Article
Radiology, Nuclear Medicine & Medical Imaging
Edgard Seif, Ziad El Bitar, Sebastien Incerti, Mario A. Bernal, Ziad Francis
Summary: This study explores different technologies to minimize simulation time for electron track generation using the Monte-Carlo method and Geant4-DNA processes. The results show that CPU simulations perform best for a small number of electrons, while GPU simulations are more suitable for a larger number of electrons. The use of a computing grid is best suited for simulations with a high number of electrons and high initial energy.
PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS
(2022)
Article
Oncology
Shannon J. Thompson, Aoife Rooney, Kevin M. Prise, Stephen J. McMahon
Summary: This study evaluates the performance of different Monte Carlo nanoscale physics models using a dataset on strand breaking in a single DNA strand. The models had similar energy distributions but made significantly different predictions for other endpoints. Multi-endpoint analysis is necessary to fully validate these models.
Article
Radiology, Nuclear Medicine & Medical Imaging
Yasmine Ali, Lucas Auzel, Caterina Monini, Kateryna Kriachok, Jean Michel Letang, Etienne Testa, Lydia Maigne, Michael Beuve
Summary: This study benchmarked two Monte Carlo track structure codes, Geant4-DNA and LPCHEM, for estimating the biological effects of ions during radiation therapy treatments. The results showed that the specific energy spectra and chemical yields obtained by the two codes were in good agreement, with LPCHEM being faster and having slightly faster recombination than Geant4-DNA.
Article
Biochemistry & Molecular Biology
Kun Zhu, Chun Wu, Xiaoyu Peng, Xuantao Ji, Siyuan Luo, Yuchen Liu, Xiaodong Wang
Summary: This study uses Monte Carlo simulations to investigate the impact of DNA damage scoring parameters on DNA damage, and accurately predicts the yield of different types of DNA damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Wook-Geun Shin, Dousatsu Sakata, Nathanael Lampe, Oleg Belov, Ngoc Hoang Tran, Ivan Petrovic, Aleksandra Ristic-Fira, Milos Dordevic, Mario A. Bernal, Marie-Claude Bordage, Ziad Francis, Ioanna Kyriakou, Yann Perrot, Takashi Sasaki, Carmen Villagrasa, Susanna Guatelli, Vincent Breton, Dimitris Emfietzoglou, Sebastien Incerti
Summary: Accurately modeling radiobiological mechanisms for DNA damage induction is a major challenge, with the Monte Carlo method being the most reliable for calculating early effects of ionizing radiation on DNA. The Geant4-DNA toolkit can simulate physical, physico-chemical, and chemical stages of water radiolysis to assess direct and indirect DNA damage. Studies have shown that Geant4-DNA can closely reproduce experimental data on double-strand break yields and support the prediction of DNA damage.
Article
Engineering, Biomedical
J. Naoki D-Kondo, Omar R. Garcia-Garcia, Jay A. LaVerne, Bruce Faddegon, Jan Schuemann, Wook-Geun Shin, Jose Ramos-Mendez
Summary: This study extended the TOPAS-nBio Monte Carlo track structure simulation code for pulsed and longtime homogeneous chemistry simulations using the Gillespie algorithm. Three different tests were conducted to assess the reliability of the implementation and its ability to accurately reproduce published experimental results. The results showed that the new implementation of TOPAS-nBio was capable of recreating the chemical evolution of water radiolysis and could be used to study the effects of FLASH dose rate on radiation chemistry.
PHYSICS IN MEDICINE AND BIOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Konstantinos P. Chatzipapas, Panagiotis Papadimitroulas, George Loudos, Niko Papanikolaou, George C. Kagadis
Summary: This study introduces a novel computational platform, IDDRRA, which utilizes Monte Carlo simulations to evaluate radiation induced DNA damage. The IDDRRA tool has been developed and demonstrated for studying various aspects of DNA irradiation experiments, and it is expandable for users to add new benchmarks and applications. Additional functionality, including quantification of indirect damage, will be incorporated over time.
Article
Radiology, Nuclear Medicine & Medical Imaging
Laura Ballisat, Lana Beck, Chiara De Sio, Susanna Guatelli, Dousatsu Sakata, Sebastien Incerti, Hoang Ngoc Tran, Jinyan Duan, Katie Maclean, Yuyao Shi, Jaap Velthuis, Anatoly Rosenfeld
Summary: Diffusing alpha-emitters radiation Therapy (DaRT) is an interstitial brachytherapy technique using 224Ra seeds. The early DNA damage and radiobiological effectiveness caused by a-particles with LET values in a certain range were calculated using Geant4-DNA. The quantity and complexity of DNA damage were found to change with LET, and the impact of DNA base pair density on DNA damage was also investigated.
PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS
(2023)
Article
Chemistry, Inorganic & Nuclear
Samer Bakr, Tibor Kibedi, Bryan Tee, David Bolst, Maarten Vos, Mohammed Alotiby, Laurent Desorgher, Dennis Herbert Wright, Alfonso Mantero, Anatoly Rosenfeld, Vladimir Ivanchenko, Sebastien Incerti, Susanna Guatelli
Summary: Auger emitting radioisotopes are crucial in targeted radiotherapy as they can deliver dose to tumor cells while sparing surrounding tissues. Geant4, a Monte Carlo code, is widely used to study the physical mechanisms involved. In this study, the modeling of Auger electron emission from various radionuclides in Geant4 was benchmarked against theoretical approaches and experimental data, showing good agreement between simulation and reference data. This is the first study to validate the emission of Auger electrons in Geant4 for radiotherapy applications.
APPLIED RADIATION AND ISOTOPES
(2021)
Article
Engineering, Biomedical
David Sarrut, Nicolas Arbor, Thomas Baudier, Damian Borys, Ane Etxebeste, Hermann Fuchs, Jan Gajewski, Loiec Grevillot, Sebastien Jan, George C. Kagadis, Han Gyu Kang, Assen Kirov, Olga Kochebina, Wojciech Krzemien, Antony Lomax, Panagiotis Papadimitroulas, Christian Pommranz, Emilie Roncali, Antoni Rucinski, Carla Winterhalter, Lydia Maigne
Summary: This paper reviews the ecosystem of GATE, an open-source Monte Carlo toolkit for medical physics. It describes the principal modules and key concepts of GATE, as well as the main source code repositories and the automated compilation and testing processes. The collaborative development of OpenGATE over the past 20 years is presented, along with the impact of GATE on medical physics and cancer research.
PHYSICS IN MEDICINE AND BIOLOGY
(2022)
Article
Instruments & Instrumentation
Sara A. Zein, Marie-Claude Bordage, Ziad Francis, Giovanni Macetti, Alessandro Genoni, Claude Dal Cappello, Wook-Geun Shin, Sebastien Incerti
Summary: The Geant4-DNA Monte Carlo toolkit has been extended to include electron interactions with the four DNA bases using cross sections from the Geant-DNA CPA100 models. The calculations for electron cross sections and other parameters in the four DNA bases are in good agreement with literature, highlighting the importance of including DNA bases cross sections in track structure codes for better estimation of radiation effects on biological material.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS
(2021)
Article
Engineering, Biomedical
Marcin Pietrzak, Monika Mietelska, Aleksandr Bancer, Antoni Rucinski, Beata Brzozowska
Summary: This study validated the calculation accuracy of nanodosimetric quantities in the Geant4-DNA track structure simulation code by implementing the Jet Counter nanodosimeter geometry and assessing the impact of physics models and detector performance on ionization cluster size distributions (ICSD). The findings showed that ICSD in JC geometry obtained from Geant4-DNA simulations corresponded well to measurements in nitrogen gas, with the best agreement for Geant4-DNA physics option 4, indicating the potential application of track structure simulation methods for treatment planning in particle therapy.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Chemistry, Physical
Payman Rafiepour, Sedigheh Sina, Seyed Mohammad Javad Mortazavi
Summary: Irradiation of foods and fruits using ionizing radiation is an effective method to eliminate pathogenic microorganisms on the surface. This study compared the dose distributions of low-energy X-rays and electrons in an apple, and calculated the DNA damages induced by secondary electrons in a bacterial cell model using a multiscale Monte Carlo simulation. The results showed that the yields of DNA breaks caused by X-rays and electrons were similar on a microscopic scale. On a macroscopic scale, a two-sided electron beam configuration combined with apple rotation provided uniform dose distribution on the surface up to a depth of 40 μm. For low-energy X-rays, apple rotation was not necessary when using a two-sided irradiation. Overall, X-rays were found to be superior to electrons for surface treatment of apples due to their lower dose uniformity ratios on the surface.
RADIATION PHYSICS AND CHEMISTRY
(2023)
Article
Engineering, Biomedical
Larissa Derksen, Tabea Pfuhl, Rita Engenhart-Cabillic, Klemens Zink, Kilian-Simon Baumann
Summary: This study aimed to investigate the feasibility of using TOPAS-nBio for track structure simulations by re-simulating GEANT4-DNA example applications and studying low-energy electron interactions. The results showed good agreement with GEANT4-DNA simulations.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Instruments & Instrumentation
Q. Gibaru, C. Inguimbert, P. Caron, M. Raine, D. Lambert, J. Puech
Summary: Several improvements have been made to the MicroElec extension of Geant4 in order to track very low energy electrons, protons and ions in different materials. The interaction processes for ions and protons have been extended down to 1 keV/nucleon, and to a few eVs for electrons. Additionally, validation has been done for silicon and several new materials, significantly expanding the capabilities of MicroElec for microdosimetry simulation and secondary electron emission applications.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS
(2021)
Article
Chemistry, Physical
Mehnaz, Bo Da, Z. J. Ding
Summary: Knowledge of absolute secondary electron yield (& delta;) is crucial for various applications of electron emission materials. However, there is a large discrepancy among the available experimental data, and simplified theories cannot accurately predict the absolute yield value. By applying machine learning (ML) models to experimental observations, we can establish the relationship between & delta; and material properties, as well as primary electron energy, providing more reliable data for different materials within the uncertainty range.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Mehnaz, L. H. Yang, B. Da, Z. J. Ding
Summary: Machine learning methods were used to predict electron stopping power for various elements over a wide energy range, showing good agreement with experimental data across all energies. Ensemble algorithms were more accurate than individual algorithms, enhancing prediction accuracy with a small training database.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)