Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application
Аутори
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
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
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-strandbreakyieldswereproducedusingeachoftheavailablegeom...etries.Theresultswerecomparedwiththeliterature,tovalidatetheexample,producinglessthan5%differenceinallcases.Conclusion:“molecularDNA”isaprototypetoolthatcanbeappliedinawidevarietyofradiobiologystudies,providingthescientificcommunitywithanopen-accessbasefor DNA damage quantification calculations. New DNA and cell geometries for the“molecularDNA”examplewillbeincludedinfutureversionsofGeant4-DNA.
Кључне речи:
DNA damage / double strand breaks / Geant4-DNA / molecularDNA / Monte Carlo simulationsИзвор:
Precision Radiation Oncology, 2023, 7, 1, 4-14Финансирање / пројекти:
- e European Space Agency for its support to Geant4-DNA through the “BioRad3” project [Contract 4000132935/21/NL/CRS, 2021–2023]
Колекције
Институција/група
VinčaTY - 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 . .