Geant4‐DNA example applications for track structure simulations in liquid water: A report from the Geant4‐DNA Project

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…). These example applications are included in the Geant4 Monte Carlo toolkit and are available in open access. Each application is described and comparisons to recent international recommendations are shown (e.g., ICRU, MIRD), when available. The influence of physics models available in Geant4-DNA for the simulation of electron interactions in liquid water is discussed. Thanks to these applications, the authors show that the most recent sets of physics models available in Geant4-DNA (the so-called "option4" and "option 6" sets) enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquid water, than the default set of models ("option 2") initially provided in Geant4-DNA. They also serve as reference applications for Geant4-DNA users interested in TS simulations.

[1]  D. Emfietzoglou.  Inelastic cross-sections for electron transport in liquid water: a comparison of dielectric models , 2003 .

[2]  M. D'Andrea,et al.  Monte Carlo dose voxel kernel calculations of beta-emitting and Auger-emitting radionuclides for internal dosimetry: A comparison between EGSnrcMP and EGS4. , 2006, Medical physics.

[3]  B. Mascialino,et al.  Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte-Carlo processes. , 2011, Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine.

[4]  J. Fernández-Varea,et al.  Monte Carlo Evaluation of Auger Electron–Emitting Theranostic Radionuclides , 2015, The Journal of Nuclear Medicine.

[5]  I. Kawrakow,et al.  The EGSnrc Code System: Monte Carlo Simulation of Electron and Photon Transport , 2016 .

[6]  V. Semenenko,et al.  Monte Carlo Simulation of Base and Nucleotide Excision Repair of Clustered DNA Damage Sites. I. Model Properties and Predicted Trends , 2005, Radiation research.

[7]  N. Lampe,et al.  The long term impact of ionising radiation on living systems , 2017 .

[8]  D. Emfietzoglou,et al.  Accurate Electron Inelastic Cross Sections and Stopping Powers for Liquid Water over the 0.1-10 keV Range Based on an Improved Dielectric Description of the Bethe Surface , 2007, Radiation research.

[9]  John E. Gillam,et al.  A low energy bound atomic electron Compton scattering model for Geant4 , 2014 .

[10]  V. Ivanchenko,et al.  Geant4 models for simulation of multiple scattering , 2010 .

[11]  David J. Carlson,et al.  Combined Use of Monte Carlo DNA Damage Simulations and Deterministic Repair Models to Examine Putative Mechanisms of Cell Killing , 2008, Radiation research.

[12]  Ritsuko Watanabe,et al.  Can Monte Carlo track structure codes reveal reaction mechanism in DNA damage and improve radiation therapy , 2008 .

[13]  Hooshang Nikjoo,et al.  Monte Carlo Electron Track Structure Calculations in Liquid Water Using a New Model Dielectric Response Function , 2017, Radiation Research.

[14]  Francis A. Cucinotta,et al.  Track-structure codes in radiation research , 2006 .

[15]  J. H. Hubbell,et al.  Tables and graphs of atomic subshell and relaxation data derived from the LLNL Evaluated Atomic Data Library (EADL), Z=1-100 , 1991 .

[16]  Francis A Cucinotta,et al.  A Complete Dielectric Response Model for Liquid Water: A Solution of the Bethe Ridge Problem , 2005, Radiation research.

[17]  S. Incerti,et al.  Geant4-DNA simulation of electron slowing-down spectra in liquid water , 2017 .

[18]  Dudley T. Goodhead,et al.  Cross-sections for water vapour for the Monte Carlo electron track structure code from 10 eV to the MeV region , 1993 .

[19]  Sébastien Incerti,et al.  Simulation of early DNA damage after the irradiation of a fibroblast cell nucleus using Geant4-DNA , 2017, Scientific Reports.

[20]  R. Nowotny.  Microdosimetry and its applications , 1997 .

[21]  D. Caruge,et al.  Recent Developments in Geant4 , 2014, ICS 2014.

[22]  Iwan Kawrakow,et al.  On the Monte Carlo simulation of electron transport in the sub-1 keV energy range. , 2011, Medical physics.

[23]  A. Ferrari,et al.  FLUKA: A Multi-Particle Transport Code , 2005 .

[24]  S. Incerti,et al.  Modeling proton and alpha elastic scattering in liquid water in Geant4-DNA , 2015 .

[25]  S. Incerti,et al.  Calculation of cellular S-values using Geant4-DNA: The effect of cell geometry. , 2015, Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine.

[26]  D. Emfietzoglou,et al.  Monte Carlo single-cell dosimetry of I-131, I-125 and I-123 for targeted radioimmunotherapy of B-cell lymphoma , 2012, International journal of radiation biology.

[27]  David Liljequist,et al.  Perspectives in radiation biophysics: From radiation track structure simulation to mechanistic models of DNA damage and repair , 2016 .

[28]  E. Bezak,et al.  Review of Geant4-DNA applications for micro and nanoscale simulations. , 2016, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[29]  Eva Forssell-Aronsson,et al.  Dosimetric characterization of radionuclides for systemic tumor therapy: influence of particle range, photon emission, and subcellular distribution. , 2006, Medical physics.

[30]  D. E. Wessol,et al.  Monte Carlo treatment planning for molecular targeted radiotherapy within the MINERVA system , 2004, Physics in medicine and biology.

[31]  S. Incerti,et al.  Simulation of Auger electron emission from nanometer-size gold targets using the Geant4 Monte Carlo simulation toolkit , 2016 .

[32]  B. Lind,et al.  Limitations (and merits) of PENELOPE as a track-structure code , 2012, International journal of radiation biology.

[33]  L. Sanche,et al.  Cross Sections for Low-Energy (1–100 eV) Electron Elastic and Inelastic Scattering in Amorphous Ice , 2003, Radiation research.

[34]  L. Toburen,et al.  Development of a Monte Carlo track structure code for low-energy protons in water , 2001, International journal of radiation biology.

[35]  Hooshang Nikjoo,et al.  The Non-homologous End-Joining (NHEJ) Mathematical Model for the Repair of Double-Strand Breaks: II. Application to Damage Induced by Ultrasoft X Rays and Low-Energy Electrons , 2013, Radiation research.

[36]  L. Quintieri,et al.  PIXE Simulation With Geant4 , 2009, IEEE Transactions on Nuclear Science.

[37]  S. Incerti,et al.  Geant4 developments and applications , 2006, IEEE Transactions on Nuclear Science.

[38]  T. Budinger,et al.  MIRD cellular S. values : self-absorbed dose per unit cumulated activity for selected radionuclides and monoenergetic electron and alpha particle emitters incorporated into different cell compartments , 1997 .

[39]  B. Faddegon,et al.  Description and dosimetric verification of the PEREGRINE Monte Carlo dose calculation system for photon beams incident on a water phantom. , 2001, Medical physics.

[40]  Herwig G. Paretzke,et al.  Electron inelastic-scattering cross sections in liquid water , 1999 .

[41]  W. Friedland,et al.  Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping , 2017, Scientific Reports.

[42]  T Liamsuwan,et al.  Radiation track, DNA damage and response—a review , 2016, Reports on progress in physics. Physical Society.

[43]  R. H. Ritchie,et al.  Comparisons of Calculations with PARTRAC and NOREC: Transport of Electrons in Liquid Water , 2008, Radiation research.

[44]  D. Emfietzoglou,et al.  Inelastic Cross Sections for Low-Energy Electrons in Liquid Water: Exchange and Correlation Effects , 2013, Radiation research.

[45]  Issam El Naqa,et al.  Monte Carlo role in radiobiological modelling of radiotherapy outcomes , 2012, Physics in medicine and biology.

[46]  S. Incerti,et al.  Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA. , 2016, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[47]  J. Fernández-Varea,et al.  A relativistic optical-data model for inelastic scattering of electrons and positrons in condensed matter , 2005 .

[48]  A. Beaudré,et al.  Simulation of Space and Time Evolution of Radiolytic Species Induced by Electrons in Water , 1990 .

[49]  V. Ivanchenko,et al.  Diffusion-controlled reactions modeling in Geant4-DNA , 2014, J. Comput. Phys..

[50]  Anatoly B. Rosenfeld,et al.  An electron-impact cross section data set (10 eV–1 keV) of DNA constituents based on consistent experimental data: A requisite for Monte Carlo simulations , 2017 .

[51]  R. T. Newman,et al.  Applied Radiation and Isotopes , 2008 .

[52]  A. Dell'Acqua,et al.  Geant4 - A simulation toolkit , 2003 .

[53]  C Villagrasa,et al.  Comparison of GEANT4 very low energy cross section models with experimental data in water. , 2010, Medical physics.

[54]  R. A. Forster,et al.  Initial MCNP6 Release Overview - MCNP6 version 1.0 , 2013 .

[55]  Ziad Francis,et al.  Stopping power and ranges of electrons, protons and alpha particles in liquid water using the Geant4-DNA package , 2011 .

[56]  T. Liamsuwan,et al.  Microdosimetry of low-energy electrons , 2012, International journal of radiation biology.

[57]  Rudd,et al.  Binary-encounter-dipole model for electron-impact ionization. , 1994, Physical review. A, Atomic, molecular, and optical physics.

[58]  J. Baró,et al.  PENELOPE: An algorithm for Monte Carlo simulation of the penetration and energy loss of electrons and positrons in matter , 1995 .

[59]  M. E. Rudd,et al.  Secondary electron spectra from charged particle interactions , 1996 .

[60]  Sébastien Incerti,et al.  Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry. , 2018, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[61]  S. Incerti,et al.  A free-parameter theoretical model for describing the electron elastic scattering in water in the Geant4 toolkit , 2009 .

[62]  D. Emfietzoglou,et al.  Inelastic scattering of low-energy electrons in liquid water computed from optical-data models of the Bethe surface , 2012, International journal of radiation biology.

[63]  V A Semenenko,et al.  NOREC, a Monte Carlo code for simulating electron tracks in liquid water , 2003, Radiation and environmental biophysics.

[64]  Michael Dingfelder,et al.  Updated model for dielectric response function of liquid water. , 2014, Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine.

[65]  L Maigne,et al.  Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. , 2015, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[66]  Oleg N Vassiliev,et al.  Electron slowing-down spectra in water for electron and photon sources calculated with the Geant4-DNA code , 2012, Physics in medicine and biology.

[67]  Peter Jacob,et al.  Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. , 2011, Mutation research.

[68]  S. Incerti,et al.  Coupling of Geant4-DNA physics models into the GATE Monte Carlo platform: Evaluation of radiation-induced damage for clinical and preclinical radiation therapy beams , 2015 .

[69]  N. Hiraoka,et al.  Accurate Measurements of Dielectric and Optical Functions of Liquid Water and Liquid Benzene in the VUV Region (1-100 eV) Using Small-Angle Inelastic X-ray Scattering. , 2015, The journal of physical chemistry. B.

[70]  C. E. Melton.  Cross Sections and Interpretation of Dissociative Attachment Reactions Producing OH−, O−, and H− in H2O , 1972 .

[71]  David Liljequist,et al.  On the validity of trajectory methods for calculating the transport of very low energy (<1 keV) electrons in liquids and amorphous media , 2014 .

[72]  S. Incerti,et al.  The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water , 2016 .

[73]  S. Incerti,et al.  Low-energy electron dose-point kernel simulations using new physics models implemented in Geant4-DNA , 2017 .

[74]  J A Gersh,et al.  Heavy ion track structure simulations in liquid water at relativistic energies. , 2006, Radiation protection dosimetry.

[75]  Hooshang Nikjoo,et al.  The Effect of Model Approximations on Single-Collision Distributions of Low-Energy Electrons in Liquid Water , 2005, Radiation research.

[76]  Harald Paganetti,et al.  Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. , 2017, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[77]  D. Emfietzoglou,et al.  Inelastic mean free path of low‐energy electrons in condensed media: beyond the standard models , 2017 .

[78]  D. Emfietzoglou,et al.  The effect of static many-body local-field corrections to inelastic electron scattering in condensed media , 2013 .

[79]  R. A. Forster,et al.  MCNP - a general Monte Carlo code for neutron and photon transport , 1985 .

[80]  Ianik Plante,et al.  Cross sections for the interactions of 1 eV–100 MeV electrons in liquid water and application to Monte-Carlo simulation of HZE radiation tracks , 2009 .

[81]  Sébastien Incerti,et al.  The Geant4-DNA Project , 2010, Int. J. Model. Simul. Sci. Comput..

[82]  S. M. Seltzer,et al.  Key Data for Ionizing-Radiation Dosimetry: Measurement Standards and Applications , 2014, Journal of the ICRU.

[83]  S. Incerti,et al.  Monte Carlo simulation of energy-deposit clustering for ions of the same LET in liquid water , 2012, Physics in medicine and biology.

[84]  S. Incerti,et al.  Technical Note: Improvements in geant4 energy-loss model and the effect on low-energy electron transport in liquid water. , 2015, Medical physics.

[85]  J. H. Hubbell,et al.  EPDL97: the evaluated photo data library `97 version , 1997 .

[86]  M. A. Cortés-Giraldo,et al.  Progress in Geant4 Electromagnetic Physics Modelling and Validation , 2015 .

[87]  C. Champion,et al.  Electron and positron elastic scattering in gaseous and liquid water: A comparative study , 2008 .

[88]  P. Barberet,et al.  Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes , 2014 .

[89]  H. Nikjoo,et al.  Repair of the double-strand breaks induced by low energy electrons: A modelling approach , 2012, International journal of radiation biology.

[90]  Fons Rademakers,et al.  ROOT — An object oriented data analysis framework , 1997 .

[91]  D. Combecher.  Measurement of W Values of Low-Energy Electrons in Several Gases , 1980 .

[92]  Susanna Guatelli,et al.  Microdosimetry of electrons in liquid water using the low-energy models of Geant4 , 2017 .

[93]  S. Incerti,et al.  Mechanistic DNA damage simulations in Geant4-DNA Part 2: Electron and proton damage in a bacterial cell. , 2018, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[94]  Peter Jacob,et al.  Simulation of DNA Damage after Proton Irradiation , 2003, Radiation research.