

Section: Monte Carlo Simulationsmentioning

confidence: 99%

Experimental benchmark data for Monte Carlo simulated radiation effects of gold nanoparticles. Part II: comparison of measured and simulated electron spectra from gold nanofoils

Borbinha¹,

Rosales

Hepperle

et al. 2023

Phys. Scr.

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Electron emission spectra of a thin gold foil after photon interaction were measured over the energy range between 50 eV and 9500 eV to provide reference data for Monte Carlo radiation-transport simulations. Experiments were performed with the HAXPES spectrometer at the PETRA III high-brilliance beamline P22 at DESY (Hamburg, Germany) for photon energies just below and above each of the gold L-edges, i.e., at 11.9 keV, 12.0 keV, 13.7 keV, 13.8 keV, 14.3 keV, and 14.4 keV. The data were analyzed to obtain the absolute values of the particle radiance of the emitted electrons per incident photon flux. Simulations of the experiment were performed using the Monte Carlo radiation-transport codes Penelope and Geant4. Comparison of the measured and simulated results shows good qualitative agreement. On an absolute scale, the experiments tend to give higher electron radiance values at the lower photon energies studied as well as at the higher photon energies for electron energies below the energy of the Au L3 photoelectron. This is attributed to the linear polarization of the photon beam in the experiments which is not considered in the simulation codes.

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Status and Extension of the Geant4-DNA Dielectric Models for Application to Electron Transport

Cited by 7 publications

References 39 publications

Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application

Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application

Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations

Experimental benchmark data for Monte Carlo simulated radiation effects of gold nanoparticles. Part II: comparison of measured and simulated electron spectra from gold nanofoils

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