TY  - JOUR
AU  - Sakata, Dousatsu
AU  - Hirayama, Ryoichi
AU  - Shin, Wook-Geun
AU  - Belli, Mauro
AU  - Tabocchini, Maria A
AU  - Stewart, Robert D
AU  - Belov, Oleg
AU  - Bernal, Mario A
AU  - Bordage, Marie-Claude
AU  - Brown, Jeremy M.C.
AU  - Đorđević, Miloš
AU  - Emfietzoglou, Dimitris
AU  - Francis, Ziad
AU  - Guatelli, Susanna
AU  - Inaniwa, Taku
AU  - Ivanchenko, Vladimir
AU  - Karamitros, Mathieu
AU  - Kyriakou, Ioanna
AU  - Lampe, Nathanael
AU  - Li, Zhuxin
AU  - Meylan, Sylvain
AU  - Michelet, Claire
AU  - Nieminen, Petteri
AU  - Perrot, Yann
AU  - Petrović, Ivan M.
AU  - Ramos-Mendez, Jose
AU  - Ristić-Fira, Aleksandra
AU  - Santin, Giovanni
AU  - Schuemann, Jan
AU  - Tran, Hoang N
AU  - Villagrasa, Carmen
AU  - Incerti, Sebastien
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10573
AB  - Purpose: Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology. Methods: We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs. Results: By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction. Conclusion: This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.
T2  - Physica Medica
T1  - Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA
VL  - 105
SP  - 102508
DO  - 10.1016/j.ejmp.2022.11.012
ER  - 

@article{
author = "Sakata, Dousatsu and Hirayama, Ryoichi and Shin, Wook-Geun and Belli, Mauro and Tabocchini, Maria A and Stewart, Robert D and Belov, Oleg and Bernal, Mario A and Bordage, Marie-Claude and Brown, Jeremy M.C. and Đorđević, Miloš and Emfietzoglou, Dimitris and Francis, Ziad and Guatelli, Susanna and Inaniwa, Taku and Ivanchenko, Vladimir and Karamitros, Mathieu and Kyriakou, Ioanna and Lampe, Nathanael and Li, Zhuxin and Meylan, Sylvain and Michelet, Claire and Nieminen, Petteri and Perrot, Yann and Petrović, Ivan M. and Ramos-Mendez, Jose and Ristić-Fira, Aleksandra and Santin, Giovanni and Schuemann, Jan and Tran, Hoang N and Villagrasa, Carmen and Incerti, Sebastien",
year = "2023",
abstract = "Purpose: Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology. Methods: We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs. Results: By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction. Conclusion: This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.",
journal = "Physica Medica",
title = "Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA",
volume = "105",
pages = "102508",
doi = "10.1016/j.ejmp.2022.11.012"
}

Sakata, D., Hirayama, R., Shin, W., Belli, M., Tabocchini, M. A., Stewart, R. D., Belov, O., Bernal, M. A., Bordage, M., Brown, J. M.C., Đorđević, M., Emfietzoglou, D., Francis, Z., Guatelli, S., Inaniwa, T., Ivanchenko, V., Karamitros, M., Kyriakou, I., Lampe, N., Li, Z., Meylan, S., Michelet, C., Nieminen, P., Perrot, Y., Petrović, I. M., Ramos-Mendez, J., Ristić-Fira, A., Santin, G., Schuemann, J., Tran, H. N., Villagrasa, C.,& Incerti, S.. (2023). Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. in Physica Medica, 105, 102508.
https://doi.org/10.1016/j.ejmp.2022.11.012

Sakata D, Hirayama R, Shin W, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage M, Brown JM, Đorđević M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Li Z, Meylan S, Michelet C, Nieminen P, Perrot Y, Petrović IM, Ramos-Mendez J, Ristić-Fira A, Santin G, Schuemann J, Tran HN, Villagrasa C, Incerti S. Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. in Physica Medica. 2023;105:102508.
doi:10.1016/j.ejmp.2022.11.012 .

Sakata, Dousatsu, Hirayama, Ryoichi, Shin, Wook-Geun, Belli, Mauro, Tabocchini, Maria A, Stewart, Robert D, Belov, Oleg, Bernal, Mario A, Bordage, Marie-Claude, Brown, Jeremy M.C., Đorđević, Miloš, Emfietzoglou, Dimitris, Francis, Ziad, Guatelli, Susanna, Inaniwa, Taku, Ivanchenko, Vladimir, Karamitros, Mathieu, Kyriakou, Ioanna, Lampe, Nathanael, Li, Zhuxin, Meylan, Sylvain, Michelet, Claire, Nieminen, Petteri, Perrot, Yann, Petrović, Ivan M., Ramos-Mendez, Jose, Ristić-Fira, Aleksandra, Santin, Giovanni, Schuemann, Jan, Tran, Hoang N, Villagrasa, Carmen, Incerti, Sebastien, "Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA" in Physica Medica, 105 (2023):102508,
https://doi.org/10.1016/j.ejmp.2022.11.012 . .

TY  - JOUR
AU  - Sakata, Dousatsu
AU  - Belov, Oleg
AU  - Bordage, Marie-Claude
AU  - Emfietzoglou, Dimitris
AU  - Guatelli, Susanna
AU  - Inaniwa, Taku
AU  - Ivanchenko, Vladimir
AU  - Karamitros, Mathieu
AU  - Kyriakou, Ioanna
AU  - Lampe, Nathanael
AU  - Petrović, Ivan M.
AU  - Ristić-Fira, Aleksandra
AU  - Shin, Wook-Geun
AU  - Incerti, Sebastien
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9751
AB  - Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation's track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic "fully integrated" MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of gamma -H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.
T2  - Scientific Reports
T1  - Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA
VL  - 10
IS  - 1
SP  - 20788
DO  - 10.1038/s41598-020-75982-x
ER  - 

@article{
author = "Sakata, Dousatsu and Belov, Oleg and Bordage, Marie-Claude and Emfietzoglou, Dimitris and Guatelli, Susanna and Inaniwa, Taku and Ivanchenko, Vladimir and Karamitros, Mathieu and Kyriakou, Ioanna and Lampe, Nathanael and Petrović, Ivan M. and Ristić-Fira, Aleksandra and Shin, Wook-Geun and Incerti, Sebastien",
year = "2020",
abstract = "Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation's track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic "fully integrated" MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of gamma -H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.",
journal = "Scientific Reports",
title = "Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA",
volume = "10",
number = "1",
pages = "20788",
doi = "10.1038/s41598-020-75982-x"
}

Sakata, D., Belov, O., Bordage, M., Emfietzoglou, D., Guatelli, S., Inaniwa, T., Ivanchenko, V., Karamitros, M., Kyriakou, I., Lampe, N., Petrović, I. M., Ristić-Fira, A., Shin, W.,& Incerti, S.. (2020). Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. in Scientific Reports, 10(1), 20788.
https://doi.org/10.1038/s41598-020-75982-x

Sakata D, Belov O, Bordage M, Emfietzoglou D, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Petrović IM, Ristić-Fira A, Shin W, Incerti S. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. in Scientific Reports. 2020;10(1):20788.
doi:10.1038/s41598-020-75982-x .

Sakata, Dousatsu, Belov, Oleg, Bordage, Marie-Claude, Emfietzoglou, Dimitris, Guatelli, Susanna, Inaniwa, Taku, Ivanchenko, Vladimir, Karamitros, Mathieu, Kyriakou, Ioanna, Lampe, Nathanael, Petrović, Ivan M., Ristić-Fira, Aleksandra, Shin, Wook-Geun, Incerti, Sebastien, "Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA" in Scientific Reports, 10, no. 1 (2020):20788,
https://doi.org/10.1038/s41598-020-75982-x . .

TY  - JOUR
AU  - Allison, John
AU  - Amako, Katsuya
AU  - Apostolakis, John
AU  - Arce, Pedro
AU  - Asai, Makoto
AU  - Aso, Tsukasa
AU  - Bagli, Enrico
AU  - Bagulya, Alexander V.
AU  - Banerjee, S
AU  - Barrand, Guy C.
AU  - Beck, Bret R.
AU  - Bogdanov, Aleksei G.
AU  - Brandt, Daniel
AU  - Brown, Jeremy Michael Cooney
AU  - Burkhardt, Helmut
AU  - Canal, Philippe
AU  - Cano-Ott, Daniel
AU  - Chauvie, S
AU  - Cho, Kihyeon
AU  - Cirrone, Giuseppe Antonio Pablo
AU  - Cooperman, Gene D.
AU  - Cortés-Giraldo, Miguel Antonio
AU  - Cosmo, Gabriele
AU  - Cuttone, Giacomo
AU  - Depaola, Gerardo O.
AU  - Desorgher, Laurent
AU  - Dong, Xin
AU  - Dotti, Andrea
AU  - Elvira, Daniel V.
AU  - Folger, Gunter
AU  - Francis, Ziad
AU  - Galoyan, Aida S.
AU  - Garnier, Laurent
AU  - Gayer, Marek
AU  - Genser, K.L.
AU  - Grichine, V.M.
AU  - Guatelli, S
AU  - Gueye, Paul L.J.
AU  - Gumplinger, Peter
AU  - Howard, Alexander S.
AU  - Hrivnacova, Ivana
AU  - Hwang, Soonwook
AU  - Incerti, Sebastien
AU  - Ivanchenko, A.
AU  - Ivanchenko, Vladimir
AU  - Jones, F.W.
AU  - Jun, S.Y.
AU  - Kaitaniemi, Pekka
AU  - Karakatsanis, Nicolas
AU  - Karamitros, M
AU  - Kelsey, M
AU  - Kimura, Akinori
AU  - Koi, Tatsumi
AU  - Kurashige, Hisaya
AU  - Lechner, Anton
AU  - Lee, Sebyeong
AU  - Longo, F
AU  - Maire, M
AU  - Mancusi, Davide
AU  - Mantero, Alfonso
AU  - Mendoza, Emilio
AU  - Morgan, Ben
AU  - Murakami, Kouichi
AU  - Nikitina, Tatiana
AU  - Pandola, Luciano
AU  - Paprocki, P
AU  - Perl, Joseph M.
AU  - Petrović, Ivan M.
AU  - Pia, Maria Grazia
AU  - Pokorski, Witold
AU  - Quesada Molina, Jose Manuel
AU  - Raine, Melanie
AU  - Reis, M.A.
AU  - Ribon, A
AU  - Ristić-Fira, Aleksandra
AU  - Romano, Francesco
AU  - Russo, Giorgio
AU  - Santin, G
AU  - Sasaki, Takashi
AU  - Sawkey, Daren L.
AU  - Shin, Jae-ik
AU  - Strakovsky, Igor I.
AU  - Taborda, Ana
AU  - Tanaka, Satoshi
AU  - Tomé, B
AU  - Toshito, T
AU  - Tran, H.N.
AU  - Truscott, Peter R.
AU  - Urban, Laszlo
AU  - Uzhinsky, Vladimir V.
AU  - Verbeke, Jerome M.
AU  - Verderi, Marc
AU  - Wendt, Brycen L.
AU  - Wenzel, Hans Joachim
AU  - Wright, Dennis Herbert
AU  - Wright, Douglas M.
AU  - Yamashita, Tomohiro
AU  - Yarba, Julia V.
AU  - Yoshida, Hajime
PY  - 2016
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8645
AB  - Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.
T2  - Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
T1  - Recent developments in Geant4
VL  - 835
SP  - 186
EP  - 225
DO  - 10.1016/j.nima.2016.06.125
ER  - 

@article{
author = "Allison, John and Amako, Katsuya and Apostolakis, John and Arce, Pedro and Asai, Makoto and Aso, Tsukasa and Bagli, Enrico and Bagulya, Alexander V. and Banerjee, S and Barrand, Guy C. and Beck, Bret R. and Bogdanov, Aleksei G. and Brandt, Daniel and Brown, Jeremy Michael Cooney and Burkhardt, Helmut and Canal, Philippe and Cano-Ott, Daniel and Chauvie, S and Cho, Kihyeon and Cirrone, Giuseppe Antonio Pablo and Cooperman, Gene D. and Cortés-Giraldo, Miguel Antonio and Cosmo, Gabriele and Cuttone, Giacomo and Depaola, Gerardo O. and Desorgher, Laurent and Dong, Xin and Dotti, Andrea and Elvira, Daniel V. and Folger, Gunter and Francis, Ziad and Galoyan, Aida S. and Garnier, Laurent and Gayer, Marek and Genser, K.L. and Grichine, V.M. and Guatelli, S and Gueye, Paul L.J. and Gumplinger, Peter and Howard, Alexander S. and Hrivnacova, Ivana and Hwang, Soonwook and Incerti, Sebastien and Ivanchenko, A. and Ivanchenko, Vladimir and Jones, F.W. and Jun, S.Y. and Kaitaniemi, Pekka and Karakatsanis, Nicolas and Karamitros, M and Kelsey, M and Kimura, Akinori and Koi, Tatsumi and Kurashige, Hisaya and Lechner, Anton and Lee, Sebyeong and Longo, F and Maire, M and Mancusi, Davide and Mantero, Alfonso and Mendoza, Emilio and Morgan, Ben and Murakami, Kouichi and Nikitina, Tatiana and Pandola, Luciano and Paprocki, P and Perl, Joseph M. and Petrović, Ivan M. and Pia, Maria Grazia and Pokorski, Witold and Quesada Molina, Jose Manuel and Raine, Melanie and Reis, M.A. and Ribon, A and Ristić-Fira, Aleksandra and Romano, Francesco and Russo, Giorgio and Santin, G and Sasaki, Takashi and Sawkey, Daren L. and Shin, Jae-ik and Strakovsky, Igor I. and Taborda, Ana and Tanaka, Satoshi and Tomé, B and Toshito, T and Tran, H.N. and Truscott, Peter R. and Urban, Laszlo and Uzhinsky, Vladimir V. and Verbeke, Jerome M. and Verderi, Marc and Wendt, Brycen L. and Wenzel, Hans Joachim and Wright, Dennis Herbert and Wright, Douglas M. and Yamashita, Tomohiro and Yarba, Julia V. and Yoshida, Hajime",
year = "2016",
abstract = "Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.",
journal = "Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment",
title = "Recent developments in Geant4",
volume = "835",
pages = "186-225",
doi = "10.1016/j.nima.2016.06.125"
}

Allison, J., Amako, K., Apostolakis, J., Arce, P., Asai, M., Aso, T., Bagli, E., Bagulya, A. V., Banerjee, S., Barrand, G. C., Beck, B. R., Bogdanov, A. G., Brandt, D., Brown, J. M. C., Burkhardt, H., Canal, P., Cano-Ott, D., Chauvie, S., Cho, K., Cirrone, G. A. P., Cooperman, G. D., Cortés-Giraldo, M. A., Cosmo, G., Cuttone, G., Depaola, G. O., Desorgher, L., Dong, X., Dotti, A., Elvira, D. V., Folger, G., Francis, Z., Galoyan, A. S., Garnier, L., Gayer, M., Genser, K.L., Grichine, V.M., Guatelli, S., Gueye, P. L.J., Gumplinger, P., Howard, A. S., Hrivnacova, I., Hwang, S., Incerti, S., Ivanchenko, A., Ivanchenko, V., Jones, F.W., Jun, S.Y., Kaitaniemi, P., Karakatsanis, N., Karamitros, M., Kelsey, M., Kimura, A., Koi, T., Kurashige, H., Lechner, A., Lee, S., Longo, F., Maire, M., Mancusi, D., Mantero, A., Mendoza, E., Morgan, B., Murakami, K., Nikitina, T., Pandola, L., Paprocki, P., Perl, J. M., Petrović, I. M., Pia, M. G., Pokorski, W., Quesada Molina, J. M., Raine, M., Reis, M.A., Ribon, A., Ristić-Fira, A., Romano, F., Russo, G., Santin, G., Sasaki, T., Sawkey, D. L., Shin, J., Strakovsky, I. I., Taborda, A., Tanaka, S., Tomé, B., Toshito, T., Tran, H.N., Truscott, P. R., Urban, L., Uzhinsky, V. V., Verbeke, J. M., Verderi, M., Wendt, B. L., Wenzel, H. J., Wright, D. H., Wright, D. M., Yamashita, T., Yarba, J. V.,& Yoshida, H.. (2016). Recent developments in Geant4. in Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 835, 186-225.
https://doi.org/10.1016/j.nima.2016.06.125

Allison J, Amako K, Apostolakis J, Arce P, Asai M, Aso T, Bagli E, Bagulya AV, Banerjee S, Barrand GC, Beck BR, Bogdanov AG, Brandt D, Brown JMC, Burkhardt H, Canal P, Cano-Ott D, Chauvie S, Cho K, Cirrone GAP, Cooperman GD, Cortés-Giraldo MA, Cosmo G, Cuttone G, Depaola GO, Desorgher L, Dong X, Dotti A, Elvira DV, Folger G, Francis Z, Galoyan AS, Garnier L, Gayer M, Genser K, Grichine V, Guatelli S, Gueye PL, Gumplinger P, Howard AS, Hrivnacova I, Hwang S, Incerti S, Ivanchenko A, Ivanchenko V, Jones F, Jun S, Kaitaniemi P, Karakatsanis N, Karamitros M, Kelsey M, Kimura A, Koi T, Kurashige H, Lechner A, Lee S, Longo F, Maire M, Mancusi D, Mantero A, Mendoza E, Morgan B, Murakami K, Nikitina T, Pandola L, Paprocki P, Perl JM, Petrović IM, Pia MG, Pokorski W, Quesada Molina JM, Raine M, Reis M, Ribon A, Ristić-Fira A, Romano F, Russo G, Santin G, Sasaki T, Sawkey DL, Shin J, Strakovsky II, Taborda A, Tanaka S, Tomé B, Toshito T, Tran H, Truscott PR, Urban L, Uzhinsky VV, Verbeke JM, Verderi M, Wendt BL, Wenzel HJ, Wright DH, Wright DM, Yamashita T, Yarba JV, Yoshida H. Recent developments in Geant4. in Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2016;835:186-225.
doi:10.1016/j.nima.2016.06.125 .

Allison, John, Amako, Katsuya, Apostolakis, John, Arce, Pedro, Asai, Makoto, Aso, Tsukasa, Bagli, Enrico, Bagulya, Alexander V., Banerjee, S, Barrand, Guy C., Beck, Bret R., Bogdanov, Aleksei G., Brandt, Daniel, Brown, Jeremy Michael Cooney, Burkhardt, Helmut, Canal, Philippe, Cano-Ott, Daniel, Chauvie, S, Cho, Kihyeon, Cirrone, Giuseppe Antonio Pablo, Cooperman, Gene D., Cortés-Giraldo, Miguel Antonio, Cosmo, Gabriele, Cuttone, Giacomo, Depaola, Gerardo O., Desorgher, Laurent, Dong, Xin, Dotti, Andrea, Elvira, Daniel V., Folger, Gunter, Francis, Ziad, Galoyan, Aida S., Garnier, Laurent, Gayer, Marek, Genser, K.L., Grichine, V.M., Guatelli, S, Gueye, Paul L.J., Gumplinger, Peter, Howard, Alexander S., Hrivnacova, Ivana, Hwang, Soonwook, Incerti, Sebastien, Ivanchenko, A., Ivanchenko, Vladimir, Jones, F.W., Jun, S.Y., Kaitaniemi, Pekka, Karakatsanis, Nicolas, Karamitros, M, Kelsey, M, Kimura, Akinori, Koi, Tatsumi, Kurashige, Hisaya, Lechner, Anton, Lee, Sebyeong, Longo, F, Maire, M, Mancusi, Davide, Mantero, Alfonso, Mendoza, Emilio, Morgan, Ben, Murakami, Kouichi, Nikitina, Tatiana, Pandola, Luciano, Paprocki, P, Perl, Joseph M., Petrović, Ivan M., Pia, Maria Grazia, Pokorski, Witold, Quesada Molina, Jose Manuel, Raine, Melanie, Reis, M.A., Ribon, A, Ristić-Fira, Aleksandra, Romano, Francesco, Russo, Giorgio, Santin, G, Sasaki, Takashi, Sawkey, Daren L., Shin, Jae-ik, Strakovsky, Igor I., Taborda, Ana, Tanaka, Satoshi, Tomé, B, Toshito, T, Tran, H.N., Truscott, Peter R., Urban, Laszlo, Uzhinsky, Vladimir V., Verbeke, Jerome M., Verderi, Marc, Wendt, Brycen L., Wenzel, Hans Joachim, Wright, Dennis Herbert, Wright, Douglas M., Yamashita, Tomohiro, Yarba, Julia V., Yoshida, Hajime, "Recent developments in Geant4" in Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 835 (2016):186-225,
https://doi.org/10.1016/j.nima.2016.06.125 . .

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 . .