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 . .