Publications

Geant4-DNA reference papers

1. Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project, H. N. Tran, J. Archer, G. Baldacchino, J. M. C. Brown, F. Chappuis, G. A. P. Cirrone, L. Desorgher, N. Dominguez, S. Fattori, S. Guatelli, V. Ivantchenko, J.-R. Méndez, P. Nieminen, Y. Perrot, D. Sakata, G. Santin, W.-G. Shin, C. Villagrasa, S. Zein, S. Incerti, Med. Phys. 51 (2024) 5873-5889 (link) - free access
2. Geant4-DNA example applications for track structure simulations in liquid water: a report from the Geant4-DNA Project, S. Incerti, I. Kyriakou, M. A. Bernal, M. C. Bordage, Z. Francis, S. Guatelli, V. Ivanchenko, M. Karamitros, N. Lampe, S. B. Lee, S. Meylan, C. H. Min, W. G. Shin, P. Nieminen, D. Sakata, N. Tang, C. Villagrasa, H. Tran, J. M. C. Brown, Med. Phys. 45 (2018) e722-e739 (link) - free access
3. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit, M. A. Bernal, M. C. Bordage, J. M. C. Brown, M. Davídková, E. Delage, Z. El Bitar, S. A. Enger, Z. Francis, S. Guatelli, V. N. Ivanchenko, M. Karamitros, I. Kyriakou, L. Maigne, S. Meylan, K. Murakami, S. Okada, H. Payno, Y. Perrot, I. Petrovic, Q.T. Pham, A. Ristic-Fira, T. Sasaki, V. Štěpán, H. N. Tran, C. Villagrasa, S. Incerti, Phys. Med. 31 (2015) 861-874 (link)
4. Comparison of Geant4 very low energy cross section models with experimental data in water, S. Incerti, A. Ivanchenko, M. Karamitros, A. Mantero, P. Moretto, H. N. Tran, B. Mascialino, C. Champion, V. N. Ivanchenko, M. A. Bernal, Z. Francis, C. Villagrasa, G. Baldacchino, P. Guèye, R. Capra, P. Nieminen, C. Zacharatou, Med. Phys. 37 (2010) 4692-4708 (link)
5. The Geant4-DNA project, S. Incerti, G. Baldacchino, M. Bernal, R. Capra, C. Champion, Z. Francis, S. Guatelli, P. Guèye, A. Mantero, B. Mascialino, P. Moretto, P. Nieminen, A. Rosenfeld, C. Villagrasa and C. Zacharatou, Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178 (link)

General scope

• Review of the Geant4-DNA simulation toolkit for radiobiological applications at the cellular and DNA level, I. Kyriakou, D. Sakata, H. N. Tran, Y. Perrot, W. G. Shin, N. Lampe, S. Zein, M. C. Bordage, S. Guatelli, C. Villagrasa, D. Emfietzoglou, S. Incerti, Cancers 14 (2022) 35 (link) - free access
• The Geant4-DNA Project in the Access to Infrastructures for Radiation protection Research (AIR2D2) / CONCERT newsletter, Issue 28 (2018) (link) - free access - and in the database - free access
• Review of Geant4-DNA applications for micro and nanoscale simulations, S. Incerti, M. Douglass, S. Penfold, S. Guatelli, E. Bezak, Phys. Med. 32(10) (2016) 1187-1200 (link)
• The Geant4-DNA Project in the CERN Knowledge Transfer 2015 report (2016) (link) - free access
• The Geant4-DNA project, M. Karamitros, S. Incerti, C. Champion, Rad. Onc. 102 S1 (2012) S191–S192 (link)
• The Geant4-DNA project, S. Incerti, G. Baldacchino, M. Bernal, R. Capra, C. Champion, Z. Francis, S. Guatelli, P. Guèye, A. Mantero, B. Mascialino, P. Moretto, P. Nieminen, A. Rosenfeld, C. Villagrasa and C. Zacharatou, Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178 (link)
• Geant4 physics processes for microdosimetry simulation : design foundation and implementation of the first set of models, S. Chauvie, Z. Francis, S. Guatelli, S. Incerti, B. Mascialino, P. Moretto, P. Nieminen, M. G. Pia, IEEE Trans. Nucl. Sci. 54 (6-2) (2007) 2619-2628 (link)
• Monte Carlo simulation of interactions of radiation with biological systems at the cellular and DNA levels : The Geant4-DNA Project, S. Chauvie, Z. Francis, S. Guatelli, S. Incerti, B. Mascialino, G. Montarou, Ph. Moretto, P. Nieminen, M. G. Pia, Rad. Res. Vol. 166 (4) (2006) 652-689 (link)

Physics processes and models

• Lithium inelastic cross-sections and their impact on micro and nano dosimetry of boron neutron capture, N. D-Kondo, R. Ortiz, B. Faddegon, S. Incerti, H. N. Tran, Z. Francis, E. Moreno Barbosa, J. Schuemann, J. Ramos-Méndez, Phys. Med. Biol. 69, 145016 (2024) (link)
• Calculation of electron interaction models in N2 and O2, F. Nicolanti, B. Caccia, A. Cartoni, D. Emfietzoglou, R. Faccini, S. Incerti, I. Kyriakou, M. Satta, H.N. Tran, C. Mancini-Terracciano, Phys. Med. 114 (2023) 102661 (link)
• Monte Carlo simulations of electron interactions with the DNA molecule: A complete set of physics models for Geant4-DNA simulation toolkit, S. A. Zein,, M.-C. Bordage, H. N. Tran, G. Macetti, A. Genoni, C. Dal Cappello, S. Incerti, Nucl. Instrum. Meth. B 542 (2023) 51-60 (link)
• Sub-keV corrections to binary encounter cross section models for electron ionization of liquid water with application to the Geant4-DNA Monte Carlo code, S. Margis, I. Kyriakou, S. Incerti, M.-C. Bordage, D. Emfietzoglou, Appl. Radiat. Isot. 194 (2023) 110693 (link)
• Intercomparison of nanodosimetric distributions in nitrogen simulated with Geant4 and PTra track structure codes, M. Pietrzak, H. Nettelbeck, Y. Perrot, C. Villagrasa, A. Bancer, M. Bug, S. Incerti, Phys. Med. 102 (2022) 103-109 (link)
• A model for Geant4-DNA to simulate ionization and excitation of liquid water by protons travelling above 100 MeV, A. D. Dominguez-Munoz, M. I. Gallardo, M. C. Bordage, Z. Francis, S. Incerti, M. A. Cortes-Giraldo, Radiat. Phys. Chem. 199 (2022) 110363 (link)
• Implementation of the EPICS2017 database for photons in Geant4, Z. Li, C. Michelet, S. Incerti, I. Ivanchenko, M. Novak, S. Guatelli, H. Seznec, Phys. Med. 95 (2022) 94-115 (link)
• Status and Extension of the Geant4-DNA Dielectric Models for Application to Electron Transport, I. Kyriakou, D. Emfietzoglou, S. Incerti, Font. Phys. 9 (2022) 711317 (link) - free access
• Electron transport in DNA bases: An extension of the Geant4-DNA Monte Carlo toolkit, S. A. Zein, M.-C. Bordage, Z. Francis, G. Macetti, A. Genoni, C. Dal Capello, W.-G. Shin, S. Incerti, Nucl. Instrum. Meth. B 488 (2021) 70-82 (link)
• Evaluation of the influence of physical and chemical parameters on water radiolysis simulations under MeV electron irradiation using Geant4-DNA, W.-G. Shin, J. Ramos-Mendez, B. Faddegon, H. N. Tran, C. Villagrasa, Y. Perrot, S. Okada, M. Karamitros, D. Emfietzoglou, I. Kyriakou, M. C. Bordage, D. Sakata, S. Guatelli, H. J. Choi, C. H. Min, S. B. Lee, S. Incerti, J. Appl. Phys. 125 (2019) 104301 (link)
• Electron track structure simulations in a gold nanoparticle using Geant4-DNA, D. Sakata, I. Kyriakou, H. N. Tran, M.-C. Bordage, A. Rosenfeld, V. Ivanchenko, S. Incerti, D. Emfietzoglou, S. Guatelli, Phys. Med. 63 (2019) 98-104 (link)
• Development of a new Geant4-DNA electron elastic scattering model for liquid-phase water using the ELSEPA code, W. G. Shin, M.-C. Bordage, D. Emfietzoglou, I. Kyriakou, D. Sakata, C. H. Min, S. B. Lee, S. Guatelli, S. Incerti, J. Appl. Phys. 124 (2018) 224901 (link)
• Geant4-DNA track-structure simulations for gold nanoparticles: the importance of electron discrete models in nanometer volumes, D. Sakata, I. Kyriakou, S. Okada, H.N. Tran, N. Lampe, S. Guatelli, M.C. Bordage, V. Ivantchenko, K. Murakami, T. Sasaki, D. Emfietzoglou, S. Incerti, Med. Phys. 45 (2018) 2230-2242 (link) - free access
• Calculation of ionisation lineal energies for water and DNA bases using the Rudd model cross sections, Z. Francis, Z. El Bitar, S. Incerti, M. A. Bernal, M. Karamitros, H. N. Tran, J. Appl. Phys. 122 (2017) 014701 (link)
• Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations, J. Ramos-Méndez, J. Schuemann, S. Incerti, H. Paganetti, R. Schulte, B. Faddegon, Phys. Med. Biol. 62 (2017) 5908-5925 (link)
• Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA, M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries, M. Bardiès, N. Lampe, S. Incerti, Phys. Med. 32(12) (2016) 1833-1840 (link)
• An implementation of discrete electron transport models for gold in the Geant4 simulation toolkit, D. Sakata, S. Incerti, M.C. Bordage, N. Lampe, S. Okada, D. Emetzoglou, I. Kyriakou, K. Murakami, T. Sasaki, H. Tran, S. Guatelli, V.N. Ivantchenko, J. Appl. Phys. 120 (2016) 244901 (link)
• The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water, I. Kyriakou, M. Sefl, V. Nourry, S. Incerti, J. Appl. Phys. 119 (2016) 194902 (link)
• Simulation of Auger electron emission from nanometer-size gold targets using the Geant4 Monte Carlo simulation toolkit, S. Incerti, B. Suerfu, J. Xu, V. Ivantchenko, A. Mantero, J.M.C. Brown, M.A. Bernal, Z. Francis, M. Karamitros, H.N. Tran, Nucl. Instrum. Meth. B 372 (2016) 91-101 (link)
• Single electron ionization and electron capture cross sections for (C6+, H2O) interaction within the Classical Trajectory Monte Carlo (CTMC) approach, H. N. Tran, D. D. Dao, S. Incerti, M. A. Bernal, M. Karamitros, T. V. Nhan Hao, T. M. Dang, Z. Francis, Nucl. Instrum. Meth. B 366 (2016) 140-144 (link)
• Improvements in Geant4 energy-loss model and the effect on low-energy electron transport in liquid water, I. Kyriakou, S. Incerti, Z. Francis, Med. Phys. 42 (2015) 3870-3876 (link)
• Modeling proton and alpha elastic scattering in liquid water in Geant4-DNA, H. N. Tran, Z. El Bitar, C. Champion, M. Karamitros, M. A. Bernal, Z. Francis, V. Ivantchenko, S. B. Lee, J. I. Shin, S. Incerti, Nucl. Instrum. and Meth. B 343 (2015) 132-137 (link)
• Advances in Computational Radiation Biophysics for Cancer Therapy: Simulating Nano-Scale Damage by Low-Energy Electrons, Z. Kuncic, Biophys. Rev. Lett. 10 (2015) 25-36 (link)
• Geant4 electromagnetic physics: improving simulation performance and accuracy, V. N. Ivanchenko, S. Incerti, J. Allison, A. Bagulya, J. M. C. Brown, C. Champion, S. Elles, Z. Francis, V. Grichine, A. Ivantchenko, J. Jacquemier, M. Karamitros, M. Maire, A. Mantero, J. P. Marques, L. Pandola, M. Raine, M. A. Reis, G. Santin, D. Sawkey, A. Schaelicke, M. Schenk, A. Taborda, L. Urban and T. Yamashita, Proceedings of the Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo 2013 (SNA + MC 2013), La Cité des Sciences et de l’Industrie, Paris, France, October 27-31 (2013) 03101 (link)
• Proton-induced ionization of isolated uracil molecules: a theory/experiment confrontation, C. Champion, M.E. Galassi, P.F. Weck, S. Incerti, R.D. Rivarola, O. Fojón, J. Hanssen, Y. Iriki, A. Itoh, Nucl. Instrum. and Meth. B 314 (2013) 66-70 (link)
• Proton transport in water and DNA components: A Geant4 Monte Carlo simulation, C. Champion, S. Incerti, H.N. Tran, M. Karamitros, J.I. Shin, S.B. Lee, H. Lekadir, M. Bernal, Z. Francis, V. Ivanchenko, O.A. Fojón, J. Hanssen, R.D. Rivarola, Nucl. Instrum. and Meth. B 306 (2013) 165-168 (link)
• Theoretical ionization and capture cross sections for DNA nucleobases impacted by light ions, C. Champion, M. E. Galassi, H. Lekadir, S. Incerti, O. Fojon, R. D. Rivarola, J. Hanssen, Int. J. Radiat. Biol. 88 (2012) 62-65 (link)
• Quantum-mechanical predictions of DNA and RNA ionization by energetic proton beams, M. E. Galassi, C. Champion, P. F. Weck, R. D. Rivarola, O. Fojon, J. Hanssen, Phys. Med. Biol. 57 (2012) 2081-2099 (link)
• Monte Carlo methods to model radiation interactions and induced damage, A. Munoz, M. C. Fuss, M. A. Cortes-Giraldo, S. Incerti, V. Ivanchenko, A. Ivanchenko, J. M. Quesada, F. Salvat, C. Champion, G. Garcia Gomez-Tejedor, Radiation Damage in Biomolecular Systems, Biological and Medical Physics, Biomedical Engineering, Part 2 (2012) 203-225 (link)
• Geant4 hadronic physics for space radiation environment, A. V. Ivanchenko, V. N. Ivanchenko, J.-M. Quesada Molina, S. L. Incerti, Int. J. Radiat. Biol. 88 (2012) 171-175 (link)
• Electron and proton elastic scattering in water vapour, C. Champion, S. Incerti, H. Tran, Z. El Bitar, Nucl. Instrum. and Meth. B 273 (2012) 98-101 (link)
• Combination of electromagnetic Physics processes for microdosimetry in liquid water with the Geant4 Monte Carlo simulation toolkit, V.N. Ivanchenko, S. Incerti, Z. Francis, H.N. Tran, M. Karamitros, M.A. Bernal, C. Champion and P. Guèye, Nucl. Instrum. and Meth. B 273 (2012) 95-97 (link)
• Recent improvements in Geant4 electromagnetic physics models and interfaces, V. Ivantchenko et al., Prog. Nucl. Sci. Tec. 2 (2011) 898-903 (link) - free access
• Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte Carlo processes, Z. Francis, S. Incerti, R. Capra, B. Mascialino, G. Montarou, V. Stepan, C. Villagrasa, Appl. Radiat. Isot. 69 (2011) 220-226 (link)
• Physical models implemented in the Geant4-DNA extension of the Geant4 toolkit for calculating initial radiation damage at the molecular level, C. Villagrasa, Z. Francis, S. Incerti, Rad. Prot. Dos. 143 (2010) 214-218 (link)
• A free-parameter theoretical model for describing the electron elastic scattering in water in the Geant4 toolkit, C. Champion, S. Incerti, H. Aouchiche, D. Oubaziz, Rad. Phys. Chem. 78 (2009) 745-750 (link)

Verification and validation of physics

• Electron absorbed fractions and S factors for intermediate size target volumes: comparison of analytic calculations and Monte Carlo simulations, C. Kotroumpelou, I. Kyriakou, V. Ivantchenko, S. Incerti, D. Emfietzoglou, Appl. Sci. 14 (2024) 2275 (link) - free access
• Space radiation quality factor for Galactic Cosmic Rays and typical space mission scenarios using a microdosimetric approach, A. Papadopoulos, I. Kyriakou, S. Incerti, G. Santin, P. Nieminen, I. A. Daglis, W. Li, D. Emfietzoglou, Radiat. Environ. Biophys. 62 (2023) 221-234 (link) - free access
• Microdosimetry study of proton quality factor using analytic model calculations, A. Papadopoulos, I. Kyriakou, Y. Matsuya, S. Incerti, I. Daglis, D. Emfietzoglou, Appl. Sci. 12 (2022) 8950 (link) - free access
• Experimental cross sections for water ionization due to the impact of light ions. A review. M. A. Bernal, J. A. Liendo, S. Incerti, Z. Francis, H. N. Tran, Nucl. Instrum. Meth. B 217 (2022) 6-15 (link)
• Report on G4‐Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group, P. Arce D. Bolst M.‐C. Bordage J. M. C. Brown P. Cirrone M. A. Cortés‐Giraldo D. Cutajar G. Cuttone L. Desorgher P. Dondero A. Dotti B. Faddegon C. Fedon S. Guatelli S. Incerti V. Ivanchenko D. Konstantinov I. Kyriakou G. Latyshev A. Le C. Mancini‐Terracciano M. Maire A. Mantero M. Novak C. Omachi L. Pandola A. Perales Y. Perrot G. Petringa J. M. Quesada J. Ramos‐Méndez F. Romano A. B. Rosenfeld L. G. Sarmiento D. Sakata T. Sasaki I. Sechopoulos E. C. Simpson T. Toshito D. H. Wright, Med. Phys. 48 (2021) 19-56 (link) - free access
• Microdosimetric calculations of the direct DNA damage induced by low energy electrons using the Geant4-DNA Monte Carlo code, S. Margis, M. Magouni, I. Kyriakou, A. G. Georgakilas, S. Incerti, D. Emfietzoglou, Phys. Med. Biol. 65 (2020) 045007 (link)
• Track structure simulations of proximity functions in liquid water using the Geant4-DNA toolkit, S. Incerti, I. Kyriakou, M. C. Bordage, S. Guatelli, V. Ivanchenko, D. Emfietzoglou, J. Appl. Phys. 125 (2019) 104301 (link)
• Influence of track structure and condensed history physics models of Geant4 to nanoscale electron transport in liquid water, I. Kyriakou, V. Ivanchenko, D. Sakata, M. C. Bordage, S. Guatelli, S. Incerti, D. Emfietzoglou, Phys. Med. 58 (2019) 149-154 (link)
• Investigation of track structure and condensed history physics models for applications in radiation dosimetry on a micro and nano scale in Geant4, P. Lazarakis, S. Incerti, V. Ivanchenko, I. Kyriakou, D. Emfietzoglou, S. Corde, A. B. Rosenfeld, M. Lerch, M. Tehei, S. Guatelli, Biomed. Phys. Eng. Express 4 (2018) 024001 (link) - free access
• Microdosimetric evaluation of alternative high and intermediate energy high dose rate brachytherapy sources - a Geant4-DNA simulation study, G. Famulari, P. Pater, S. A. Enger, Int. J. Radiat. Oncol. Biol. Phys. 100 (2018) 270-277 (link)
• Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm, G. Famulari, P. Pater, S. A. Enger, Phys. Med. Biol., 62 (2017) 5495-5508 (link)
• Microdosimetry of electrons in liquid water using the low-energy models of Geant4, I. Kyriakou, D. Emfietzoglou, V. Ivanchenko, M. C. Bordage, S. Guatelli, P. Lazarakis, H. N. Tran, S. Incerti, J. Appl. Phys. 122 (2017) 024303 (link)
• Low-energy electron dose-point kernel simulations using new physics models implemented in Geant4-DNA, J. Bordes, S. Incerti, N. Lampe, M. Bardies, M.-C. Bordage, Nucl. Instrum. Meth. B 398 (2017) 13-20 (link)
• Geant4-DNA simulation of electron slowing-down spectra in liquid water, S. Incerti, I. Kyriakou, H. N. Tran, Nucl. Instrum. and Meth. B 397 (2017) 45-50 (link)
• Calculation of cellular S-values using Geant4-DNA: The effect of cell geometry, M. Šefl, S. Incerti, G. Papamichael, D. Emfietzoglou Appl. Radiat. Isot. 69 (2015) 113-123 (link)
• Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study, S. Incerti, M. Psaltaki, P. Gillet, Ph. Barberet, M. Bardiès, M.A. Bernal, M.-C. Bordage, V. Breton, M. Davidkova, E. Delage, Z. El Bitar, Z. Francis, S. Guatelli, A. Ivanchenko, V. Ivanchenko, M. Karamitros, S.B. Lee, L. Maigne, S. Meylan, K. Murakami, P. Nieminen, H. Payno, Y. Perrot, I. Petrovic, Q.T. Pham, A. Ristic-Fira, G. Santin, T. Sasaki, H. Seznec, J.I. Shin, V. Stepan, H.N. Tran, C. Villagras, Nucl. Instrum. and Meth. B 333 (2014) 92-98 (link)
• Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes, T. André, F. Morini, M. Karamitros, R. Delorme, C. Le Loirec, L. Campos, C. Champion, J.-E. Groetz, M. Fromm, M.-C. Bordage, Y. Perrot, Ph. Barberet, M.A. Bernal, J.M.C. Brown, M.S. Deleuze, Z. Francis, V. Ivanchenko, B. Mascialino, C. Zacharatou, M. Bardiès, S. Incerti, Nucl. Instrum. and Meth. B 319 (2014) 87-94 (link)
• Dose point kernels in liquid water: An intra-comparison between GEANT4-DNA and a variety of Monte Carlo codes, C. Champion, S. Incerti, Y. Perrot, R. Delorme, M.C. Bordage, M. Bardiès, B. Mascialino, H.N. Tran, V. Ivanchenko, M. Bernal, Z. Francis, J.-E. Groetz, M. Fromm, L. Campos, Appl. Radiat. Isot. 83 (2014) 137-141 (link)
• Monte Carlo simulation of energy-deposit clustering for ions with the same LET in liquid water, Z. Francis, S. Incerti, V. Ivanchenko, C. Champion, M. Karamitros, M. Bernal, Z. El Bitar, Phys. Med. Biol. 57 (2012) 209-224 (link)
• Stopping power and ranges of electrons, protons and alpha particles in liquid water using the Geant4-DNA package, Z. Francis, S. Incerti, M. Karamitros, H.N. Tran, C. Villagrasa, Nucl. Instrum. and Meth. B 269 (2011) 2307-2311 (link)
• Comparison of Geant4 very low energy cross section models with experimental data in water, S. Incerti, A. Ivanchenko, M. Karamitros, A. Mantero, P. Moretto, H. N. Tran, B. Mascialino, C. Champion, V. N. Ivanchenko, M. A. Bernal, Z. Francis, C. Villagrasa, G. Baldacchino, P. Guèye, R. Capra, P. Nieminen, C. Zacharatou, Med. Phys. 37 (2010) 4692-4708 (link)

Physico-chemistry and chemistry processes and models

• Investigating ultra-high dose rate water radiolysis using the Geant4-DNA toolkit and a Geant4 model of the Oriatron eRT6 electron linac, F. Chappuis, H. N. Tran, P. G. Jorge, S. A. Zein, I. Kyriakou, D. Emfietzoglou, C. Bailat, F. Bochud, S. Incerti, L. Desorgher, Sc. Rep. 14 (2024) 26707 (link) - free access
• Modeling water radiolysis with Geant4-DNA: Impact of the temporal structure of the irradiation pulse under oxygen conditions, T. A. Le, H. N. Tran, S. Fattori, V. C. Phan, S. Incerti (2024) (arXiv:2409.11993)
• Monte Carlo simulations of microdosimetry and radiolytic species production at long time post proton irradiation using GATE and Geant4-DNA, G. R. Fois, H. N. Tran, V. Fiegel, G. Blain, S. Chiavassa, E. Craff, G. Delpon, M. Evin, F. Haddad, S. Incerti, C. Koumeir, V. Métivier, Q. Mouchard, F. Poirier, V. Potiron, N. Servagent, J. Vandenborre, L. Maigne, Med. Phys. 51 (2024) 7500-7510 (link)
• The general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension to investigate mechanisms underlying the FLASH effect in radiotherapy: current status and challenges, F. Chappuis, H. N. Tran, S. A. Zein, C. Bailat, S. Incerti, F. Bochud, L. Desorgher, Phys. Med. 110 (2023) 102601 (link) - free access
• Modeling of scavenging systems for water radiolysis with Geant4-DNA, F. Chappuis, V. Grilj, H. N. Tran, S. Zein, F. Bochud, C. Bailat, S. Incerti, L. Desorgher, Phys. Med. 108 (2023) 102549 (link)
• Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields, W.-G. Shin, J. Ramos-Mendez, N. H. Tran, S. Okada, Y. Perrot, C. Villagrasa, S. Incerti, Phys. Med. 88 (2021) 86-90 (link)
• Geant4-DNA modeling of water radiolysis beyond the microsecond : an on-lattice stochastic approach, H. N. Tran, F. Chappuis, S. Incerti, F. Bochud, L. Desorgher, Int. J. Mol. Sci. 22 (2021) 6023 (link) and in Encyclopedia (2021) 12236 (link) - free access
• Le code Geant4-DNA : simuler les premiers instants de la radiolyse de l’eau, W. G. Shin, H. Tran, J. Ramos-Méndez, Y. Perrot, G. Montarou, Z. Francis, G. Baldacchino, B. Faddegon, C. Villagrasa, S. Incerti, L'actualité chimique (2021) 460-461 (link) - in French
• Assessment of DNA damage with a new Independent Reaction Time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber, H. N. Tran, J. R. Mendez, W. G. Shin, Y. Perrot, B. Faddegon, S. Okada, M. Karamitros, M. Davidkova, V. Stepan, S. Incerti, C. Villagrasa, Med. Phys. 48 (2021) 890-901 (link) - free access
• Independent Reaction Times method in Geant4-DNA: implementation and performance, J. Ramos-Mendez, W.-G. Shin, J. Domínguez-Kondo, S. Incerti, H. Tran, C. Villagrasa, Y. Perrot, V. Stepan, M. Karamitros, S. Okada, E. Moreno-Barbosa, B. Faddegon, Med. Phys. 47 (2020) 5919-5930 (link)
• Implementing the Independent Reaction Time method in Geant4 for radiation chemistry simulations, M. Karamitros, J. M. C. Brown, N. Lampe, D. Sakata, N. H. Tran, W.-G. Shin, J. R. Mendez, S. Guatelli, S. Incerti, J. A. LaVerne, arXiv:2006.14225 (2020) (link)
• Validation and investigation of reactive species yields of Geant4-DNA chemistry models, D. Peukert, S. Incerti, I. Kempson, M. Douglass, M. Karamitros, G. Baldacchino, E. Bezak, Med. Phys. 46 (2019) 983-998 (link)
• Diffusion-controlled reactions modeling in Geant4-DNA, M. Karamitros, S. Luan, M.A. Bernal, J. Allison, G. Baldacchino, M. Davidkova, Z. Francis, W. Friedland, V. Ivantchenko, A. Ivantchenko, A. Mantero, P. Nieminem, G. Santin, H.N. Tran, V. Stepan, S. Incerti, J. Comput. Phys. 274 (2014) 841-882 (link)
• Geometric algorithms and data structures for simulating diffusion-limited reactions, S. Bloom, M. Karamitros, S. Incerti, S. Luan, Simulation Series 46 (2014) 7-14 (link)
• Geant4 electromagnetic physics: improving simulation performance and accuracy, V. N. Ivanchenko, S. Incerti, J. Allison, A. Bagulya, J. M. C. Brown, C. Champion, S. Elles, Z. Francis, V. Grichine, A. Ivantchenko, J. Jacquemier, M. Karamitros, M. Maire, A. Mantero, J. P. Marques, L. Pandola, M. Raine, M. A. Reis, G. Santin, D. Sawkey, A. Schaelicke, M. Schenk, A. Taborda, L. Urban and T. Yamashita, Proceedings of the Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo 2013 (SNA + MC 2013), La Cité des Sciences et de l’Industrie, Paris, France, October 27-31 (2014) 03101 (link)
• Modeling radiation chemistry in the Geant4 toolkit, M. Karamitros et al., Prog. Nucl. Sci. Tec. 2 (2011) 503-508 (link) - free access

Geometries of biological targets

• Monte Carlo dosimetry of a realistic multicellular model of follicular lymphoma in a context of radioimmunotherapy, J. Bordes, S. Incerti, E. Mora-Ramirez, J. Tranel, C. Rossi, C. Bezombes, J. Bordenave, M. Bardiès, M.-C. Bordage, Med. Phys. 47 (2020) 5222-5234 (link)
• Influence of chromatin compaction on simulated early radiation-induced DNA damage using Geant4-DNA, N. Tang, M. Bueno, S. Meylan, S. Incerti, A. Vaurijoux, G. Gruel, C. Villagrasa, Med. Phys. 46 (2019) 1501-1511 (link) - free access
• Simulation of early radiation-induced DNA damage on different types of cell nuclei, N. Tang, M. Bueno, S. Meylan, S. Incerti, I. Clairand, C. Villagrasa, Radiat. Prot. Dosim. 183 (2018) 26-31 (link)
• Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit, A. L. McNamara, J. R. Mendez, J. Perl, K. Held, N. Dominguez, E. Moreno, N. T. Henthorn, S. Meylan, C. Villagrasa, S. Incerti, B. Faddegon, H. Paganetti, J. Schuemann, Phys. Med. Biol. 63 (2018) 175018 (link)
• Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool, S. Meylan, U. Vimont, S. Incerti, I. Clairand, C. Villagrasa, Comput. Phys. Commun. 204 (2016) 159-169 (link)
• PDB4DNA: implementation of DNA geometry from Protein Data Bank (pdb) description for Geant4-DNA Monte-Carlo simulations, E. Delage, Q. T. Pham, M. Karamitros, V. Stepan, S. Incerti, L. Maigne, Y. Perrot, Comput. Phys. Commun. 192 (2015) 282-288 (link)
• Influence of the chromatin density on the number of direct clustered damages calculated for proton and alpha irradiations using a Monte Carlo code, M. Dos Santos, C. Villagrasa, I. Clairand and S. Incerti , Prog. Nucl. Sci. Tech. 4, (2014) 449-453 (link) - free access
• Performance of a new atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations, M. A. Bernal, D. Sikansi, F. Cavalcante, S. Incerti, C. Champion, V. Ivanchenko, Z. Francis, M. Karamitros, J. Phys.: Conf. Ser. 490 (2014) 012150 (link)
• Influence of the DNA density on the number of clustered damages created by protons of different energies, M. Dos Santos, C. Villagrasa, I. Clairand, S. Incerti, Nucl. Instrum. and Meth. B 298 (2013) 47-54 (link)
• An atomistic geometrical model of the B-DNA configuration for DNA–radiation interaction simulations, M.A. Bernal, D. Sikansi, F. Cavalcante, S. Incerti, C. Champion, V. Ivanchenko, Z. Francis, Comp. Phys. Comm. 184 (2013) 2840-2847 (link)

Multi-scale applications

• Development of a novel computational technique to create DNA and cell geometrical models for Geant4-DNA, K. Chatzipapas, H. N. Tran, M. Dordevic, D. Sakata, S. Incerti, D. Visvikis, J. Bert, Phys. Med. 127 (2024) 104389 (link)
• « dsbandrepair » - an updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair, A. Le Tuan, N. H. Tran, Y. Thibaut, K. Chatzipapas, D. Sakata, S. Incerti, C. Villagrasa, Y. Perrot, Phys. Med. 124, 103422 (2024) (link) - free access
• Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation, Y. Thibaut, G. Gonon, J. S. Martinez, M. Petit, R. Babut, A. Vaurijoux, G. Gruel, C. Villagrasa, S. Incerti, Y. Perrot, Phys. Med. Biol. 68 (2023) 225008 (link)
• In-silico calculations of DNA damage induced by alpha-particles in the 224Ra DaRT decay chain for a better understanding of the radiobiological effectiveness of this treatment, L. Ballisat, L. Beck, C. De Sio, S. Guatelli, D. Sakata, S. Incerti, H. N. Tran, J. Duan, K. Maclean, Y. Shi, J. Velthuis, A. Rozenfeld, Phys. Med. 112 (2023) 102626 (link) - free access
• Geant4-DNA simulation of human cancer cells irradiation with helium ion beams, K. Chatzipapas, M. Dordevic, S. Zivkovic, N. H. Tran, N. Lampe, D. Sakata, I. Petrovic, A. Ristic-Fira, W.-G. Shin, S. Zein, J. M. C. Brown, I. Kyriakou, D. Emfietzoglou, S. Guatelli, S. Incerti, Phys. Med. 112 (2023) 102613 (link)
• Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application, K. P. Chatzipapas, N. H. Tran, M. Dordevic, S. Zivkovic, S. Zein, W.-G. Shin, D. Sakata, N. Lampe, J. M. C. Brown, A. Ristic-Fira, I. Petrovic, I. Kyriakou, D. Emfietzoglou, S. Guatelli, S. Incerti, Prec. Radiat. Oncol. 7 (2023) 4-14 (link) - free access
• MINAS TIRITH: A new tool for simulating radiation-induced DNA damage at the cell population level, Y. Thibaut, G. Gonon, J. Martinez-Guerrero, M. Petit, A. Vaurijoux, G. Gruel, C. Villagrasa, S. Incerti, Y. Perrot, Phys. Med. Biol. 68 (2023) 034002 (2023) (link) - free access
• Prediction of DNA rejoining kinetics and cell survival for V79 cells using Geant4-DNA, D. Sakata, R. Hirayama, W.-G. Shin, M. Belli, M. A. Tabocchini, O. Belov, M. A. Bernal, M.-C. Bordage, J. M. C. Brown, F. Chappuis, L. Desorgher, D. Emfietzoglou, Z. Francis, S. Guatelli, T. Inaniwa, V. Ivanchenko, M. Karamitros, I. Kyriakou, Z. Li, S. Meylan, C. Michelet, N. Lampe, K. Murakami, S. Okada, Y. Perrot, I. Petrovic, J. Ramos-Mendez, A. Ristic-Fira, G. Santin, T. Sasaki, J. Schuemann, H. N. Tran, C. Villagrasa, S. Incerti, Phys. Med. (2023) 102508 (link) - corrigendum - Galileo Galilei Award 2023 of the European Journal of Medical Physics
• Nanodosimetric calculations of radiation-induced DNA damage in a new nucleus geometrical model, Y. Thibaut, N. Tang, H. N. Tran, A. Vaurijoux, C. Villagrasa, S. Incerti, Y. Perrot, Int. J. Mol. Sci. 23, 3770 (2022) (link) - free access
• DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions, N. D-Kondo, E. Moreno-Barbosa, V. Štěphán, K. Stefanová, Y. Perrot, C. Villagrasa, S. Incerti, B. De Celis Alonso, J. Schuemann, B. Faddegon, J. Ramos-Méndez, Phys. Med. Biol. 66 (2021) 245017 (link)
• Performance evaluation for repair of HSGc-C5 carcinoma cell using Geant4-DNA, D. Sakata, M. Suzuki, R. Hirayama, Y. Abe, M. Muramatsu, S. Sato, O. Belov, I. Kyriakou, D. Emfietzoglou, S. Guatelli, S. Incerti, T. Inaniwa, Cancers 13 (2021) 6046 (link) - free access
• A Geant4-DNA evaluation of radiation-induced DNA damage on a human fibroblast, W.-G. Shin, D. Sakata, N. Lampe, O. Belov, H. N. Tran, I. Petrovic, A. Ristic-Fira, M. Dordevic, M. Bernal, M.-C. Bordage, Z. Francis, I. Kyriakou, Y. Perrot, T. Sasaki, C. Villagrasa, S. Guatelli, V. Breton, D. Emfietzoglou, S. Incerti, Cancers 13 (2021) 4940 (link) - free access
• TOPAS-nBio validation for simulating water radiolysis and DNA damage under Low-LET irradiation, J. Ramos-Méndez, J. LaVerne, N. Domínguez-Kondo, J. Milligan, V. Štěphán, M. Šefl, Y. Perrot, C. Villagrasa, W-G. Shin, S. Incerti, A. McNamara, H. Paganetti, J. Perl, J. Schuemann, B. Faddegon, Phys. Med. Biol. 66 (2021) 175026 (link)
• Monte Carlo simulation of SARS-CoV-2 radiation-induced inactivation for vaccine development, Z. Francis, S. Incerti, S. A. Zein, N. Lampe, C. A. Guzman, M. Durante, Rad. Res. 195 (2021) 221-229 (link) - Radiation Research journal cover page (link) - free access
• Full integrated Monte Carlo simulation for evaluating radiation induced DNA damage and following repair using Geant4-DNA, D.Sakata, O. Belov, M.-C. Bordage, D. Emfietzoglou, S. Guatelli, T. Inaniwa, V. Ivantchenko, M. Karamitros, I. Kyriakou, N. Lampe, I. Petrovic, A. Ristic-Fira, W.-G. Shin, S. Incerti, Sc. Rep. 10 (2020) 20788 (link) - free access
• Cosmic-Ray Tracks in Astrophysical Ices: Modeling with the Geant4-DNA Monte Carlo Toolkit, C. N. Shingledecker, S. Incerti, A. Ivlev, D. Emfietzoglou, I. Kyriakou, A. Vasyunin, P. Caselli , ApJ 904 (2020) 189 (link)
• Advances in modelling gold nanoparticle radio-sensitisation using new Geant4-DNA physics models, E. Engels, S. Bakr, D. Bolst, D. Sakata, N. Li, P. Lazarakis, S. McMahon, V. Ivanchenko, A. Rosenfeld, S. Incerti, I. Kyriakou, D. Emfietzoglou, M. L. F. Lerch, M. Tehei, S. Corde, S. Guatelli, Phys. Med. Biol. 65 (2020) 225017 (link)
• Advances in Geant4 applications in medicine, S. Incerti, J.M.C. Brown, S.Guatelli, Phys. Med. 70 (2020) 224-227 (link)
• Determination of fast neutron RBE using a fully mechanistic computational model, A. Zabihi, J. Tello, S. Incerti, Z. Francis, G. Forozani, F. Semsarha, A. Moslehi, M. A. Bernal, Appl. Radiat. Isot. 156 (2020) 108952 (link)
• Assessment of the biological response of endothelial cells irradiated with 40 kVp, 220 kVp and 4 MV X-rays by means of micro and nanodosimetric calculations, N. Tang, M. Bueno, S. Meylan, Y. Perrot, H. N. Tran, A. Freneau, M. Dos Santos, A. Vaurijoux, G. Gruel, M. A. Bernal, M.-C. Bordage, D. Emfietzoglou, Z. Francis, S. Guatelli, V. Ivanchenko, M. Karamitros, I. Kyriakou, W.-G. Shin, S. Incerti, C. Villagrasa, Int. J. Mol. Sci. 20 (2019) 6204 (link)
• A simulation study of gold nanoparticles localisation effects on radiation enhancement at the mitochondrion scale, Z. Francis, G. Montarou, S. Incerti, M. Bernal, S. Zein, Phys. Med. 67 (2019) 148-154 (link)
• Monte-Carlo dosimetry and real-time imaging of targeted irradiation consequences in 2-cell stage Caenorhabditis elegans embryo, E. Torfeh, M. Simon , G. Muggiolu , G. Devès , F. Vianna , S. Bourret , S. Incerti , P. Barberet, H. Seznec, Sc. Rep. 9 (2019) 10568 (link) - free access
• Evaluation of Radiation DNA Damage in a Fractal Cell Nucleus model using Geant4-DNA, D. Sakata, N. Lampe, M. Karamitos, I. Kyriakou, O. Belov, M. Bernal, M.-C. Bordage, J. M. C. Brown, Z. Francis, V. Ivantchenko, K. Murakami, S. Okada, I. Petrovic, A. Ristic-Fira, T. Sasaki, W.-G. Shin, N. Tang, H. N. Tran, C. Villagrasa, D. Emfietzoglou, P. Nieminen, S. Guatelli, S. Incerti, Phys. Med. 62 (2019) 152-157 (link) - free access - see press announcement in the Summer 2019 issue of the EFOMP European Medical Physics News and in the September 2019 ESTRO Newsletter
• Computational approach to determine the relative biological effectiveness of fast neutrons using the Geant4-DNA toolkit and a DNA atomic model from the Protein Data Bank, A. Zabihi, S. Incerti, Z. Francis, G. Forozani, F. Semsarha, A. Moslehi, P. Rezaeian, M. A. Bernal, Phys. Rev. E 99 (2019) 052404 (link)
• TOPAS-nBio – An extension to the TOPAS simulation toolkit for (sub-)cellular radiobiology, J. Schuemann, A. McNamara, J. Ramos, J. Perl, K. Held, H. Paganetti, S. Incerti, B. Faddegon, Rad. Res. 191 (2019) 125-139 (link) - free access
• A new standard DNA damage (SDD) data format, J. Schuemann, A. L. McNamara, J. W. Warmenhoven, N. T. Henthorn, K. Kirkby, M. J. Merchant, S. Ingram, H. Paganetti, K. D. Held, J. Ramos-Mendez, B. Faddegon, J. Perl, D. T. Goodhead, I. Plante, H. Rabus, H. Nettelbeck, W. Friedland, P. Kundrat, A. Ottolenghi, G. Baiocco, S. Barbieri, M. Dingfelder, S. Incerti, C. Villagrasa, M. Bueno, M. A. Bernal, S. Guatelli, D. Sakata, J. M. C. Brown, Z. Francis, I. Kyriakou, N. Lampe, F. Ballarini, M. P. Carante, M. Davidkova, V. Štěpan, X. Jia, F. A. Cucinotta, R. Schulte, R. D. Stewart, D. J. Carlson, S. Galer, Z. Kuncic, S. Lacombe, J. Milligan, S. H. Cho, G. Sawakuchi, T. Inaniwa, T. Sato, W. Li, A. V. Solov’yov, E. Surdutovich, M. Durante, K. Prise and S. J. McMahon, Rad. Res. 191 (2019) 76-92 (link) - free access
• Accounting for radiation-induced indirect damage on DNA with the Geant4-DNA code, L. de la Fuente Rosales, S. Incerti, Z. Francis, M. A. Bernal, Phys. Med. 51 (2018) (link)
• Mechanistic DNA Damage Simulations in Geant4-DNA Part 2: Electron and Proton Damage in a Bacterial Cell, N. Lampe, M. Karamitros, V. Breton, J. M. C. Brown, D. Sakata, D. Sarramia, S. Incerti, Phys. Med. 48 (2018) 146-155 (link)
• Mechanistic DNA Damage Simulations in Geant4-DNA Part 1: A parameter study in a simplified geometry, N. Lampe, M. Karamitros, V. Breton, J. M. C. Brown, I. Kyriakou, D. Sakata, D. Sarramia, S. Incerti, Phys. Med. 48 (2018) 135-145 (link)
• Numerical insight into the dual radiation action theory, J. J. Tello, S. Incerti, Z. Francis, H. Tran, M. A. Bernal, Phys. Med. 43 (2017) 120-126 (link)
• Simulation of early DNA damage after the irradiation of a Fibroblast cell nucleus using Geant4-DNA, S. Meylan, S. Incerti, M. Karamitros, N. Tang, M. Bueno, I. Clairand, C. Villagrasa, Sc. Rep. 7 (2017) 11923 (link)
• Simulating the Impact of the Natural Radiation Background on Bacterial Systems: Implications for Very Low Radiation Biological Experiments, N. Lampe, D. G. Biron, J. M. C. Brown, S. Incerti, P. Marin, L. Maigne, D. Sarramia, H. Seznec, V. Breton, PLoS One 11(11) (2016) e0166364 (link) - free access
• Radiation damage to neuronal cells: simulating the energy deposition and water radiolysis in a small neural network, O. V. Belov, M. Batmunkh, S. Incerti, O. Lkhagva, Phys. Med. 32 (2016) 1510-1520 (link)
• Optimizing dose enhancement with Ta2O5 nanoparticles for synchrotron microbeam activated radiation therapy, E. Engels, S. McKinnon, M. Tehei, K. Konstantinov, S. Incerti, A. Rosenfeld, M. Lerch, S. Corde, S. Guatelli, Phys. Med. 32 (2016) 1852-1861 (link)
• Local dose enhancement of proton therapy by ceramic oxide nanoparticles investigated with Geant4 simulations, S. McKinnon, M. Tehei, K. Konstantinov, S. Incerti, A. Rosenfeld, M. Lerch, S. Corde, S. Guatelli, Phys. Med. 32(12) (2016) 1584-1593 (link)
• Study of the effect of ceramic Ta2O5 nanoparticle distribution on cellular dose enhancement in a kilovoltage photon field, S. McKinnon, E. Engels, M. Tehei, K. Konstantinov, S. Corde, S. Oktaria, S. Incerti, M. Lerch, A. Rosenfeld, S. Guatelli, Phys. Med. 32(10) (2016) 1216-1224 (link)
• Geant4 Monte Carlo simulation of absorbed dose and radiolysis yields enhancement from a gold nanoparticle under MeV proton irradiation, H. N. Tran, M. Karamitros, V. Ivantchenko, S. Guatelli, S. McKinnon, K. Murakami, T. Sasaki, S. Okada, M.C. Bordage, Z. Francis, Z. EL Bitar, M. A. Bernal, J. I. Shin, S. B. Lee, Ph. Barberet, T.T. Tran, J. M. C. Brown, S. Incerti, Nucl. Instrum. Meth. B 373 (2016) 126-139 (link)
• Complex cell geometry and sources distribution model for Monte Carlo single cell dosimetry with iodine 125 radioimmunotherapy, F. X. Arnaud, S. Paillas, J. P. Pouget, S. Incerti, M. Bardiès, M. C. Bordage, Nucl. Instrum. Meth. B 366 (2016) 227-233 (link)
• Coupling of Geant4-DNA physics models into the GATE Monte Carlo platform: Evaluation of radiation-induced damage for clinical and preclinical radiation therapy beams, Q.T. Pham, A. Anne, M. Bony, E. Delage, D. Donnarieix, A. Dufaure, M. Gautier, S.B. Lee, P. Micheau, G. Montarou, Y. Perrot, J.I. Shin, S. Incerti, L. Maigne, Nucl. Instrum. Meth. B 353 (2015) 46-55 (link)
• The influence of DNA configuration on the direct strand break yield, M. A. Bernal, C. E. deAlmeida, S. Incerti, C. Champion, V. Ivanchenko, Z. Francis, Comp. Math. Meth. Med. (2015) 417501 (link) - free access
• The cytoplasm as a radiation target: an in silico study of microbeam cell irradiation, H. L. Byrne, W. Domanova, A. L. McNamara, S. Incerti., Z. Kuncic, Phys. Med. Biol. 60 (2015) 2325-2338 (link)
• Carbon ion fragmentation effects on the nanometric level behind the Bragg peak depth, Z. Francis, E. Seif, S. Incerti, C. Champion, M. Karamitros, M. A. Bernal, V. N. Ivanchenko, A. Mantero, H. N. Tran, Z. El Bitar, Phys. Med. Biol. 59 (2014) 7691-7702 (link)
• Extending Geant4 at the Physics-Medicine-Biology frontier, V. Breton, C. Champion, Z. El Bitar, M. Karamitros, S. B. Lee, L. Maigne, Y. Perrot, Q. T. Pham, J. I. Shin, H. N. Tran, S. Incerti, Trends in Computational Science and Engineering 3 (2013) 21-41 (link)
• Energy deposition in small-scale targets of liquid water using the very low energy electromagnetic physics processes of the Geant4 toolkit, S. Incerti, C. Champion, H.N. Tran, M. Karamitros, M. Bernal, Z. Francis, V. Ivanchenko, A. Mantero, Nucl. Instrum. and Meth. B 306 (2013) 158-164 (link)
• In Silico nanodosimetry: new insights into non-targeted biological responses to radiation, Z. Kuncic, H. L. Byrne, A. L. McNamara, S. Guatelli, W. Domanova, S. Incerti, Comp. Math. Meth. Med. (2012) 147252 (link) - free access
• Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha-particle, P. Barberet, F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H. Seznec, Phys. Med. Biol. 57 (2012) 2189-2207 (link)
• The invariance of the total direct DNA strand break yield, M. A. Bernal, C. E. de Almeida, C. S. Sampaio, S. Incerti, C. Champion, P. Nieminen, Med. Phys. 38 (2011) 4147-4153 (link)
• Effect of a magnetic field on the track structure of low-energy electrons: a Monte Carlo study, M. U. Bug, E. Gargioni, S. Guatelli, S. Incerti, H. Rabus, R. Schulte, A. B. Rosenfeld, Eur. Phys. J. D 60 (2010) 85-92 (link)
• Monte Carlo dosimetry for targeted irradiation of individual cells using a microbeam facility, S. Incerti, H. Seznec, M. Simon, Ph. Barberet, C. Habchi, Ph. Moretto, Rad. Prot. Dos. 133 (2009) 2-11 (link)
• A comparison of cellular irradiation techniques with alpha particles using the Geant4 Monte Carlo simulation toolkit, S. Incerti, N. Gault, C. Habchi, J. L. Lefaix, Ph. Moretto, T. Pouthier, H. Seznec, Rad. Prot. Dos. 122 (2006) 327-329 (link)

Radiobiology experiments

• In vitro validation of helium ion irradiations as a function of Linear Energy Transfer in radioresistant human malignant cells, A. M. Ristić Fira, O. D. Keta, V. D. Petković, M. Đorđević, G. Petringa, S. Fattori, R. Catalano, P. Cirrone, G. Cuttone, D. Sakata, N. H. Tran, K. Chatzipapas, S. Incerti, I. M. Petrović, Int. J. Radiat. Biol. 100 (2024) 1426-1437 (link)
• Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations, P. Beaudier, S. A. Zein, K. Chatzipapas, H. Tran, G. Devès, L. Plawinski, R. Liénard, D. Dupuy, Ph. Barberet, S. Incerti, F. Gobet, H. Seznec, Sc. Rep. 10 (2024) 20788 (link) - free access
• DNA double-strand breaks in cancer cells as a function of proton linear energy transfer and its variation in time, O. Keta, V. Petković, P. Cirrone, G. Petringa, G. Cuttone, D. Sakata, W.-G. Shin, S. Incerti, I. Petrović, A. Ristić-Fira, Int. J. Radiat. Biol. 97 (2021) 1229-1240 (link)
• DNA damage assessment of human breast and lung carcinoma cells irradiated with protons and carbon ions, A. M. Ristić Fira, O. D. Keta, V. D. Petković, F. P. Cammarata, G. Petringa, P. G.A. Cirrone, G. Cuttone, S. Incerti, I. M. Petrović, J. Radiat. Res. Appl. Sci. 13 (2020) 672-687 (link) - free access
• Biological outcomes of Gamma-radiation induced DNA damages in breast and lung cancer cells pretreated with free radical scavengers, V. D. Petković, O. D. Keta, M. Z. Vidosavljević, S. Incerti, A. M. Ristić Fira, I. M. Petrović, Int. J. Radiat. Biol. 95 (2019) 274-285 (link)
• The impact of autophagy on cell death modalities in CRL-5876 lung adenocarcinoma cells after their exposure to γ-rays and/or erlotinib, O. Keta, T. Bulat, I. Golić, S. Incerti, A. Korać, I. Petrović, A. Ristić-Fira, Cell Biol. Toxicol. 32 (2016) 83-101 (link)
• Contribution of indirect effects to clustered damage in DNA irradiated with protons, K. Pachnerová Brabcová, V. Štěpán, M. Karamitros, M. Karabín, P. Dostálek, S. Incerti, M. Davídková, L. Sihver, Radiat. Prot. Dosim. 166 (2015) 44-48 (link)
• Proton-induced direct and indirect damage of plasmid DNA, L. Vyšín, K. Pachnerová Brabcová, V. Štěpán, P. Moretto-Capelle, B. Bugler, G. Legube, P. Caffarelli, R. Casta, J. P. Champeaux, M. Sence, M. Vlk, R. Wagner, J. Štursa, V. Zach, S. Incerti, L. Juha, M. Davídková, Radiat. Environ. Biophys 54 (2015) 343-352 (link)

Computing performance

• Electron tracks simulation in water: performance comparison between GPU, CPU and the EUMED grid installation, E. Seif, Z. El Bitar, S. Incerti, M. A. Bernal, Z. Francis, Phys. Med. 104 (2022) 56-66 (link)
• MPEXS-DNA, A new GPU-based Monte Carlo simulator for radiophysics and chemistry at subcellular scale, S. Okada, K. Murakami, S. Incerti, K. Amako, T. Sasaki, Med. Phys. 46 (2019) 1483-1500 (link) - free access
• GPU Acceleration of Monte Carlo Simulation at the Cellular and DNA Levels, S. Okada, K. Murakami, K. Amako, T. Sasaki, S. Incerti, M. Karamitros, N. Henderson, M. Gerritsen, M. Asai, A. Dotti, Smart Innovation, Systems and Technologies 45 (2016) 323-332 (link)

Selection of movies

• Example of movies by N. Lampe: fractal based geometries (2019)
• Example of movie by V. Stepan : 50 MeV, 100 MeV and 1 GeV proton tracks in liquid water (2014)
• Example of movie by V. Stepan : 20 keV electron and 200 keV alpha tracks in 10 micrometer cube of liquid water, generated using Geant4 10.0p2 microdosimetry example (2014)
• Example of movie by V. Stepan : 20 keV electron and 20 MeV alpha tracks in 10 micrometer cube of liquid water, generated using Geant4 10.0p2 microdosimetry example (2014)
• Example of movie by V. Stepan : 1 keV electron in 150 nm liquid water sphere, including chemistry (2014)
• Example of movie by M. Karamitros for the transport of radicals from a single proton track in liquid water (2012)

PhD theses on Geant4-DNA

1. Microdosimetric calculations at DNA level for the determination of safe radiation dose limits for manned long-term space missions, A. Papadopoulos, Ioannina University, Greece - on-going
2. Modélisation de l'évolution des dommages précoces radio-induits au sein d'une population cellulaire, Y. Thibaut, Bordeaux University, France (2023) (link) - in French
3. Implementation of the EPICS2017 electron-photon database in Geant4 : developments and applications, Z. Li, Bordeaux University, France (2023) (link)
4. Development and application of the Geant4-DNA toolkit for the simulation of radiobiological effects at the sub-cellular scale, W. G. Shin, Bordeaux University, France & Yonsei U., Republic of Korea (2020) (link) - 2019 FKPPL Young Researcher Award
5. Monte Carlo microdosimetry of charged-particle microbeam irradiations, E. Torfeh, Bordeaux University, France (2019) (link)
6. Évaluation, à partir de modélisations nanodosimétriques, de l'influence de la compaction de la chromatine sur les effets radio-induits précoces et extension aux effets tardifs (réparation des dommages à l’ADN et mort cellulaire), N. Tang, Bordeaux University, France (2019) (link) - in French
7. A Monte Carlo study of the direct and indirect DNA damage induced by ionizing radiation, L. de la Fuente Rosales, Unicamp, Brazil (2018) (link)
8. Modélisation du transport des électrons de basse énergie avec des modèles physiques alternatifs dans le code Geant4-DNA et application à la radioimmunothérapie, J. Bordes, Paul Sabatier University, France (2017) (link) - in French
9. De l’impact à long terme des radiations ionisantes sur les systèmes vivants, N. Lampe, Blaise Pascal University, France (2017) (link) - 2017 Daniel Blanc Award
10. Développement d’un outil de simulation multi-échelle adapté au calcul des dommages radio-induits précoces dans des cellules exposées à des irradiations d’ions légers (proton et alpha), S. Meylan, Bordeaux University, France (2016) (link) - in French
11. Couplage et validation de l’extension Geant4-DNA dans la plateforme de simulation Monte Carlo GATE pour l’irradiation de molécules d’ADN dans un environnement de grille de calcul­, Q. T. Pham, Blaise Pascal University, France (2014) (link) - in French
12. Modélisation de la topologie des dépôts d’énergie créés par un rayonnement ionisant à l’échelle nanométrique dans les noyaux cellulaires et relation avec les événements précoces radio-­induits, M. Dos Santos, Bordeaux 1 University, France (2013) (link) - in French
13. Extension de l'outil Monte Carlo généraliste Geant4 pour la simulation de la radiolyse de l'eau dans le cadre du projet Geant4-DNA, M. Karamitros, Bordeaux 1 University, France (2012) (link) - in French
14. Extension et validation de l'outil Geant4 dans le cadre du projet Geant4-DNA pour la prédiction des dommages biologiques radio-induits à l'échelle cellulaire, H. N. Tran, Bordeaux 1 University, France (2012) (link) - in French
15. Simulations Monte-Carlo et étude microdosimétrique pour des irradiations cellulaires à faibles doses en neutrons de 14 MeV, Z. Francis, Blaise Pascal University, France (2007) (link) - in French