Comparison and assessment of electron cross sections for Monte Carlo track structure codes.

The purpose of this study was to make an intercomparison and assessment of cross sections for electrons in water used in electron track structure codes. This study is intended to shed light on the extent to which the differences between the input data and physical and chemical assumptions influence the outcome in biophysical modeling of radiation effects. Ionization cross sections and spectra of secondary electrons were calculated by various theories. The analyses were carried out for water vapor cross sections, as these are more abundant and readily available. All suitable published experimental total ionization cross sections were fitted by an appropriate function and used for generation of electron tracks. Three sets of compiled data were used for comparison of total excitation cross sections and mean excitation energy. The tracks generated by a Monte Carlo track code, using various combinations of cross sections, were compared in terms of radial distributions of interactions and point kernels. The spectrum of secondary electrons emitted by the ionization process was found to be the factor that has the most influence on these quantities. A different set of cross sections for excitation and elastic scattering did not affect the electron track structure as much as did ionization cross sections. It is concluded that all codes, using different cross sections and in different phase, currently used for biophysical modeling exhibit close similarities for energy deposition in larger size targets while appreciable differences are observed in B-DNA-size targets. We recommend fitted functions to all available suitable experimental data for the total ionization and elastic cross sections. We conclude that most codes produce tracks in reasonable agreement with the macroscopic quantities such as total stopping power and total yield of strand breaks. However, we predict differences in frequencies of clustering in tracks from the different models.     

A Monte Carlo code for the simulation of heavy-ion tracks in water

TILDA, a new Monte Carlo track structure code for ions in gaseous water that is valid for both high-LET (approximately 10(4) keV/microm) and low-LET ions, is presented. It is specially designed for a comparison of the patterns of energy deposited by a large range of ions. Low-LET ions are described in a perturbative frame, whereas heavy ions with a very high stopping power are treated using the Lindhard local density approximation and the Russek and Meli statistical method. Ionization cross sections singly differential with energy compare well with the experiment. As an illustration of the non-perturbative interaction of high-LET ions, a comparison between the ion tracks of light and heavy ions with the same specific energy is presented (1.4 MeV/nucleon helium and uranium ions). The mean energy for ejected electrons was found to be approximately four times larger for uranium than for helium, leading to a much larger track radius in the first case. For electrons, except for the excitation cross sections that are deduced from experimental fits, cross sections are derived analytically. For any orientation of the target molecule, the code calculates multiple differential cross sections as a function of the ejection and scattering angles and of the energy transfer. The corresponding singly differential and total ionization cross sections are in good agreement with experimental data. The angular distribution of secondary electrons is shown to depend strongly on the orientation of the water molecule.     

Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment

In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40–70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20–40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A–T.     

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.     

A track structure model for simulation of strand breaks in plasmid DNA after heavy ion irradiation

We present a track structure model based on the local dose deposited around heavy ion tracks to explain the cross sections for single-strand and double-strand break induction in plasmid DNA in different aqueous buffers. The model is based only on measurable quantities, namely the effect distribution for inducing strand breaks after x-ray irradiation as a function of dose, and the radial dose distribution of the heavy ion track. The effect of indirect DNA damage mediated by free radicals produced in the water surrounding the DNA is accounted for by allowing the radial dose distribution to be smeared in space by an effective target size corresponding to the squared sum of the geometrical extension of the plasmid molecule and the mean free drift path of the radicals in the buffer solution. Our calculations reproduce well the measured cross sections for single-strand and double-strand break induction in SV40 plasmid DNA in various buffer solutions both as a function of the LET and of the specific energy of the heavy ion.     

A new calculation on spectrum of direct DNA damage induced by low-energy electrons

In this work, direct DNA damage induced by low-energy electrons (<5 keV) is simulated using Monte Carlo methods, and the resulting yield of various strand breaks and base damages in cellular environment is presented. The simulation is based on a new inelastic cross section for the production of electron track structure in liquid water, and on ionization cross sections of DNA bases to generate base radical. Especially, a systematic approach of simulating detailed base damage is suggested. This approach includes improvement of a volume model of DNA, generation of the DNA base sequence, conversion of ionization events in liquid water at hit site to the ionization interaction of electrons with DNA bases and development of an algorithm to convert a base radical to a damage. The results obtained in terms of strand breaks are compared with those of experiments and other theoretical calculations, and good agreement was obtained. The yield of detailed base damages and clustered DNA damages caused by the combination of various strand breaks and base damages is presented, and the corresponding distribution characteristics are analyzed. The influence of the relative content of base pairs A-T and G-C in a DNA segment on the yield of both strand breaks and base damages is also explored. The present work provides fundamental information on DNA damage and represents the first effort toward the goal of obtaining the spectrum of clustered DNA damage including detailed base damages, for the mechanistic interpretation and prediction of radiation effects.     

Cross sections for low-energy (10-50 eV) electron damage to DNA

We report direct measurements of the formation of single-, double- and multiple strand breaks in pure plasmid DNA as a function of exposure to 10-50 eV electrons. The effective cross sections to produce these different types of DNA strand breaks were determined and were found to range from approximately 10(-17) to 3 x 10(-15) cm(2). The total effective cross section and the effective range for destruction of supercoiled DNA extend from 3.4 to 4.4 x 10(-15) cm(2) and 12 to 14 nm, respectively, over the range 10-50 eV. The variation of the effective cross sections with electron energy is discussed in terms of the electron's inelastic mean free path, penetration depth, and dissociation mechanisms, including resonant electron capture; the latter is found to dominate the effective cross sections for single- and double-strand breaks at 10 eV. The most striking observations are that (1) supercoiled DNA is approximately one order of magnitude more sensitive to the formation of double-strand breaks by low-energy electrons than is relaxed circular DNA, and (2) the dependence of the effective cross sections on the incident electron energy is unrelated to the corresponding ionization cross sections. This finding suggests that the traditional notion that radiobiological damage is related to the number of ionization events would not apply at very low energies.     

Electron temperature in nitrogen afterglow: Dependence of theoretical results on the adopted set of cross sections and on the type of molecular distribution over vibrational levels

The electron energy distribution function in nitrogen afterglow is simulated using different available sets of cross sections for electron scattering by vibrationally excited molecules. The calculations are performed for two types of molecular distribution over vibrational levels, namely, for the Boltzmann and Treanor-Gordiets distributions. It is shown that the calculated values of the electron temperature in nitrogen afterglow depend strongly on the set of cross sections used and on the type of molecular distribution over vibrational levels. The validity of comparison between theoretical and experimental results is discussed.     

Optical diffraction of the Z lattice in canine cardiac muscle

Optical diffraction patterns from electron micrographs of both longitudinal and cross sections of normal and anomalous canine cardiac Z bands have been compared. The data indicate that anomalous cardiac Z bands resembling nemaline rods are structurally related to Z bands in showing a repeating lattice common to both. In thin sections transverse to the myofibril axis, both electron micrographs and optical diffraction patterns of the Z structure reveal a square lattice of 24 nm. This lattice is simple at the edge of each I band and centered in the interior of the Z band, where two distinct lattice forms have been observed. In longitudinal sections, oblique filaments visible in the electron micrographs correspond to a 38-nm axial periodicity in diffraction patterns of both Z band and Z rod. We conclude that the Z rods will be useful for further analysis and reconstruction of the Z lattice by optical diffraction techniques.     

Root-soil contact of maize,as measured by a thin-section technique

In models of oxygen, water and nutrient uptake by plant roots, the degree of root-soil contact is an important parameter. An observation technique is required to evaluate to what extent root-soil contact depends on plant species, soil texture and structure. Thin sections for studying soil structure may be used for this purpose, provided that roots do not shrink during section preparation, and that all root cross sections are recognized.Maize was grown in pots with soil aggregates obtained by sieving and compacting to three bulk densities. Thin sections were made by freeze-drying samples before impregnating the soil with resin. Two checks were made on the validity of the method. Firstly, visual appearance of roots with intact epidermis, cortex and other tissues did not show signs of shrinkage. Secondly, the agreement was checked between root lengths obtained by washing duplicate soil samples and the number of root cross sections counted on horizonal and vertical thin sections. For the latter, the angle at which roots intersected the thin-section plane was determined from the shape of the cross sections. The frequency distribution of calculated angles was in agreement with the frequency distribution expected for a randomly oriented set of cylinders when an error term was included in the simulated measurements.Some results are presented for a field test of the thin-section method with barley on a calcareous marine sandy loam. Root hairs, apparently undamaged by sample preparation, are important for bridging the gap between roots and soil in this situation. According to the experience presented, the thin-section technique is suitable to derive the degree of root-soil contact, as influenced by species, soil texture and structure, in samples obtained from pot or field experiments.Communication No. 43 of the Dutch Programme on Soil Ecology of Arable Farming Systems.Communication No. 43 of the Dutch Programme on Soil Ecology of Arable Farming Systems.     

Cross sections for low-energy (1-100 eV) electron elastic and inelastic scattering in amorphous ice

We report the integral cross sections per scatterer (i.e. elastic collision, phonon excitations, vibrational excitations, electronic excitations and ionization) for 1-100 eV electron scattering in an amorphous film of ice condensed at a temperature of 14 K. The integral cross sections are determined relative to the total from a two-stream multiple-scattering analysis of the electron energy distribution backscattered from the film. Their energy dependence is obtained from both the analysis of the elastic electron reflectivity as a function of the film thickness and the vibrational electron energy-loss spectra measured for several incident energies and large film thickness. The magnitude and various features found in the energy dependence of the cross sections are discussed, whenever possible, by comparison with data and with scattering mechanisms available in the gas phase. Microcospic effects, which are implicitly included in cross sections determined in this way, are discussed in terms of interference and coherent multiple-scattering contributions among the scattering sites as well as interactions of the scattering sites with their neighbors in the condensed phase.     

Track structures and dose distributions from decays of (131)I and (125)I in and around water spheres simulating micrometastases of differentiated thyroid cancer

The disintegration of the radionuclides (131)I and (125)I and the subsequent charged-particle tracks left behind in water (as a model substance for a biological cell) are simulated by the Monte Carlo track structure simulation code PARTRAC, using new inelastic electron scattering cross sections for condensed water. Every photon and electron emitted was followed in detail, event by event, down to 10 eV. From the spatial information on the track structures, absorbed dose distributions per (131)I and (125)I decay were calculated in and around water spheres simulating micrometastases as well as in the tissue surrounding such metastases. These radionuclides were assumed to be distributed uniformly inside spheres of different diameters (0.01, 0.03, 0.1, 0.3, 1.0 and 3.0 mm). The respective electron degradation spectra, the nearest-neighbor distance distributions between inelastic events, and the distance distributions for all activations for both iodine radionuclides were calculated. The absorbed fractions of the initial electron energies, absorbed doses and energy depositions, and single-event distributions, F(1)(epsilon), inside the six water spheres described above and in the surrounding tissue were also calculated. The absorbed doses per decay inside the six water spheres, i.e., the calculated S values (listed from 0.01 to 3.0 mm), were 6.8 x 10(-4), 7.2 x 10(-5), 5.5 x 10(-6), 4.9 x 10(-7), 3.1 x 10(-8) and 1.8 x 10(-9) Gy Bq(-1) s(-1) for (131)I, and 3.4 x 10(-3), 1.7 x 10(-4), 5.1 x 10(-6), 2.0 x 10(-7), 5.6 x 10(-9) and 2.2 x 10(-10) Gy Bq(-1) s(-1) for (125)I. It is concluded that, in the treatment of thyroid cancer, the geometrical track structure properties of (125)I might be superior to those of (131)I in micrometastases with diameters less than 0.1 mm; however, in this medical context, many other factors also have to be considered.     

Monte Carlo transport of swift protons and light ions in water: The influence of excitation cross sections,relativistic effects,and Auger electron emission in w-values

PurposeTo develop a particle transport code to compute w-values and stopping power of swift ions in liquid water and gases of interest for reference dosimetry in hadrontherapy. To analyze the relevance of inelastic and post-collisional processes considered.MethodsThe Monte Carlo code MDM was extended to the case of swift ion impact on liquid water (MDM-Ion). Relativistic corrections in the inelastic cross sections and the post-collisional Auger emission were considered. The effects of introducing different electronic excitation cross sections were also studied.ResultsThe stopping power of swift ions on liquid water, calculated with MDM-Ion, are in excellent agreement with recommended data. The w-values show a strong dependence on the electronic excitation cross sections and on the Auger electron emission. Comparisons with other Monte Carlo codes show the relevance of both the processes considered and of the cross sections employed. W and w-values for swift electron, proton, and carbon ions calculated with the MDM and MDM-Ion codes are in very close agreement with each other and with the 20.8 eV experimental value.ConclusionWe found that w-values in liquid water are independent of ion charge and energy, as assumed in reference dosimetry for hadrontherapy from sparse experimental results for electron and ion impact on gases. Excitation cross sections and Auger emission included in Monte Carlo codes are critical in w-values calculations. The computation of this physical parameter should be used as a benchmark for micro-dosimetry investigations, to assess the reliability of the cross sections employed.     

Cross section calculations for electron scattering from DNA and RNA bases

Differential and integral cross sections for elastic electron collisions with uracil, cytosine, guanine, adenine and thymine have been calculated using the independent atom method with a static-polarization model potential for incident energies ranging from 50 to 4000 eV. Total cross sections for single electron-impact ionization of selected DNA and RNA bases have also been calculated with the binary-encounter-Bethe model from the ionization threshold up to 5000 eV. Cross sections within the investigated energy range, can be related to the molecular symmetry, the number of target electrons and molecular size; elastic and ionization processes are most efficient for guanine and adenine molecules, while the lowest cross sections were obtained for the uracil molecule. The ionization cross sections for cytosine, thymine, adenine and guanine are compared with those recently obtained with a semi-classical and binary-encounter-Bethe formalisms. No theoretical and experimental data for elastic electron scattering from DNA and RNA bases are available, but comparisons with calculations for molecules of similar size and geometry allows the validity of the theoretical approach to be verified.     

Analysis of Data on the Cross Sections for Electron-Impact Ionization and Excitation of Electronic States of Atomic Hydrogen (Review)

A review is given of experimental and theoretical data on the cross sections for ionization, excitation, and deexcitation of atomic hydrogen. The set of the cross sections required to calculate the electron energy distribution function and find the level-to-level rate coefficients needed to solve balance equations for the densities of neutral and charged particles in hydrogen plasma is determined.     

The Z lattice in canine cardiac muscle

Filtered images of mammalian cardiac Z bands were reconstructed from optical diffraction patterns from electron micrographs. Reconstructed images from longitudinal sections show connecting filaments at each 38-nm axial repeat in an array consistent with cross-sectional data. Some reconstructed images from cross sections indicate two distinctly different optical diffraction patterns, one for each of two lattice forms (basket weave and small square). Other images are more complex and exhibit composite diffraction patterns. Thus, the two lattice forms co-exist, interconvert, or represent two different aspects of the same details within the lattice. Two three-dimensional models of the Z lattice are presented. Both include the following features: a double array of axial filaments spaced at 24 nm, successive layers of tetragonally arrayed connecting filaments, projected fourfold symmetry in cross section, and layers of connecting filaments spaced at intervals of 38 nm along the myofibril axis. Projected views of the models are compared to electron micrographs and optically reconstructed images of the Z lattice in successively thicker cross sections. The entire Z band is rarely a uniform lattice regardless of plane of section or section thickness. Optical reconstructions strongly suggest two types of variation in the lattice substructure: (a) in the arrangement of connecting filaments, and (b) in the arrangement of units added side-to-side to make larger myofilament bundles and/or end-to-end to make wider Z bands. We conclude that the regular arrangement of axial and connecting filaments generates a dynamic Z lattice.     

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

Electron inelastic cross sections and stopping powers for liquid water over the 0.1-10 keV range are presented based on a recently developed dielectric response model for liquid water (D. Emfietzoglou, F. Cucinotta and H. Nikjoo, Radiat. Res. 164, 202-211, 2005) that is consistent with the experimental data over the whole energy-momentum plane. Both exchange and second-order Born corrections are included in a material-specific way using the dielectric functions of liquid water. The numerical results are fitted by simple analytic functions to facilitate their further use. Compared to previous studies, differential cross sections are shifted toward smaller energy losses resulting in smaller inelastic and stopping cross sections with differences reaching, on average, the approximately 20% and approximately 50% level, respectively. Contrary to higher energies, it is shown that the dispersion model for the momentum dependence of the dielectric functions (Bethe ridge) is as important as the optical model used. Within the accuracy of the experimental data (a few percent) upon which our dielectric model is based, the calculations are "exact" to first order, while the uncertainty of the results beyond first order is estimated at the 5-10% level. The present work overcomes the limitations of Bethe's theory at low energies by a self-consistent account of inner-shell effects and may serve to extend the ICRU electron stopping power database for liquid water down to 100 eV with a level of uncertainty similar to that for the higher-energy values.     

The lid forming apparatus in cysts of the green algaAcetabularia mediterranea

Summary Cross sections and cross tangential sections of 1 to 3-day-old cysts (gametangia) ofAcetabularia mediterranea were examined by electron microscopy. In a defined zone of the peripheral cytoplasm of the cysts, where the lid is to be formed, a characteristic circular band-like structure, the putative lid forming apparatus, can be identified. In 1 -day-old cysts this structure is characterized by two electron dense amorphous layers close and parallel to the plasma membrane. In 3-day-old cysts the lower layer consists of rod-like structures. The position of the circular band-like lid forming apparatus is correlated to the position of the cyst organizing secondary nucleus which occupies a non central position. Usually the center of the lid forming apparatus lies on the shortest line between the secondary nucleus and the cyst wall. This suggests that the cyst organizing secondary nucleus plays an important role in the formation of the cyst lid.