Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC.

This review describes the PARTRAC suite of comprehensive Monte Carlo simulation tools for calculations of track structures of a variety of ionizing radiation qualities and their biological effects. A multi-scale target model characterizes essential structures of the whole genomic DNA within human fibroblasts and lymphocytes in atomic resolution. Calculation methods and essential results are recapitulated regarding the physical, physico-chemical and chemical stage of track structure development of radiation damage induction. Recent model extension towards DNA repair processes extends the time dimension by about 12 orders of magnitude and paves the way for superior predictions of radiation risks.

[1]  K. Prise,et al.  Quantification of DNA damage by PFGE: development of an analytical approach to correct for the background distribution. , 2000, International journal of radiation biology.

[2]  H. Paretzke,et al.  Monte Carlo simulation of the production of short DNA fragments by low-linear energy transfer radiation using higher-order DNA models. , 1998, Radiation research.

[3]  J. Little,et al.  Induction of sister chromatid exchanges by extremely low doses of alpha-particles. , 1992, Cancer research.

[4]  Richard M. Noyes,et al.  Effects of diffusion rates on chemical kinetics , 1961 .

[5]  R. Stewart,et al.  On the biophysical interpretation of lethal DNA lesions induced by ionising radiation. , 2005, Radiation protection dosimetry.

[6]  Ioanna Tzoulaki,et al.  A Model of Cardiovascular Disease Giving a Plausible Mechanism for the Effect of Fractionated Low-Dose Ionizing Radiation Exposure , 2009, PLoS Comput. Biol..

[7]  R. Stewart,et al.  Monte Carlo simulation of DNA damage induction by x-rays and selected radioisotopes , 2008, Physics in medicine and biology.

[8]  Jan Christian Kaiser,et al.  Possible expressions of radiation-induced genomic instability, bystander effects or low-dose hypersensitivity in cancer epidemiology. , 2010, Mutation research.

[9]  M. Löbrich,et al.  Spatial Distribution and Yield of DNA Double-Strand Breaks Induced by 3–7 MeV Helium Ions in Human Fibroblasts , 2002, Radiation research.

[10]  P. Kundrát.  Detailed analysis of the cell-inactivation mechanism by accelerated protons and light ions , 2005, Physics in medicine and biology.

[11]  A. M. Stoneham.  Kinetics of Nonhomogeneous Processes: Ed. G.R. Freeman (John Wiley and Sons, New York, Chichester, 1987); Price: -P95.50 , 1987 .

[12]  P O'Neill,et al.  Computational Approach for Determining the Spectrum of DNA Damage Induced by Ionizing Radiation , 2001, Radiation research.

[13]  S. Ritter,et al.  Cell cycle arrest and aberration yield in normal human fibroblasts. I. Effects of X‐rays and 195 MeV u−1 C ions , 2004, International journal of radiation biology.

[14]  D. Goodhead.  Understanding and characterisation of the risks to human health from exposure to low levels of radiation. , 2009, Radiation protection dosimetry.

[15]  S. Pimblott,et al.  Hydrated electron yields in the heavy ion radiolysis of water. , 2005, The journal of physical chemistry. A.

[16]  C Cremer,et al.  Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code. , 2004, Biophysical journal.

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

[18]  G. Barendsen.  RBE-LET relationships for different types of lethal radiation damage in mammalian cells: comparison with DNA dsb and an interpretation of differences in radiosensitivity. , 1994, International journal of radiation biology.

[19]  M. Ljungman,et al.  DNA-bound proteins contribute much more than soluble intracellular compounds to the intrinsic protection against radiation-induced DNA strand breaks in human cells. , 1991, Radiation research.

[20]  K. Hieda,et al.  DNA damage induced by vacuum and soft X-ray photons from synchrotron radiation. , 1994, International journal of radiation biology.

[21]  D. Goodhead,et al.  Modelling of radiation-induced DNA damage: the early physical and chemical event. , 1994, International journal of radiation biology.

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

[23]  H. Paretzke,et al.  Simulation of light ion induced DNA damage patterns. , 2006, Radiation protection dosimetry.

[24]  P. Schopfer,et al.  Effects of Ionising Radiation , 1995 .

[25]  M G Stabin,et al.  Monte Carlo simulation of diffusion and reaction in water radiolysis – a study of reactant `jump through' and jump distances , 1998, Radiation and environmental biophysics.

[26]  W Friedland,et al.  Simulation of DNA fragment distributions after irradiation with photons , 1999, Radiation and environmental biophysics.

[27]  K M Prise,et al.  Critical energies for SSB and DSB induction in plasmid DNA by low-energy photons: action spectra for strand-break induction in plasmid DNA irradiated in vacuum. , 2000, International journal of radiation biology.

[28]  Burkhard Jakob,et al.  Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks , 2007, The Journal of cell biology.

[29]  G. Iliakis,et al.  Extensive Repair of DNA Double-Strand Breaks in Cells Deficient in the DNA-PK-Dependent Pathway of NHEJ after Exclusion of Heat-Labile Sites , 2009, Radiation research.

[30]  J F Ziegler,et al.  Comments on ICRU report no. 49: stopping powers and ranges for protons and alpha particles. , 1999, Radiation research.

[31]  C. Kao,et al.  The complete optical spectrum of liquid water measured by inelastic x-ray scattering. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A. Kuzin.  On the role of DNA in the radiation damage of the cell. , 1963, International Journal of Radiation Biology and Related Studies in Physics Chemistry and Medicine.

[33]  H. Paretzke,et al.  Time- and space-resolved Monte Carlo study of water radiolysis for photon, electron and ion irradiation , 2009, Radiation and environmental biophysics.

[34]  V. Ramakrishnan,et al.  Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[35]  L. Toburen,et al.  Electron Emission from Foils and Biological Materials after Proton Impact. , 2008, Radiation physics and chemistry.

[36]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[37]  M. Dingfelder.  Cross section calculations in condensed media: charged particles in liquid water. , 2002, Radiation protection dosimetry.

[38]  V. Semenenko,et al.  Fast Monte Carlo simulation of DNA damage formed by electrons and light ions , 2006, Physics in medicine and biology.

[39]  P. Hahnfeldt,et al.  A Robust Procedure for Removing Background Damage in Assays of Radiation-Induced DNA Fragment Distributions , 2006, Radiation research.

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

[41]  M. Hill,et al.  Dependence of the Yield of DNA Double-Strand Breaks in Chinese Hamster V79-4 Cells on the Photon Energy of Ultrasoft X Rays , 2001, Radiation research.

[42]  H. Eisenberg,et al.  Nucleosome core particle structure and structural changes in solution. , 1985, Journal of molecular biology.

[43]  D. Goodhead,et al.  Effects of Radiations of Different Qualities on Cells: Molecular Mechanisms of Damage and Repair , 1993 .

[44]  F Ballarini,et al.  Modelling study on the protective role of OH radical scavengers and DNA higher‐order structures in induction of single‐ and double‐strand break by gamma‐radiation , 2003, International journal of radiation biology.

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

[46]  M. Terrissol.  Modelling of radiation damage by 125I on a nucleosome. , 1994, International journal of radiation biology.

[47]  Monte Carlo simulation of DNA strand breaks induced by monoenergetic electrons using higher-order structure models of DNA. , 1994, International journal of radiation biology.

[48]  H. Paretzke,et al.  Energy deposition in small cylindrical targets by monoenergetic electrons. , 1991, International journal of radiation biology.

[49]  J. Jay-Gerin,et al.  Low-Energy Electron Penetration Range in Liquid Water , 2002, Radiation research.

[50]  J. Sempau,et al.  PENELOPE-2006: A Code System for Monte Carlo Simulation of Electron and Photon Transport , 2009 .

[51]  P. Cooper,et al.  Dose-Dependent Misrejoining of Radiation-Induced DNA Double-Strand Breaks in Human Fibroblasts: Experimental and Theoretical Study for High- and Low-LET Radiation , 2004, Radiation research.

[52]  B. Stenerlöw,et al.  Induction and Rejoining of DNA Double-Strand Breaks in Normal Human Skin Fibroblasts after Exposure to Radiation of Different Linear Energy Transfer: Possible Roles of Track Structure and Chromatin Organization , 2001, Radiation research.

[53]  J. Thacker,et al.  Mutation and inactivation of cultured mammalian cells exposed to beams of accelerated heavy ions. II. Chinese hamster V79 cells. , 1979, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[54]  R Eils,et al.  Compartmentalization of interphase chromosomes observed in simulation and experiment. , 1999, Journal of molecular biology.

[55]  B. Stenerlöw,et al.  Rejoining of DNA fragments produced by radiations of different linear energy transfer. , 2000, International journal of radiation biology.

[56]  Herman Yagoda,et al.  Nuclear Research Emulsions , 1964 .

[57]  I. Petsalakis,et al.  Semi-empirical dielectric descriptions of the Bethe surface of the valence bands of condensed water , 2008 .

[58]  E Pomplun,et al.  A new DNA target model for track structure calculations and its first application to I-125 Auger electrons. , 1991, International journal of radiation biology.

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

[60]  B. Rydberg,et al.  Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. II. Experimental detection. , 1996, Radiation research.

[61]  D. T. Goodhead,et al.  Quantitative modelling of DNA damage using Monte Carlo track structure method , 1999, Radiation and environmental biophysics.

[62]  B. Stevens,et al.  Progress in reaction kinetics , 1961 .

[63]  M. Suzuki,et al.  LET and Ion Species Dependence for Cell Killing in Normal Human Skin Fibroblasts , 2005, Radiation research.

[64]  K. Baverstock.  Why do we need a new paradigm in radiobiology? , 2010, Mutation research.

[65]  I. Mian,et al.  Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber. , 1998, Journal of molecular biology.

[66]  R. H. Ritchie,et al.  Spatial distributions of inelastic events produced by electrons in gaseous and liquid water. , 1991, Radiation research.

[67]  R. Cox,et al.  Mutation and inactivation of cultured mammalian cells exposed to beams of accelerated heavy ions. III. Human diploid fibroblasts. , 1979, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[68]  M. Löbrich,et al.  Non-random distribution of DNA double-strand breaks induced by particle irradiation. , 1996, International journal of radiation biology.

[69]  H. Paretzke,et al.  Interaction of ion tracks in spatial and temporal proximity , 2009, Radiation and environmental biophysics.

[70]  Aloke Chatterjee,et al.  Clusters of DNA Damage Induced by Ionizing Radiation: Formation of Short DNA Fragments. I. Theoretical Modeling , 1996 .

[71]  D. Hunting,et al.  Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. , 2000, Science.

[72]  H Nikjoo,et al.  Calculation of initial yields of single- and double-strand breaks in cell nuclei from electrons, protons and alpha particles. , 1989, International journal of radiation biology.

[73]  H. Paretzke,et al.  Modeling of ultrasoft X-ray induced DNA damage using structured higher order DNA targets , 2003 .

[74]  K M Prise,et al.  A review of dsb induction data for varying quality radiations. , 1998, International journal of radiation biology.

[75]  V Michalik,et al.  Computer-aided stochastic modeling of the radiolysis of liquid water. , 1998, Radiation research.

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

[77]  Wei Bo Li,et al.  Track Structures and Dose Distributions from Decays of 131I and 125I in and around Water Spheres Simulating Micrometastases of Differentiated Thyroid Cancer , 2001, Radiation research.

[78]  M. Ljungman,et al.  Chromatin structure and radiation-induced DNA strand breaks in human cells: soluble scavengers and DNA-bound proteins offer a better protection against single- than double-strand breaks. , 1995, International journal of radiation biology.

[79]  D T Goodhead,et al.  Energy deposition in small cylindrical targets by ultrasoft x-rays. , 1989, Physics in medicine and biology.

[80]  D T Goodhead,et al.  Initial events in the cellular effects of ionizing radiations: clustered damage in DNA. , 1994, International journal of radiation biology.

[81]  R. Mortimer,et al.  A quantitative model of DNA fragments generated by ionizing radiation, and possible experimental applications. , 1991, Radiation research.

[82]  P. Hahnfeldt,et al.  Subtraction of background damage in PFGE experiments on DNA fragment-size distributions , 2007, Radiation and environmental biophysics.

[83]  G. Buxton,et al.  Critical Review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals (⋅OH/⋅O− in Aqueous Solution , 1988 .

[84]  L Kissel,et al.  EPDL97 The Evaluated Data Library, '97 Version , 1997 .

[85]  C.K.C. Wang,et al.  The progress of radiobiological models in modern radiotherapy with emphasis on the uncertainty issue. , 2010, Mutation research.

[86]  A. Campa,et al.  Modeling of DNA fragmentation induced in human fibroblasts by 56Fe ions , 2007 .

[87]  D. T. Goodhead,et al.  Microdosimetry: An interdisciplinary approach , 1997 .

[88]  H. Paretzke,et al.  Calculation of electron impact ionization cross sections of DNA using the Deutsch–Märk and Binary–Encounter–Bethe formalisms , 2003 .

[89]  W Friedland,et al.  Mechanistic simulation of radiation damage to DNA and its repair: on the track towards systems radiation biology modelling. , 2011, Radiation protection dosimetry.

[90]  R K Sachs,et al.  Locations of radiation-produced DNA double strand breaks along chromosomes: a stochastic cluster process formalism. , 1999, Mathematical biosciences.

[91]  G. Moschini,et al.  DNA fragmentation in mammalian cells exposed to various light ions. , 2001, Advances in space research : the official journal of the Committee on Space Research.

[92]  A. Campa,et al.  DNA Fragmentation Induced in Human Fibroblasts by 56Fe Ions: Experimental Data and Monte Carlo Simulations , 2009, Radiation research.

[93]  M. Durante,et al.  Live cell microscopy analysis of radiation-induced DNA double-strand break motion , 2009, Proceedings of the National Academy of Sciences.

[94]  E. Höglund.  DNA fragmentation in cultured cells exposed to high linear energy transfer , 2000 .

[95]  Herwig G. Paretzke,et al.  Inelastic-collision cross sections of liquid water for interactions of energetic protons , 2000 .

[96]  M. Terrissol,et al.  Low-energy electrons inside active DNA models: A tool to elucidate the radiation action mechanisms , 1994, Radiation and environmental biophysics.

[97]  K. Prise,et al.  DNA double-strand break distributions in X-ray and alpha-particle irradiated V79 cells: evidence for non-random breakage. , 1997, International journal of radiation biology.

[98]  D. Charlton,et al.  A method of calculating initial DNA strand breakage following the decay of incorporated 125I. , 1988, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[99]  P O'Neill,et al.  Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events. , 1997, International journal of radiation biology.

[100]  A. Campa,et al.  DNA DSB induced in human cells by charged particles and gamma rays: Experimental results and theoretical approaches , 2005, International journal of radiation biology.

[101]  David J. Chen,et al.  Repair of HZE-Particle-Induced DNA Double-Strand Breaks in Normal Human Fibroblasts , 2008, Radiation research.

[102]  H. Paretzke,et al.  First steps towards systems radiation biology studies concerned with DNA and chromosome structure within living cells , 2008, Radiation and environmental biophysics.

[103]  Peter Jacob,et al.  Stochastic Simulation of DNA Double-Strand Break Repair by Non-homologous End Joining Based on Track Structure Calculations , 2010, Radiation research.

[104]  S. L. McLawhorn,et al.  Electron Emission from Amorphous Solid Water Induced by Passage of Energetic Protons and Fluorine Ions , 2010, Radiation research.

[105]  A. Kellerer,et al.  Concepts of microdosimetry , 1975, Radiation and environmental biophysics.

[106]  Michael Scholz,et al.  Biophysical models in ion beam radiotherapy , 2007 .

[107]  D. T. Goodhead,et al.  Transmission of chromosomal instability after plutonium α-particle irradiation , 1992, Nature.

[108]  K. Prise,et al.  The relationship between radiation-induced DNA double-strand breaks and cell kill in hamster V79 fibroblasts irradiated with 250 kVp X-rays, 2.3 MeV neutrons or 238Pu alpha-particles. , 1987, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[109]  A. Campa,et al.  DNA fragmentation in V79 cells irradiated with light ions as measured by pulsed‐field gel electrophoresis. II. Simulation with a generalized broken stick model , 2004, International journal of radiation biology.

[110]  E. Bothe,et al.  Single- and double-strand break formation in DNA irradiated in aqueous solution: dependence on dose and OH radical scavenger concentration. , 1987, Radiation research.

[111]  P. O'Neill,et al.  A Sting in the Tail of Electron Tracks , 2000, Science.

[112]  D T Goodhead,et al.  Monte Carlo track structure studies of energy deposition and calculation of initial DSB and RBE. , 1994, Advances in space research : the official journal of the Committee on Space Research.

[113]  H. Paretzke,et al.  Calculated DNA double-strand break and fragmentation yields after irradiation with He ions , 2005 .

[114]  Peter Jacob,et al.  Stochastic modelling of DSB repair after photon and ion irradiation , 2012, International journal of radiation biology.

[115]  W. Friedland,et al.  Modelling of intercellular induction of apoptosis in oncogenic transformed cells and radiation effects on the phenomenon. , 2011, Radiation protection dosimetry.

[116]  Yunmei Ma,et al.  Mechanism and regulation of human non-homologous DNA end-joining , 2003, Nature Reviews Molecular Cell Biology.

[117]  H. J. Brede,et al.  Induction of DNA double-strand breaks by 1H and 4He lons in primary human skin fibroblasts in the LET range of 8 to 124 keV/microm. , 1999, Radiation research.

[118]  I. Radford.  Evidence for a general relationship between the induced level of DNA double-strand breakage and cell-killing after X-irradiation of mammalian cells. , 1986, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[119]  B. Stenerlöw,et al.  Repair of Radiation-Induced Heat-Labile Sites is Independent of DNA-PKcs, XRCC1 and PARP , 2008, Radiation research.

[120]  A. Ottolenghi,et al.  Effects of Ionizing Radiation on Cell-to-Cell Communication , 2010, Radiation research.

[121]  A. Campa,et al.  A Monte Carlo Study of the Radiation Quality Dependence of DNA Fragmentation Spectra , 2010, Radiation research.

[122]  K. H. Chadwick,et al.  Biophysical modelling of radiation effects , 1992 .

[123]  Simon Bouffler,et al.  Assessing cancer risks of low-dose radiation , 2009, Nature Reviews Cancer.

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

[125]  H. Rossi.  INTERPRETATION OF BIOLOGICAL RESPONSE IN TERMS OF MICRODOSIMETRY * , 1969, Annals of the New York Academy of Sciences.

[126]  R. N. Hamm,et al.  Collective oscillation in liquid water , 1974 .

[127]  F Ballarini,et al.  Stochastic aspects and uncertainties in the prechemical and chemical stages of electron tracks in liquid water: a quantitative analysis based on Monte Carlo simulations , 2000, Radiation and environmental biophysics.

[128]  M. Sevilla,et al.  Radiation-induced DNA damage as a function of hydration. I. Release of unaltered bases. , 1992, Radiation research.

[129]  S. P. Williams,et al.  Small angle x-ray scattering of chromatin. Radius and mass per unit length depend on linker length. , 1991, Biophysical journal.

[130]  Yunmei Ma,et al.  Analysis of the kinetic and equilibrium binding of Ku protein to DNA. , 2002, Journal of theoretical biology.