Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA.

A new alternative set of elastic and inelastic cross sections has been added to the very low energy extension of the Geant4 Monte Carlo simulation toolkit, Geant4-DNA, for the simulation of electron interactions in liquid water. These cross sections have been obtained from the CPA100 Monte Carlo track structure code, which has been a reference in the microdosimetry community for many years. They are compared to the default Geant4-DNA cross sections and show better agreement with published data. In order to verify the correct implementation of the CPA100 cross section models in Geant4-DNA, simulations of the number of interactions and ranges were performed using Geant4-DNA with this new set of models, and the results were compared with corresponding results from the original CPA100 code. Good agreement is observed between the implementations, with relative differences lower than 1% regardless of the incident electron energy. Useful quantities related to the deposited energy at the scale of the cell or the organ of interest for internal dosimetry, like dose point kernels, are also calculated using these new physics models. They are compared with results obtained using the well-known Penelope Monte Carlo code.

Pitfalls and modelling inconsistencies in computational radiation dosimetry: lessons learnt from the QUADOS intercomparison. Part I: Neutrons and uncertainties.

The QUADOS EU cost shared action conducted an intercomparison on the usage of numerical methods in radiation protection and dosimetry. The eight problems proposed were intended to test the usage of Monte Carlo and deterministic methods by assessing the accuracy with which the codes are applied and also the methods used to evaluate uncertainty in the answer gained through these methods. The overall objective was to spread good practice through the community and give users information on how to assess the uncertainties associated with their calculated results.

Computer simulation of 57Fe bleomycin auger effects in DNA.

The antibiotic bleomycin binds to the DNA and induces double strand breaks (DSBs). To increase the cleavages. 57Fe is used to form a complex suitable for Mössbauer effect. The de-excitation of the resonant excited 57Fe nucleus releases Auger electrons and X rays. The goal of this work is to evaluate the increase in yield of DSBs due to the 57Fe, using Monte Carlo simulation methods. Particles spectra and the yields of single strand breaks (SSBs) and DSBs were calculated by considering direct events on DNA and reaction of all radical species generated in the radiolysis of its environment. The Auger spectrum shows a large number of electrons with energies below 100 eV, mainly responsible for direct damage, while another group around 600-700 eV is responsible for indirect damage effects. Bleomycin receives about one fourth of the energy deposited in DNA and an average of 0.65 DSB per de-excitation is observed.

A method for radioprobing DNA structures using Auger electrons.

PURPOSE: To present a new method for radioprobing a DNA triple helix structure by Auger electrons emitted in the decay of 125I using theoretical/computational approaches. MATERIALS AND METHODS: A Monte Carlo track structure method was used to simulate the damage to a triplex resulting from Auger electrons emitted in the decay of an incorporated 125I atom in plasmid DNA. Comparison of the theoretical frequency distributions of single-strand breaks induced on the Pu and Py strands with the experimental data and a knowledge of the distances from the strand breaks to the iodine provide information on the structures otherwise difficult to obtain with X-ray crystallography. RESULTS: In comparing theoretical frequency distributions of single-strand breaks with the experimental data it is found that the results are very sensitive to the conformation of the triplex model used. It is found that the best fit to the experimental data results from using a hybrid triplex model, in which the base-step geometry is A-like, while the sugar puckers adopt the B-like C2'-endo conformation. CONCLUSIONS: The approach and technique presented here represent a valuable new addition to the methods available for DNA structure determination since they provide information on medium-range structure otherwize difficult to obtain in the absence of X-ray crystallography. It is concluded that currently accepted models for triplex structure are not optimal, and a modified structure is proposed that fits the radioprobing results better, while maintaining agreement with the fibre diffraction and NMR data. Although the method has proved to be very useful for scoring alternative trial solutions, further studies combining experimental data from multiple iodine positions with track structure modelling are required for directing structural optimization.

Quantitative modelling of DNA damage using Monte Carlo track structure method.

This paper presents data on modelling of DNA damage induced by electrons, protons and alpha-particles to provide an insight into factors which determine the biological effectiveness of radiations of high and low linear energy transfer (LET). These data include the yield of single- and double-strand breaks (ssb, dsb) and base damage in a cellular environment. We obtain a ratio of 4-15 for ssb:dsb for solid and cellular DNA and a preliminary ratio of about 2 for base damage to strand breakage. Data are also given on specific characteristics of damage at the DNA level in the form of clustered damage of varying complexity, that challenge the repair processes and if not processed adequately could lead to the observed biological effects. It is shown that nearly 30% of dsb are of complex form for low-LET radiation, solely by virtue of additional breaks, rising to about 70% for high-LET radiation. Inclusion of base damage increases the complex proportion to about 60% and 90% for low- and high-LET radiation, respectively. The data show a twofold increase in frequencies of complex dsb from low-LET radiation when base damage is taken into account. It is shown that most ssb induced by high-LET radiation have associated base damages, and also a substantial proportion is induced by low-energy electrons.

Modelling of Auger-induced DNA damage by incorporated 125I.

We have analyzed a newly available high resolution and precision repeat of the original Martin and Haseltine experiment which includes the influence of DMSO on the results. The new model includes the production and diffusion of radical species and .OH radical attack on DNA as well as the direct hits. Calculations of single-strand breaks use individual Auger electron along with the tracks of electrons and radical species superimposed on an atomistic model of B-DNA. Comparison of the preliminary calculations with the experiment supports the earlier choice of data for the amount of energy required to produce a single-strand break, i.e. 17.5 eV. In a separate simulation we found that an average of less than two ionizations inducing a single-strand break gave the best fit to experimental data. Direct hits were found to be predominantly occurring at short range while the damage by .OH radicals was mainly of the long-range type.

Modelling of radiation damage by 125I on a nucleosome.

Studies of early physical interactions of ionizing radiation in biological medium have evolved from water cylinders or spheres to structured volumes representing nucleosomal DNA, based on spatial co-ordinates for each individual atom. Regarding the physico-chemical and chemical stages, the models of DNA have evolved from inactive geometrical objects to active participation of DNA in the reactions with the radical species. In this paper data are presented on the modelling of the interaction of low energy electrons with nucleosomal DNA. The nucleosome core unit has been modelled as a 146-bp helical DNA, containing > 9000 atoms, wound around the core unit. The yields of strand breaks for low energy electrons has been obtained by placing the nucleosome target in a liquid water environment and introducing a number of assumptions for the induction of strand breaks. The calculated results for the induction of ssb and dsb by 125I decays agree with experimental data, confirming the plausibility of this nucleosome model as well as the characterization of the interaction of ionizing radiation in terms of the energy deposition and the assumptions made for the strand breaks.

Modelling of radiation-induced DNA damage: the early physical and chemical event.

A Monte Carlo track structure calculation of single- and double-strand breaks induced by direct energy deposition in DNA and by interacting diffusible .OH radicals with DNA has been made for low energy electrons. The .OH radicals generated within 4 nm of linear segments of DNA were diffused in order to mimic the mean diffusion distance in the cellular environment. The reactions of the radical species .OH, .H and e-aq were included in this study. The calculated values for the yield of single- and double-strand breaks have been compared with experimentally determined values from the literature. The calculations indicate, too, that the majority of dsb have additional associated damage, constituting clustered lesions of varying complexity.

A nucleosome model for the simulation of DNA strand break experiments.

Using a set of Monte Carlo simulation models, track structures of 125I Auger electrons generated in liquid water are superimposed on a nucleosome DNA model able to precisely localize energy deposition events on sub-molecular units of the DNA strands. After scoring direct hits taking place during the physical phase (at about 10(-15) s) the radiation chemistry of the whole system is simulated between 10(-12) and 10(-8) s, taking into account all reactions between water radio-chemical species, radicals, sub-molecular units of DNA (Ribose, Adenine, Thymine, Guanine, and Cytosine), and scavengers like Tris or Formate ions. The model's possibility to distinguish between direct and indirect hits has been utilized to introduce different assumptions for strand break induction by both hit modes. The number of SSB and DSB as well as their local distribution will be given and compared with experimental and theoretical results from the literature.