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 . .