Journal ArticleDOI
Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit
Mario A. Bernal,Marie-Claude Bordage,Jeremy M. C. Brown,Jeremy M. C. Brown,Marie Davídková,E. Delage,Z. El Bitar,Shirin A. Enger,Ziad Francis,Susanna Guatelli,Vladimir Ivanchenko,M. Karamitros,Ioanna Kyriakou,Lydia Maigne,Sylvain Meylan,K. Murakami,Shogo Okada,H. Payno,Yann Perrot,Ivan Petrović,Q.T. Pham,Aleksandra Ristić-Fira,Takashi Sasaki,Václav Štěpán,H.N. Tran,Carmen Villagrasa,Sebastien Incerti +26 more
TLDR
This paper presents the most recent review of the Geant4-DNA extension, as available to Geant 4 users since June 2015 (release 10.2 Beta), and includes the description of new physical models for thedescription 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.About:
This article is published in Physica Medica.The article was published on 2015-12-01. It has received 370 citations till now. The article focuses on the topics: Monte Carlo method.read more
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Journal ArticleDOI
Recent developments in GEANT4
John Allison,K. Amako,John Apostolakis,Pedro Arce,Makoto Asai,Tsukasa Aso,Enrico Bagli,Alexander Bagulya,Sw. Banerjee,G. Barrand,B. R. Beck,Alexey Bogdanov,D. Brandt,Jeremy M. C. Brown,Helmut Burkhardt,Ph Canal,D. Cano-Ott,Stephane Chauvie,Kyung-Suk Cho,G.A.P. Cirrone,Gene Cooperman,M. A. Cortés-Giraldo,G. Cosmo,Giacomo Cuttone,G.O. Depaola,Laurent Desorgher,X. Dong,Andrea Dotti,Victor Daniel Elvira,Gunter Folger,Ziad Francis,A. Galoyan,L. Garnier,M. Gayer,K. Genser,Vladimir Grichine,Vladimir Grichine,Susanna Guatelli,Susanna Guatelli,Paul Gueye,P. Gumplinger,Alexander Howard,Ivana Hřivnáčová,S. Hwang,Sebastien Incerti,Sebastien Incerti,A. Ivanchenko,Vladimir Ivanchenko,F.W. Jones,S. Y. Jun,Pekka Kaitaniemi,Nicolas A. Karakatsanis,Nicolas A. Karakatsanis,M. Karamitrosi,M.H. Kelsey,Akinori Kimura,Tatsumi Koi,Hisaya Kurashige,A. Lechner,S. B. Lee,Francesco Longo,M. Maire,Davide Mancusi,A. Mantero,E. Mendoza,B. Morgan,K. Murakami,T. Nikitina,Luciano Pandola,P. Paprocki,J Perl,Ivan Petrović,Maria Grazia Pia,W. Pokorski,J. M. Quesada,M. Raine,Maria A.M. Reis,Alberto Ribon,A. Ristic Fira,Francesco Romano,Giorgio Ivan Russo,Giovanni Santin,Takashi Sasaki,D. Sawkey,J. I. Shin,Igor Strakovsky,A. Taborda,Satoshi Tanaka,B. Tome,Toshiyuki Toshito,H.N. Tran,Pete Truscott,L. Urbán,V. V. Uzhinsky,Jerome Verbeke,M. Verderi,B. Wendt,H. Wenzel,D. H. Wright,Douglas Wright,T. Yamashita,J. Yarba,H. Yoshida +102 more
TL;DR: Geant4 as discussed by the authors is a software toolkit for the simulation of the passage of particles through matter, which 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.
Journal ArticleDOI
Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project.
Sebastien Incerti,Sebastien Incerti,Ioanna Kyriakou,Mario A. Bernal,Marie-Claude Bordage,Marie-Claude Bordage,Ziad Francis,Susanna Guatelli,Susanna Guatelli,Vladimir Ivanchenko,M. Karamitros,Nathanael Lampe,Sang Bae Lee,Sylvain Meylan,Chul Hee Min,Wook Geun Shin,Pentti Nieminen,Dosatsu Sakata,Dosatsu Sakata,Dosatsu Sakata,Nicolas Tang,Carmen Villagrasa,H.N. Tran,Jeremy M. C. Brown +23 more
TL;DR: This Special Report presents a description of Geant4-DNA user applications dedicated to the simulation of track structures (TS) in liquid water and associated physical quantities (e.g., range, stopping power, mean free path…) and shows that the most recent sets of physics models available in Geant 4-DNA enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquidWater.
Journal ArticleDOI
A Thermodynamic Study on Hydration and Dehydration of DNA and RNA Amphiphile Complexes
TL;DR: In this paper, the adhesion of DNA and RNA−amphiphile complexes to non-modified glasses, glasses containing phenylboronic acid (PBA) attached via 3-GPTMS, and glasses containing grafted DMAA-AAPBA copolymer (DMAA-APBA-glasses) were studied.
Journal ArticleDOI
TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology
Jan Schuemann,Aimee L. McNamara,José Ramos-Méndez,J Perl,Kathryn D. Held,Harald Paganetti,Sebastien Incerti,Bruce A. Faddegon +7 more
TL;DR: The TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells.
Journal ArticleDOI
Simulation of early DNA damage after the irradiation of a fibroblast cell nucleus using Geant4-DNA.
Sylvain Meylan,Sebastien Incerti,M. Karamitros,Nicolas Tang,M. Bueno,Isabelle Clairand,Carmen Villagrasa +6 more
TL;DR: This work presents for the first time the simulation of the physical, physicochemical and chemical stages of early radiation damage at the scale of an entire human genome and using Geant4-DNA models.
References
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Geant4—a simulation toolkit
S. Agostinelli,John Allison,K. Amako,J. Apostolakis,Henrique Araujo,P. Arce,Makoto Asai,D. Axen,S. Banerjee,G. Barrand,F. Behner,Lorenzo Bellagamba,J. Boudreau,L. Broglia,A. Brunengo,H. Burkhardt,Stephane Chauvie,J. Chuma,R. Chytracek,Gene Cooperman,G. Cosmo,P. V. Degtyarenko,Andrea Dell'Acqua,G. Depaola,D. Dietrich,R. Enami,A. Feliciello,C. Ferguson,H. Fesefeldt,Gunter Folger,Franca Foppiano,Alessandra Forti,S. Garelli,S. Gianì,R. Giannitrapani,D. Gibin,J. J. Gomez Y Cadenas,I. González,G. Gracia Abril,G. Greeniaus,Walter Greiner,Vladimir Grichine,A. Grossheim,Susanna Guatelli,P. Gumplinger,R. Hamatsu,K. Hashimoto,H. Hasui,A. Heikkinen,A. S. Howard,Vladimir Ivanchenko,A. Johnson,F.W. Jones,J. Kallenbach,Naoko Kanaya,M. Kawabata,Y. Kawabata,M. Kawaguti,S.R. Kelner,Paul R. C. Kent,A. Kimura,T. Kodama,R. P. Kokoulin,M. Kossov,Hisaya Kurashige,E. Lamanna,Tapio Lampén,V. Lara,Veronique Lefebure,F. Lei,M. Liendl,W. S. Lockman,Francesco Longo,S. Magni,M. Maire,E. Medernach,K. Minamimoto,P. Mora de Freitas,Yoshiyuki Morita,K. Murakami,M. Nagamatu,R. Nartallo,Petteri Nieminen,T. Nishimura,K. Ohtsubo,M. Okamura,S. W. O'Neale,Y. Oohata,K. Paech,J Perl,Andreas Pfeiffer,Maria Grazia Pia,F. Ranjard,A.M. Rybin,S.S Sadilov,E. Di Salvo,Giovanni Santin,Takashi Sasaki,N. Savvas,Y. Sawada,Stefan Scherer,S. Sei,V. Sirotenko,David J. Smith,N. Starkov,H. Stoecker,J. Sulkimo,M. Takahata,Satoshi Tanaka,E. Tcherniaev,E. Safai Tehrani,M. Tropeano,P. Truscott,H. Uno,L. Urbán,P. Urban,M. Verderi,A. Walkden,W. Wander,H. Weber,J.P. Wellisch,Torre Wenaus,D.C. Williams,Douglas Wright,T. Yamada,H. Yoshida,D. Zschiesche +126 more
TL;DR: The Gelfant 4 toolkit as discussed by the authors is a toolkit for simulating the passage of particles through matter, including a complete range of functionality including tracking, geometry, physics models and hits.
Proceedings Article
A density-based algorithm for discovering clusters a density-based algorithm for discovering clusters in large spatial databases with noise
TL;DR: In this paper, a density-based notion of clusters is proposed to discover clusters of arbitrary shape, which can be used for class identification in large spatial databases and is shown to be more efficient than the well-known algorithm CLAR-ANS.
Proceedings Article
A density-based algorithm for discovering clusters in large spatial Databases with Noise
TL;DR: DBSCAN, a new clustering algorithm relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape, is presented which requires only one input parameter and supports the user in determining an appropriate value for it.
Journal ArticleDOI
Geant4 developments and applications
John Allison,K. Amako,John Apostolakis,Henrique Araujo,P.A. Dubois,Makoto Asai,G. Barrand,R. Capra,Stephane Chauvie,R Chytracek,G.A.P. Cirrone,Gene Cooperman,G. Cosmo,Giacomo Cuttone,G.G. Daquino,M. Donszelmann,M. Dressel,Gunter Folger,Franca Foppiano,J. Generowicz,Vladimir Grichine,Susanna Guatelli,P. Gumplinger,A. Heikkinen,Ivana Hrivnacova,A. S. Howard,Sebastien Incerti,Vladimir Ivanchenko,T. Johnson,F.W. Jones,Tatsumi Koi,R. P. Kokoulin,M. Kossov,Hisaya Kurashige,V. Lara,S.A. Larsson,Fan Lei,O. Link,Francesco Longo,M. Maire,A. Mantero,B. Mascialino,I. McLaren,Patricia Mendez Lorenzo,K. Minamimoto,K. Murakami,Petteri Nieminen,Luciano Pandola,S. Parlati,Luis Peralta,J Perl,Andreas Pfeiffer,Maria Grazia Pia,Alberto Ribon,Pedro Rodrigues,Giorgio Ivan Russo,S.S Sadilov,Giovanni Santin,Takashi Sasaki,David J. Smith,N. Starkov,Satoshi Tanaka,E. Tcherniaev,B. Tome,A. Trindade,Pete Truscott,L. Urbán,M. Verderi,A. Walkden,J.P. Wellisch,D.C. Williams,Douglas Wright,H. Yoshida +72 more
TL;DR: GeGeant4 as mentioned in this paper 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.
Journal ArticleDOI
ROOT — An object oriented data analysis framework
Rene Brun,Fons Rademakers +1 more
TL;DR: ROOT, written in C++, contains an efficient hierarchical OO database, a C++ interpreter, advanced statistical analysis (multi-dimensional histogramming, fitting, minimization, cluster finding algorithms) and visualization tools.
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Geant4—a simulation toolkit
S. Agostinelli,John Allison,K. Amako,J. Apostolakis,Henrique Araujo,P. Arce,Makoto Asai,D. Axen,S. Banerjee,G. Barrand,F. Behner,Lorenzo Bellagamba,J. Boudreau,L. Broglia,A. Brunengo,H. Burkhardt,Stephane Chauvie,J. Chuma,R. Chytracek,Gene Cooperman,G. Cosmo,P. V. Degtyarenko,Andrea Dell'Acqua,G. Depaola,D. Dietrich,R. Enami,A. Feliciello,C. Ferguson,H. Fesefeldt,Gunter Folger,Franca Foppiano,Alessandra Forti,S. Garelli,S. Gianì,R. Giannitrapani,D. Gibin,J. J. Gomez Y Cadenas,I. González,G. Gracia Abril,G. Greeniaus,Walter Greiner,Vladimir Grichine,A. Grossheim,Susanna Guatelli,P. Gumplinger,R. Hamatsu,K. Hashimoto,H. Hasui,A. Heikkinen,A. S. Howard,Vladimir Ivanchenko,A. Johnson,F.W. Jones,J. Kallenbach,Naoko Kanaya,M. Kawabata,Y. Kawabata,M. Kawaguti,S.R. Kelner,Paul R. C. Kent,A. Kimura,T. Kodama,R. P. Kokoulin,M. Kossov,Hisaya Kurashige,E. Lamanna,Tapio Lampén,V. Lara,Veronique Lefebure,F. Lei,M. Liendl,W. S. Lockman,Francesco Longo,S. Magni,M. Maire,E. Medernach,K. Minamimoto,P. Mora de Freitas,Yoshiyuki Morita,K. Murakami,M. Nagamatu,R. Nartallo,Petteri Nieminen,T. Nishimura,K. Ohtsubo,M. Okamura,S. W. O'Neale,Y. Oohata,K. Paech,J Perl,Andreas Pfeiffer,Maria Grazia Pia,F. Ranjard,A.M. Rybin,S.S Sadilov,E. Di Salvo,Giovanni Santin,Takashi Sasaki,N. Savvas,Y. Sawada,Stefan Scherer,S. Sei,V. Sirotenko,David J. Smith,N. Starkov,H. Stoecker,J. Sulkimo,M. Takahata,Satoshi Tanaka,E. Tcherniaev,E. Safai Tehrani,M. Tropeano,P. Truscott,H. Uno,L. Urbán,P. Urban,M. Verderi,A. Walkden,W. Wander,H. Weber,J.P. Wellisch,Torre Wenaus,D.C. Williams,Douglas Wright,T. Yamada,H. Yoshida,D. Zschiesche +126 more
Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project.
Sebastien Incerti,Sebastien Incerti,Ioanna Kyriakou,Mario A. Bernal,Marie-Claude Bordage,Marie-Claude Bordage,Ziad Francis,Susanna Guatelli,Susanna Guatelli,Vladimir Ivanchenko,M. Karamitros,Nathanael Lampe,Sang Bae Lee,Sylvain Meylan,Chul Hee Min,Wook Geun Shin,Pentti Nieminen,Dosatsu Sakata,Dosatsu Sakata,Dosatsu Sakata,Nicolas Tang,Carmen Villagrasa,H.N. Tran,Jeremy M. C. Brown +23 more
Geant4 developments and applications
John Allison,K. Amako,John Apostolakis,Henrique Araujo,P.A. Dubois,Makoto Asai,G. Barrand,R. Capra,Stephane Chauvie,R Chytracek,G.A.P. Cirrone,Gene Cooperman,G. Cosmo,Giacomo Cuttone,G.G. Daquino,M. Donszelmann,M. Dressel,Gunter Folger,Franca Foppiano,J. Generowicz,Vladimir Grichine,Susanna Guatelli,P. Gumplinger,A. Heikkinen,Ivana Hrivnacova,A. S. Howard,Sebastien Incerti,Vladimir Ivanchenko,T. Johnson,F.W. Jones,Tatsumi Koi,R. P. Kokoulin,M. Kossov,Hisaya Kurashige,V. Lara,S.A. Larsson,Fan Lei,O. Link,Francesco Longo,M. Maire,A. Mantero,B. Mascialino,I. McLaren,Patricia Mendez Lorenzo,K. Minamimoto,K. Murakami,Petteri Nieminen,Luciano Pandola,S. Parlati,Luis Peralta,J Perl,Andreas Pfeiffer,Maria Grazia Pia,Alberto Ribon,Pedro Rodrigues,Giorgio Ivan Russo,S.S Sadilov,Giovanni Santin,Takashi Sasaki,David J. Smith,N. Starkov,Satoshi Tanaka,E. Tcherniaev,B. Tome,A. Trindade,Pete Truscott,L. Urbán,M. Verderi,A. Walkden,J.P. Wellisch,D.C. Williams,Douglas Wright,H. Yoshida +72 more