Journal Articles
2017
Famulari, Gabriel; Pater, Piotr; Enger, Shirin A.
Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm Journal Article
In: Physics in Medicine and Biology, vol. 62, no. 13, pp. 5495–5508, 2017, ISSN: 1361-6560.
Abstract | Links | BibTeX | Tags: Algorithms, DNA, DNA Damage, Electrons, Imaging, Monte Carlo Method, Phantoms, Photons, Radiometry
@article{famulari_microdosimetry_2017,
title = {Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm},
author = {Gabriel Famulari and Piotr Pater and Shirin A. Enger},
doi = {10.1088/1361-6560/aa71f6},
issn = {1361-6560},
year = {2017},
date = {2017-07-01},
journal = {Physics in Medicine and Biology},
volume = {62},
number = {13},
pages = {5495--5508},
abstract = {The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(textgreaterE)/f(textgreater0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.},
keywords = {Algorithms, DNA, DNA Damage, Electrons, Imaging, Monte Carlo Method, Phantoms, Photons, Radiometry},
pubstate = {published},
tppubtype = {article}
}
The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(textgreaterE)/f(textgreater0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.2016
Pater, Piotr; Bäckstöm, Gloria; Villegas, Fernanda; Ahnesjö, Anders; Enger, Shirin A.; Seuntjens, Jan; Naqa, Issam El
Proton and light ion RBE for the induction of direct DNA double strand breaks Journal Article
In: Medical Physics, vol. 43, no. 5, pp. 2131–2140, 2016, ISSN: 2473-4209, (_eprint: https://aapm.onlinelibrary.wiley.com/doi/pdf/10.1118/1.4944870).
Abstract | Links | BibTeX | Tags: biological effects of ionising particles, biomolecular effects of radiation, Cell Nucleus, cell nucleus model, cellular effects of radiation, DNA, DNA double-strand breaks, Dosimetry, Dosimetry/exposure assessment, Energy transfer, Genomics, Ion beams, Ion radiation effects, Monte Carlo calculations, Monte Carlo methods, Monte Carlo simulations, Monte Carlo track structure, Protons, RBE, Schottky barriers, Scintigraphy
@article{pater_proton_2016b,
title = {Proton and light ion RBE for the induction of direct DNA double strand breaks},
author = {Piotr Pater and Gloria Bäckstöm and Fernanda Villegas and Anders Ahnesjö and Shirin A. Enger and Jan Seuntjens and Issam El Naqa},
url = {https://aapm.onlinelibrary.wiley.com/doi/abs/10.1118/1.4944870},
doi = {10.1118/1.4944870},
issn = {2473-4209},
year = {2016},
date = {2016-01-01},
urldate = {2021-09-07},
journal = {Medical Physics},
volume = {43},
number = {5},
pages = {2131--2140},
abstract = {Purpose: To present and characterize a Monte Carlo (MC) tool for the simulation of the relative biological effectiveness for the induction of direct DNA double strand breaks () for protons and light ions. Methods: The MC tool uses a pregenerated event-by-event tracks library of protons and light ions that are overlaid on a cell nucleus model. The cell nucleus model is a cylindrical arrangement of nucleosome structures consisting of 198 DNA base pairs. An algorithm relying on k-dimensional trees and cylindrical symmetries is used to search coincidences of energy deposition sites with volumes corresponding to the sugar–phosphate backbone of the DNA molecule. Strand breaks (SBs) are scored when energy higher than a threshold is reached in these volumes. Based on the number of affected strands, they are categorized into either single strand break (SSB) or double strand break (DSB) lesions. The number of SBs composing each lesion (i.e., its size) is also recorded. is obtained by taking the ratio of DSB yields of a given radiation field to a 60Co field. The MC tool was used to obtain SSB yields, DSB yields, and as a function of linear energy transfer (LET) for protons (1H+), 4He2+, 7Li3+, and 12C6+ ions. Results: For protons, the SSB yields decreased and the DSB yields increased with LET. At ≈24.5 keV μm−1, protons generated 15% more DSBs than 12C6+ ions. The varied between 1.24 and 1.77 for proton fields between 8.5 and 30.2 keV μm−1, and it was higher for iso-LET ions with lowest atomic number. The SSB and DSB lesion sizes showed significant differences for all radiation fields. Generally, the yields of SSB lesions of sizes ≥2 and the yields of DSB lesions of sizes ≥3 increased with LET and increased for iso-LET ions of lower atomic number. On the other hand, the ratios of SSB to DSB lesions of sizes 2–4 did not show variability with LET nor projectile atomic number, suggesting that these metrics are independent of the radiation quality. Finally, a variance of up to 8% in the DSB yields was observed as a function of the particle incidence angle on the cell nucleus. This simulation effect is due to the preferential alignment of ion tracks with the DNA nucleosomes at specific angles. Conclusions: The MC tool can predict SSB and DSB yields for light ions of various LET and estimate . In addition, it can calculate the frequencies of different DNA lesion sizes, which is of interest in the context of biologically relevant absolute dosimetry of particle beams.},
note = {_eprint: https://aapm.onlinelibrary.wiley.com/doi/pdf/10.1118/1.4944870},
keywords = {biological effects of ionising particles, biomolecular effects of radiation, Cell Nucleus, cell nucleus model, cellular effects of radiation, DNA, DNA double-strand breaks, Dosimetry, Dosimetry/exposure assessment, Energy transfer, Genomics, Ion beams, Ion radiation effects, Monte Carlo calculations, Monte Carlo methods, Monte Carlo simulations, Monte Carlo track structure, Protons, RBE, Schottky barriers, Scintigraphy},
pubstate = {published},
tppubtype = {article}
}
Purpose: To present and characterize a Monte Carlo (MC) tool for the simulation of the relative biological effectiveness for the induction of direct DNA double strand breaks () for protons and light ions. Methods: The MC tool uses a pregenerated event-by-event tracks library of protons and light ions that are overlaid on a cell nucleus model. The cell nucleus model is a cylindrical arrangement of nucleosome structures consisting of 198 DNA base pairs. An algorithm relying on k-dimensional trees and cylindrical symmetries is used to search coincidences of energy deposition sites with volumes corresponding to the sugar–phosphate backbone of the DNA molecule. Strand breaks (SBs) are scored when energy higher than a threshold is reached in these volumes. Based on the number of affected strands, they are categorized into either single strand break (SSB) or double strand break (DSB) lesions. The number of SBs composing each lesion (i.e., its size) is also recorded. is obtained by taking the ratio of DSB yields of a given radiation field to a 60Co field. The MC tool was used to obtain SSB yields, DSB yields, and as a function of linear energy transfer (LET) for protons (1H+), 4He2+, 7Li3+, and 12C6+ ions. Results: For protons, the SSB yields decreased and the DSB yields increased with LET. At ≈24.5 keV μm−1, protons generated 15% more DSBs than 12C6+ ions. The varied between 1.24 and 1.77 for proton fields between 8.5 and 30.2 keV μm−1, and it was higher for iso-LET ions with lowest atomic number. The SSB and DSB lesion sizes showed significant differences for all radiation fields. Generally, the yields of SSB lesions of sizes ≥2 and the yields of DSB lesions of sizes ≥3 increased with LET and increased for iso-LET ions of lower atomic number. On the other hand, the ratios of SSB to DSB lesions of sizes 2–4 did not show variability with LET nor projectile atomic number, suggesting that these metrics are independent of the radiation quality. Finally, a variance of up to 8% in the DSB yields was observed as a function of the particle incidence angle on the cell nucleus. This simulation effect is due to the preferential alignment of ion tracks with the DNA nucleosomes at specific angles. Conclusions: The MC tool can predict SSB and DSB yields for light ions of various LET and estimate . In addition, it can calculate the frequencies of different DNA lesion sizes, which is of interest in the context of biologically relevant absolute dosimetry of particle beams.
Journal Articles
2017
Famulari, Gabriel; Pater, Piotr; Enger, Shirin A.
Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm Journal Article
In: Physics in Medicine and Biology, vol. 62, no. 13, pp. 5495–5508, 2017, ISSN: 1361-6560.
Abstract | Links | BibTeX | Tags: Algorithms, DNA, DNA Damage, Electrons, Imaging, Monte Carlo Method, Phantoms, Photons, Radiometry
@article{famulari_microdosimetry_2017,
title = {Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm},
author = {Gabriel Famulari and Piotr Pater and Shirin A. Enger},
doi = {10.1088/1361-6560/aa71f6},
issn = {1361-6560},
year = {2017},
date = {2017-07-01},
journal = {Physics in Medicine and Biology},
volume = {62},
number = {13},
pages = {5495--5508},
abstract = {The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(textgreaterE)/f(textgreater0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.},
keywords = {Algorithms, DNA, DNA Damage, Electrons, Imaging, Monte Carlo Method, Phantoms, Photons, Radiometry},
pubstate = {published},
tppubtype = {article}
}
The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(textgreaterE)/f(textgreater0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.
2016
Pater, Piotr; Bäckstöm, Gloria; Villegas, Fernanda; Ahnesjö, Anders; Enger, Shirin A.; Seuntjens, Jan; Naqa, Issam El
Proton and light ion RBE for the induction of direct DNA double strand breaks Journal Article
In: Medical Physics, vol. 43, no. 5, pp. 2131–2140, 2016, ISSN: 2473-4209, (_eprint: https://aapm.onlinelibrary.wiley.com/doi/pdf/10.1118/1.4944870).
Abstract | Links | BibTeX | Tags: biological effects of ionising particles, biomolecular effects of radiation, Cell Nucleus, cell nucleus model, cellular effects of radiation, DNA, DNA double-strand breaks, Dosimetry, Dosimetry/exposure assessment, Energy transfer, Genomics, Ion beams, Ion radiation effects, Monte Carlo calculations, Monte Carlo methods, Monte Carlo simulations, Monte Carlo track structure, Protons, RBE, Schottky barriers, Scintigraphy
@article{pater_proton_2016b,
title = {Proton and light ion RBE for the induction of direct DNA double strand breaks},
author = {Piotr Pater and Gloria Bäckstöm and Fernanda Villegas and Anders Ahnesjö and Shirin A. Enger and Jan Seuntjens and Issam El Naqa},
url = {https://aapm.onlinelibrary.wiley.com/doi/abs/10.1118/1.4944870},
doi = {10.1118/1.4944870},
issn = {2473-4209},
year = {2016},
date = {2016-01-01},
urldate = {2021-09-07},
journal = {Medical Physics},
volume = {43},
number = {5},
pages = {2131--2140},
abstract = {Purpose: To present and characterize a Monte Carlo (MC) tool for the simulation of the relative biological effectiveness for the induction of direct DNA double strand breaks () for protons and light ions. Methods: The MC tool uses a pregenerated event-by-event tracks library of protons and light ions that are overlaid on a cell nucleus model. The cell nucleus model is a cylindrical arrangement of nucleosome structures consisting of 198 DNA base pairs. An algorithm relying on k-dimensional trees and cylindrical symmetries is used to search coincidences of energy deposition sites with volumes corresponding to the sugar–phosphate backbone of the DNA molecule. Strand breaks (SBs) are scored when energy higher than a threshold is reached in these volumes. Based on the number of affected strands, they are categorized into either single strand break (SSB) or double strand break (DSB) lesions. The number of SBs composing each lesion (i.e., its size) is also recorded. is obtained by taking the ratio of DSB yields of a given radiation field to a 60Co field. The MC tool was used to obtain SSB yields, DSB yields, and as a function of linear energy transfer (LET) for protons (1H+), 4He2+, 7Li3+, and 12C6+ ions. Results: For protons, the SSB yields decreased and the DSB yields increased with LET. At ≈24.5 keV μm−1, protons generated 15% more DSBs than 12C6+ ions. The varied between 1.24 and 1.77 for proton fields between 8.5 and 30.2 keV μm−1, and it was higher for iso-LET ions with lowest atomic number. The SSB and DSB lesion sizes showed significant differences for all radiation fields. Generally, the yields of SSB lesions of sizes ≥2 and the yields of DSB lesions of sizes ≥3 increased with LET and increased for iso-LET ions of lower atomic number. On the other hand, the ratios of SSB to DSB lesions of sizes 2–4 did not show variability with LET nor projectile atomic number, suggesting that these metrics are independent of the radiation quality. Finally, a variance of up to 8% in the DSB yields was observed as a function of the particle incidence angle on the cell nucleus. This simulation effect is due to the preferential alignment of ion tracks with the DNA nucleosomes at specific angles. Conclusions: The MC tool can predict SSB and DSB yields for light ions of various LET and estimate . In addition, it can calculate the frequencies of different DNA lesion sizes, which is of interest in the context of biologically relevant absolute dosimetry of particle beams.},
note = {_eprint: https://aapm.onlinelibrary.wiley.com/doi/pdf/10.1118/1.4944870},
keywords = {biological effects of ionising particles, biomolecular effects of radiation, Cell Nucleus, cell nucleus model, cellular effects of radiation, DNA, DNA double-strand breaks, Dosimetry, Dosimetry/exposure assessment, Energy transfer, Genomics, Ion beams, Ion radiation effects, Monte Carlo calculations, Monte Carlo methods, Monte Carlo simulations, Monte Carlo track structure, Protons, RBE, Schottky barriers, Scintigraphy},
pubstate = {published},
tppubtype = {article}
}
Purpose: To present and characterize a Monte Carlo (MC) tool for the simulation of the relative biological effectiveness for the induction of direct DNA double strand breaks () for protons and light ions. Methods: The MC tool uses a pregenerated event-by-event tracks library of protons and light ions that are overlaid on a cell nucleus model. The cell nucleus model is a cylindrical arrangement of nucleosome structures consisting of 198 DNA base pairs. An algorithm relying on k-dimensional trees and cylindrical symmetries is used to search coincidences of energy deposition sites with volumes corresponding to the sugar–phosphate backbone of the DNA molecule. Strand breaks (SBs) are scored when energy higher than a threshold is reached in these volumes. Based on the number of affected strands, they are categorized into either single strand break (SSB) or double strand break (DSB) lesions. The number of SBs composing each lesion (i.e., its size) is also recorded. is obtained by taking the ratio of DSB yields of a given radiation field to a 60Co field. The MC tool was used to obtain SSB yields, DSB yields, and as a function of linear energy transfer (LET) for protons (1H+), 4He2+, 7Li3+, and 12C6+ ions. Results: For protons, the SSB yields decreased and the DSB yields increased with LET. At ≈24.5 keV μm−1, protons generated 15% more DSBs than 12C6+ ions. The varied between 1.24 and 1.77 for proton fields between 8.5 and 30.2 keV μm−1, and it was higher for iso-LET ions with lowest atomic number. The SSB and DSB lesion sizes showed significant differences for all radiation fields. Generally, the yields of SSB lesions of sizes ≥2 and the yields of DSB lesions of sizes ≥3 increased with LET and increased for iso-LET ions of lower atomic number. On the other hand, the ratios of SSB to DSB lesions of sizes 2–4 did not show variability with LET nor projectile atomic number, suggesting that these metrics are independent of the radiation quality. Finally, a variance of up to 8% in the DSB yields was observed as a function of the particle incidence angle on the cell nucleus. This simulation effect is due to the preferential alignment of ion tracks with the DNA nucleosomes at specific angles. Conclusions: The MC tool can predict SSB and DSB yields for light ions of various LET and estimate . In addition, it can calculate the frequencies of different DNA lesion sizes, which is of interest in the context of biologically relevant absolute dosimetry of particle beams.