TY  - JOUR
AU  - Chatzipapas, Konstantinos P.
AU  - Tran, Ngoc Hoang
AU  - Đorđević, Miloš
AU  - Živković, Sara
AU  - Zein, Sara
AU  - Shin, Wook‐Geun
AU  - Sakata, Dousatsu
AU  - Lampe, Nathanael
AU  - Brown, Jeremy M. C.
AU  - Ristić‐Fira, Aleksandra
AU  - Petrović, Ivan
AU  - Kyriakou, Ioanna
AU  - Emfietzoglou, Dimitris
AU  - Guatelli, Susanna
AU  - Incerti, Sébastien
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/12968
AB  - Purpose:ThescientificcommunityshowsgreatinterestinthestudyofDNAdamageinduction,DNAdamagerepair,andthebiologicaleffectsoncellsandcellularsystemsafterexposuretoionizingradiation.Severalin silicomethodshavebeenproposedsofar to study these mechanisms using Monte Carlo simulations. This study outlinesaGeant4-DNAexampleapplication,named“molecularDNA”,publiclyreleasedinthe11.1versionofGeant4(December2022).Methods:ItwasdevelopedfornoviceGeant4usersandrequiresonlyabasicunder-standing of scripting languages to get started. The example includes two differentDNA-scalegeometriesofbiologicaltargets,namely“cylinders”and“humancell”.Thispublicversionisbasedonapreviousprototypeandincludesnewfeatures,suchas:theadoptionofanewapproachforthemodelingofthechemicalstage,theuseofthestan-dardDNAdamageformattodescriberadiation-inducedDNAdamage,andupgradedcomputationaltoolstoestimateDNAdamageresponse.Results:Simulationdataintermsofsingle-strandbreakanddouble-strandbreakyieldswereproducedusingeachoftheavailablegeometries.Theresultswerecomparedwiththeliterature,tovalidatetheexample,producinglessthan5%differenceinallcases.Conclusion:“molecularDNA”isaprototypetoolthatcanbeappliedinawidevarietyofradiobiologystudies,providingthescientificcommunitywithanopen-accessbasefor DNA damage quantification calculations. New DNA and cell geometries for the“molecularDNA”examplewillbeincludedinfutureversionsofGeant4-DNA.
T2  - Precision Radiation Oncology
T1  - Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application
VL  - 7
IS  - 1
SP  - 4
EP  - 14
DO  - 10.1002/pro6.1186
ER  - 

@article{
author = "Chatzipapas, Konstantinos P. and Tran, Ngoc Hoang and Đorđević, Miloš and Živković, Sara and Zein, Sara and Shin, Wook‐Geun and Sakata, Dousatsu and Lampe, Nathanael and Brown, Jeremy M. C. and Ristić‐Fira, Aleksandra and Petrović, Ivan and Kyriakou, Ioanna and Emfietzoglou, Dimitris and Guatelli, Susanna and Incerti, Sébastien",
year = "2023",
abstract = "Purpose:ThescientificcommunityshowsgreatinterestinthestudyofDNAdamageinduction,DNAdamagerepair,andthebiologicaleffectsoncellsandcellularsystemsafterexposuretoionizingradiation.Severalin silicomethodshavebeenproposedsofar to study these mechanisms using Monte Carlo simulations. This study outlinesaGeant4-DNAexampleapplication,named“molecularDNA”,publiclyreleasedinthe11.1versionofGeant4(December2022).Methods:ItwasdevelopedfornoviceGeant4usersandrequiresonlyabasicunder-standing of scripting languages to get started. The example includes two differentDNA-scalegeometriesofbiologicaltargets,namely“cylinders”and“humancell”.Thispublicversionisbasedonapreviousprototypeandincludesnewfeatures,suchas:theadoptionofanewapproachforthemodelingofthechemicalstage,theuseofthestan-dardDNAdamageformattodescriberadiation-inducedDNAdamage,andupgradedcomputationaltoolstoestimateDNAdamageresponse.Results:Simulationdataintermsofsingle-strandbreakanddouble-strandbreakyieldswereproducedusingeachoftheavailablegeometries.Theresultswerecomparedwiththeliterature,tovalidatetheexample,producinglessthan5%differenceinallcases.Conclusion:“molecularDNA”isaprototypetoolthatcanbeappliedinawidevarietyofradiobiologystudies,providingthescientificcommunitywithanopen-accessbasefor DNA damage quantification calculations. New DNA and cell geometries for the“molecularDNA”examplewillbeincludedinfutureversionsofGeant4-DNA.",
journal = "Precision Radiation Oncology",
title = "Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application",
volume = "7",
number = "1",
pages = "4-14",
doi = "10.1002/pro6.1186"
}

Chatzipapas, K. P., Tran, N. H., Đorđević, M., Živković, S., Zein, S., Shin, W., Sakata, D., Lampe, N., Brown, J. M. C., Ristić‐Fira, A., Petrović, I., Kyriakou, I., Emfietzoglou, D., Guatelli, S.,& Incerti, S.. (2023). Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. in Precision Radiation Oncology, 7(1), 4-14.
https://doi.org/10.1002/pro6.1186

Chatzipapas KP, Tran NH, Đorđević M, Živković S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristić‐Fira A, Petrović I, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. in Precision Radiation Oncology. 2023;7(1):4-14.
doi:10.1002/pro6.1186 .

Chatzipapas, Konstantinos P., Tran, Ngoc Hoang, Đorđević, Miloš, Živković, Sara, Zein, Sara, Shin, Wook‐Geun, Sakata, Dousatsu, Lampe, Nathanael, Brown, Jeremy M. C., Ristić‐Fira, Aleksandra, Petrović, Ivan, Kyriakou, Ioanna, Emfietzoglou, Dimitris, Guatelli, Susanna, Incerti, Sébastien, "Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application" in Precision Radiation Oncology, 7, no. 1 (2023):4-14,
https://doi.org/10.1002/pro6.1186 . .

TY  - JOUR
AU  - Chatzipapas, Konstantinos P.
AU  - Tran, Ngoc Hoang
AU  - Đorđević, Miloš
AU  - Živković, Sara
AU  - Zein, Sara
AU  - Shin, Wook-Geun
AU  - Sakata, Dousatsu
AU  - Lampe, Nathanael
AU  - Brown, Jeremy M. C.
AU  - Ristić-Fira, Aleksandra
AU  - Petrović, Ivan M.
AU  - Kyriakou, Ioanna
AU  - Emfietzoglou, Dimitris
AU  - Guatelli, Susanna
AU  - Incerti, Sebastien
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10661
AB  - 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.
T2  - Precision Radiation Oncology
T1  - Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application
VL  - 7
IS  - 1
SP  - 4
EP  - 14
DO  - 10.1002/pro6.1186
ER  - 

@article{
author = "Chatzipapas, Konstantinos P. and Tran, Ngoc Hoang and Đorđević, Miloš and Živković, Sara and Zein, Sara and Shin, Wook-Geun and Sakata, Dousatsu and Lampe, Nathanael and Brown, Jeremy M. C. and Ristić-Fira, Aleksandra and Petrović, Ivan M. and Kyriakou, Ioanna and Emfietzoglou, Dimitris and Guatelli, Susanna and Incerti, Sebastien",
year = "2023",
abstract = "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.",
journal = "Precision Radiation Oncology",
title = "Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application",
volume = "7",
number = "1",
pages = "4-14",
doi = "10.1002/pro6.1186"
}

Chatzipapas, K. P., Tran, N. H., Đorđević, M., Živković, S., Zein, S., Shin, W., Sakata, D., Lampe, N., Brown, J. M. C., Ristić-Fira, A., Petrović, I. M., Kyriakou, I., Emfietzoglou, D., Guatelli, S.,& Incerti, S.. (2023). Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application. in Precision Radiation Oncology, 7(1), 4-14.
https://doi.org/10.1002/pro6.1186

Chatzipapas KP, Tran NH, Đorđević M, Živković S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristić-Fira A, Petrović IM, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application. in Precision Radiation Oncology. 2023;7(1):4-14.
doi:10.1002/pro6.1186 .

Chatzipapas, Konstantinos P., Tran, Ngoc Hoang, Đorđević, Miloš, Živković, Sara, Zein, Sara, Shin, Wook-Geun, Sakata, Dousatsu, Lampe, Nathanael, Brown, Jeremy M. C., Ristić-Fira, Aleksandra, Petrović, Ivan M., Kyriakou, Ioanna, Emfietzoglou, Dimitris, Guatelli, Susanna, Incerti, Sebastien, "Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application" in Precision Radiation Oncology, 7, no. 1 (2023):4-14,
https://doi.org/10.1002/pro6.1186 . .

TY  - JOUR
AU  - Chatzipapas, Konstantinos
AU  - Đorđević, Miloš
AU  - Živković, Sara
AU  - Tran, Ngoc Hoang
AU  - Lampe, Nathanael
AU  - Sakata, Dousatsu
AU  - Petrović, Ivan
AU  - Ristić-Fira, Aleksandra
AU  - Shin, Wook-Geun
AU  - Zein, Sara
AU  - Brown, Jeremy M.C.
AU  - Kyriakou, Ioanna
AU  - Emfietzoglou, Dimitris
AU  - Guatelli, Susanna
AU  - Incerti, Sebastien
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/11202
AB  - Purpose: This study aimed to develop a computational environment for the accurate simulation of human cancer cell irradiation using Geant4-DNA. New cell geometrical models were developed and irradiated by alpha particle beams to induce DNA damage. The proposed approach may help further investigation of the benefits of external alpha irradiation therapy. Methods: The Geant4-DNA Monte Carlo (MC) toolkit allows the simulation of cancer cell geometries that can be combined with accurate modelling of physical, physicochemical and chemical stages of liquid water irradiation, including radiolytic processes. Geant4-DNA is used to calculate direct and non-direct DNA damage yields, such as single and double strand breaks, produced by the deposition of energy or by the interaction of DNA with free radicals. Results: In this study, the “molecularDNA” example application of Geant4-DNA was used to quantify early DNA damage in human cancer cells upon irradiation with alpha particle beams, as a function of linear energy transfer (LET). The MC simulation results are compared to experimental data, as well as previously published simulation data. The simulation results agree well with the experimental data on DSB yields in the lower LET range, while the experimental data on DSB yields are lower than the results obtained with the “molecularDNA” example in the higher LET range. Conclusion: This study explored and demonstrated the possibilities of the Geant4-DNA toolkit together with the “molecularDNA” example to simulate the helium beam irradiation of cancer cell lines, to quantify the early DNA damage, or even the following DNA damage response. © 2023 Associazione Italiana di Fisica Medica e Sanitaria
T2  - Physica Medica
T1  - Geant4-DNA simulation of human cancer cells irradiation with helium ion beams
VL  - 112
DO  - 10.1016/j.ejmp.2023.102613
ER  - 

@article{
author = "Chatzipapas, Konstantinos and Đorđević, Miloš and Živković, Sara and Tran, Ngoc Hoang and Lampe, Nathanael and Sakata, Dousatsu and Petrović, Ivan and Ristić-Fira, Aleksandra and Shin, Wook-Geun and Zein, Sara and Brown, Jeremy M.C. and Kyriakou, Ioanna and Emfietzoglou, Dimitris and Guatelli, Susanna and Incerti, Sebastien",
year = "2023",
abstract = "Purpose: This study aimed to develop a computational environment for the accurate simulation of human cancer cell irradiation using Geant4-DNA. New cell geometrical models were developed and irradiated by alpha particle beams to induce DNA damage. The proposed approach may help further investigation of the benefits of external alpha irradiation therapy. Methods: The Geant4-DNA Monte Carlo (MC) toolkit allows the simulation of cancer cell geometries that can be combined with accurate modelling of physical, physicochemical and chemical stages of liquid water irradiation, including radiolytic processes. Geant4-DNA is used to calculate direct and non-direct DNA damage yields, such as single and double strand breaks, produced by the deposition of energy or by the interaction of DNA with free radicals. Results: In this study, the “molecularDNA” example application of Geant4-DNA was used to quantify early DNA damage in human cancer cells upon irradiation with alpha particle beams, as a function of linear energy transfer (LET). The MC simulation results are compared to experimental data, as well as previously published simulation data. The simulation results agree well with the experimental data on DSB yields in the lower LET range, while the experimental data on DSB yields are lower than the results obtained with the “molecularDNA” example in the higher LET range. Conclusion: This study explored and demonstrated the possibilities of the Geant4-DNA toolkit together with the “molecularDNA” example to simulate the helium beam irradiation of cancer cell lines, to quantify the early DNA damage, or even the following DNA damage response. © 2023 Associazione Italiana di Fisica Medica e Sanitaria",
journal = "Physica Medica",
title = "Geant4-DNA simulation of human cancer cells irradiation with helium ion beams",
volume = "112",
doi = "10.1016/j.ejmp.2023.102613"
}

Chatzipapas, K., Đorđević, M., Živković, S., Tran, N. H., Lampe, N., Sakata, D., Petrović, I., Ristić-Fira, A., Shin, W., Zein, S., Brown, J. M.C., Kyriakou, I., Emfietzoglou, D., Guatelli, S.,& Incerti, S.. (2023). Geant4-DNA simulation of human cancer cells irradiation with helium ion beams. in Physica Medica, 112.
https://doi.org/10.1016/j.ejmp.2023.102613

Chatzipapas K, Đorđević M, Živković S, Tran NH, Lampe N, Sakata D, Petrović I, Ristić-Fira A, Shin W, Zein S, Brown JM, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Geant4-DNA simulation of human cancer cells irradiation with helium ion beams. in Physica Medica. 2023;112.
doi:10.1016/j.ejmp.2023.102613 .

Chatzipapas, Konstantinos, Đorđević, Miloš, Živković, Sara, Tran, Ngoc Hoang, Lampe, Nathanael, Sakata, Dousatsu, Petrović, Ivan, Ristić-Fira, Aleksandra, Shin, Wook-Geun, Zein, Sara, Brown, Jeremy M.C., Kyriakou, Ioanna, Emfietzoglou, Dimitris, Guatelli, Susanna, Incerti, Sebastien, "Geant4-DNA simulation of human cancer cells irradiation with helium ion beams" in Physica Medica, 112 (2023),
https://doi.org/10.1016/j.ejmp.2023.102613 . .

TY  - JOUR
AU  - Shin, Wook-Geun
AU  - Sakata, Dousatsu
AU  - Lampe, Nathanael
AU  - Belov, Oleg
AU  - Tran, Ngoc Hoang
AU  - Petrović, Ivan M.
AU  - Ristić-Fira, Aleksandra
AU  - Đorđević, Miloš
AU  - Bernal, Mario A.
AU  - Bordage, Marie-Claude
AU  - Francis, Ziad
AU  - Kyriakou, Ioanna
AU  - Perrot, Yann
AU  - Sasaki, Takashi
AU  - Villagrasa, Carmen
AU  - Guatelli, Susanna
AU  - Breton, Vincent
AU  - Emfietzoglou, Dimitris
AU  - Incerti, Sebastien
PY  - 2021
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9961
AB  - Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.
T2  - Cancers
T2  - Cancers
T1  - A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast
VL  - 13
IS  - 19
SP  - 4940
DO  - 10.3390/cancers13194940
ER  - 

@article{
author = "Shin, Wook-Geun and Sakata, Dousatsu and Lampe, Nathanael and Belov, Oleg and Tran, Ngoc Hoang and Petrović, Ivan M. and Ristić-Fira, Aleksandra and Đorđević, Miloš and Bernal, Mario A. and Bordage, Marie-Claude and Francis, Ziad and Kyriakou, Ioanna and Perrot, Yann and Sasaki, Takashi and Villagrasa, Carmen and Guatelli, Susanna and Breton, Vincent and Emfietzoglou, Dimitris and Incerti, Sebastien",
year = "2021",
abstract = "Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.",
journal = "Cancers, Cancers",
title = "A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast",
volume = "13",
number = "19",
pages = "4940",
doi = "10.3390/cancers13194940"
}

Shin, W., Sakata, D., Lampe, N., Belov, O., Tran, N. H., Petrović, I. M., Ristić-Fira, A., Đorđević, M., Bernal, M. A., Bordage, M., Francis, Z., Kyriakou, I., Perrot, Y., Sasaki, T., Villagrasa, C., Guatelli, S., Breton, V., Emfietzoglou, D.,& Incerti, S.. (2021). A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. in Cancers, 13(19), 4940.
https://doi.org/10.3390/cancers13194940

Shin W, Sakata D, Lampe N, Belov O, Tran NH, Petrović IM, Ristić-Fira A, Đorđević M, Bernal MA, Bordage M, Francis Z, Kyriakou I, Perrot Y, Sasaki T, Villagrasa C, Guatelli S, Breton V, Emfietzoglou D, Incerti S. A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. in Cancers. 2021;13(19):4940.
doi:10.3390/cancers13194940 .

Shin, Wook-Geun, Sakata, Dousatsu, Lampe, Nathanael, Belov, Oleg, Tran, Ngoc Hoang, Petrović, Ivan M., Ristić-Fira, Aleksandra, Đorđević, Miloš, Bernal, Mario A., Bordage, Marie-Claude, Francis, Ziad, Kyriakou, Ioanna, Perrot, Yann, Sasaki, Takashi, Villagrasa, Carmen, Guatelli, Susanna, Breton, Vincent, Emfietzoglou, Dimitris, Incerti, Sebastien, "A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast" in Cancers, 13, no. 19 (2021):4940,
https://doi.org/10.3390/cancers13194940 . .

TY  - JOUR
AU  - Bernal, Mario A.
AU  - Bordage, Marie Claude
AU  - Brown, Jeremy Michael Cooney
AU  - Davídková, Marie
AU  - Delage, E.
AU  - El Bitar, Ziad Ei
AU  - Enger, Shirin A.
AU  - Francis, Ziad
AU  - Guatelli, Susanna
AU  - Ivanchenko, Vladimir N.
AU  - Karamitros, Mathieu
AU  - Kyriakou, Ioanna
AU  - Maigne, Lydia
AU  - Meylan, Sylvain
AU  - Murakami, Kouichi
AU  - Okada, Shogo
AU  - Payno, H.
AU  - Perrot, Yann
AU  - Petrović, Ivan M.
AU  - Pham, Q. T.
AU  - Ristić-Fira, Aleksandra
AU  - Sasaki, Takashi
AU  - Stepan, Vaclav
AU  - Tran, Ngoc Hoang
AU  - Villagrasa, Carmen
AU  - Incerti, Sebastien
PY  - 2015
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/859
AB  - Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of todays radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described.
T2  - Physica Medica
T1  - Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit
VL  - 31
IS  - 8
SP  - 861
EP  - 874
DO  - 10.1016/j.ejmp.2015.10.087
ER  - 

@article{
author = "Bernal, Mario A. and Bordage, Marie Claude and Brown, Jeremy Michael Cooney and Davídková, Marie and Delage, E. and El Bitar, Ziad Ei and Enger, Shirin A. and Francis, Ziad and Guatelli, Susanna and Ivanchenko, Vladimir N. and Karamitros, Mathieu and Kyriakou, Ioanna and Maigne, Lydia and Meylan, Sylvain and Murakami, Kouichi and Okada, Shogo and Payno, H. and Perrot, Yann and Petrović, Ivan M. and Pham, Q. T. and Ristić-Fira, Aleksandra and Sasaki, Takashi and Stepan, Vaclav and Tran, Ngoc Hoang and Villagrasa, Carmen and Incerti, Sebastien",
year = "2015",
abstract = "Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of todays radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described.",
journal = "Physica Medica",
title = "Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit",
volume = "31",
number = "8",
pages = "861-874",
doi = "10.1016/j.ejmp.2015.10.087"
}

Bernal, M. A., Bordage, M. C., Brown, J. M. C., Davídková, M., Delage, E., El Bitar, Z. E., Enger, S. A., Francis, Z., Guatelli, S., Ivanchenko, V. N., Karamitros, M., Kyriakou, I., Maigne, L., Meylan, S., Murakami, K., Okada, S., Payno, H., Perrot, Y., Petrović, I. M., Pham, Q. T., Ristić-Fira, A., Sasaki, T., Stepan, V., Tran, N. H., Villagrasa, C.,& Incerti, S.. (2015). Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. in Physica Medica, 31(8), 861-874.
https://doi.org/10.1016/j.ejmp.2015.10.087

Bernal MA, Bordage MC, Brown JMC, Davídková M, Delage E, El Bitar ZE, Enger SA, Francis Z, Guatelli S, Ivanchenko VN, Karamitros M, Kyriakou I, Maigne L, Meylan S, Murakami K, Okada S, Payno H, Perrot Y, Petrović IM, Pham QT, Ristić-Fira A, Sasaki T, Stepan V, Tran NH, Villagrasa C, Incerti S. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. in Physica Medica. 2015;31(8):861-874.
doi:10.1016/j.ejmp.2015.10.087 .

Bernal, Mario A., Bordage, Marie Claude, Brown, Jeremy Michael Cooney, Davídková, Marie, Delage, E., El Bitar, Ziad Ei, Enger, Shirin A., Francis, Ziad, Guatelli, Susanna, Ivanchenko, Vladimir N., Karamitros, Mathieu, Kyriakou, Ioanna, Maigne, Lydia, Meylan, Sylvain, Murakami, Kouichi, Okada, Shogo, Payno, H., Perrot, Yann, Petrović, Ivan M., Pham, Q. T., Ristić-Fira, Aleksandra, Sasaki, Takashi, Stepan, Vaclav, Tran, Ngoc Hoang, Villagrasa, Carmen, Incerti, Sebastien, "Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit" in Physica Medica, 31, no. 8 (2015):861-874,
https://doi.org/10.1016/j.ejmp.2015.10.087 . .

TY  - JOUR
AU  - Incerti, Sebastien
AU  - Psaltaki, Maria G.
AU  - Gillet, Pierre
AU  - Barberet, Ph.
AU  - Bardies, M.
AU  - Bernal, Mario A.
AU  - Bordage, Marie Claude
AU  - Breton, Vincent
AU  - Davídková, Marie
AU  - Delage, E.
AU  - El Bitar, Ziad Ei
AU  - Francis, Ziad
AU  - Guatelli, Susanna
AU  - Ivanchenko, A.
AU  - Ivanchenko, Vladimir
AU  - Karamitros, Mathieu
AU  - Lee, Sebyeong
AU  - Maigne, Lydia
AU  - Meylan, Sylvain
AU  - Murakami, Kouichi
AU  - Nieminen, Petteri H.
AU  - Payno, H.
AU  - Perrot, Yann
AU  - Petrović, Ivan M.
AU  - Pham, Q. T.
AU  - Ristić-Fira, Aleksandra
AU  - Santin, Giovanni
AU  - Sasaki, Takashi
AU  - Seznec, Herve
AU  - Shin, Jae-ik
AU  - Stepan, Vaclav
AU  - Tran, Ngoc Hoang
AU  - Villagrasa, Carmen
AU  - Geant4-DNA Collaboration
PY  - 2014
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/6073
AB  - An accurate modeling of radial energy deposition around ion tracks is a key requirement of radiation transport software used for simulations in radiobiology at the sub-cellular scale. The work presented in this paper is part of the on-going benchmarking of the Geant4-DNA physics processes and models, which are available in the Geant4 Monte Carlo simulation toolkit for the low energy transport of particles in liquid water. We present for the first time radial dose distributions of incident ion tracks simulated with Geant4-DNA. Simulation results are compared to other results available in the literature, obtained from analytical calculations, step-by-step Monte Carlo simulations and measurements. They show a reasonable agreement with reference data. (C) 2014 Elsevier B.V. All rights reserved.
T2  - Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms
T1  - Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study
VL  - 333
SP  - 92
EP  - 98
DO  - 10.1016/j.nimb.2014.04.025
ER  - 

@article{
author = "Incerti, Sebastien and Psaltaki, Maria G. and Gillet, Pierre and Barberet, Ph. and Bardies, M. and Bernal, Mario A. and Bordage, Marie Claude and Breton, Vincent and Davídková, Marie and Delage, E. and El Bitar, Ziad Ei and Francis, Ziad and Guatelli, Susanna and Ivanchenko, A. and Ivanchenko, Vladimir and Karamitros, Mathieu and Lee, Sebyeong and Maigne, Lydia and Meylan, Sylvain and Murakami, Kouichi and Nieminen, Petteri H. and Payno, H. and Perrot, Yann and Petrović, Ivan M. and Pham, Q. T. and Ristić-Fira, Aleksandra and Santin, Giovanni and Sasaki, Takashi and Seznec, Herve and Shin, Jae-ik and Stepan, Vaclav and Tran, Ngoc Hoang and Villagrasa, Carmen and Geant4-DNA Collaboration",
year = "2014",
abstract = "An accurate modeling of radial energy deposition around ion tracks is a key requirement of radiation transport software used for simulations in radiobiology at the sub-cellular scale. The work presented in this paper is part of the on-going benchmarking of the Geant4-DNA physics processes and models, which are available in the Geant4 Monte Carlo simulation toolkit for the low energy transport of particles in liquid water. We present for the first time radial dose distributions of incident ion tracks simulated with Geant4-DNA. Simulation results are compared to other results available in the literature, obtained from analytical calculations, step-by-step Monte Carlo simulations and measurements. They show a reasonable agreement with reference data. (C) 2014 Elsevier B.V. All rights reserved.",
journal = "Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms",
title = "Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study",
volume = "333",
pages = "92-98",
doi = "10.1016/j.nimb.2014.04.025"
}

Incerti, S., Psaltaki, M. G., Gillet, P., Barberet, Ph., Bardies, M., Bernal, M. A., Bordage, M. C., Breton, V., Davídková, M., Delage, E., El Bitar, Z. E., Francis, Z., Guatelli, S., Ivanchenko, A., Ivanchenko, V., Karamitros, M., Lee, S., Maigne, L., Meylan, S., Murakami, K., Nieminen, P. H., Payno, H., Perrot, Y., Petrović, I. M., Pham, Q. T., Ristić-Fira, A., Santin, G., Sasaki, T., Seznec, H., Shin, J., Stepan, V., Tran, N. H., Villagrasa, C.,& Geant4-DNA Collaboration. (2014). Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study. in Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms, 333, 92-98.
https://doi.org/10.1016/j.nimb.2014.04.025

Incerti S, Psaltaki MG, Gillet P, Barberet P, Bardies M, Bernal MA, Bordage MC, Breton V, Davídková M, Delage E, El Bitar ZE, Francis Z, Guatelli S, Ivanchenko A, Ivanchenko V, Karamitros M, Lee S, Maigne L, Meylan S, Murakami K, Nieminen PH, Payno H, Perrot Y, Petrović IM, Pham QT, Ristić-Fira A, Santin G, Sasaki T, Seznec H, Shin J, Stepan V, Tran NH, Villagrasa C, Geant4-DNA Collaboration. Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study. in Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms. 2014;333:92-98.
doi:10.1016/j.nimb.2014.04.025 .

Incerti, Sebastien, Psaltaki, Maria G., Gillet, Pierre, Barberet, Ph., Bardies, M., Bernal, Mario A., Bordage, Marie Claude, Breton, Vincent, Davídková, Marie, Delage, E., El Bitar, Ziad Ei, Francis, Ziad, Guatelli, Susanna, Ivanchenko, A., Ivanchenko, Vladimir, Karamitros, Mathieu, Lee, Sebyeong, Maigne, Lydia, Meylan, Sylvain, Murakami, Kouichi, Nieminen, Petteri H., Payno, H., Perrot, Yann, Petrović, Ivan M., Pham, Q. T., Ristić-Fira, Aleksandra, Santin, Giovanni, Sasaki, Takashi, Seznec, Herve, Shin, Jae-ik, Stepan, Vaclav, Tran, Ngoc Hoang, Villagrasa, Carmen, Geant4-DNA Collaboration, "Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study" in Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms, 333 (2014):92-98,
https://doi.org/10.1016/j.nimb.2014.04.025 . .