Model for radial dependence of frequency distributions for energy imparted in nanometer volumes from HZE particles

This paper develops a deterministic model of frequency distributions for energy imparted (total energy deposition) in small volumes similar to DNA molecules from high-energy ions of interest for space radiation protection and cancer therapy. Frequency distributions for energy imparted are useful for considering radiation quality and for modeling biological damage produced by ionizing radiation. For high-energy ions, secondary electron (delta-ray) tracks originating from a primary ion track make dominant contributions to energy deposition events in small volumes. Our method uses the distribution of electrons produced about an ion's path and incorporates results from Monte Carlo simulation of electron tracks to predict frequency distributions for ions, including their dependence on radial distance. The contribution from primary ion events is treated using an impact parameter formalism of spatially restricted linear energy transfer (LET) and energy-transfer straggling. We validate our model by comparing it directly to results from Monte Carlo simulations for proton and alpha-particle tracks. We show for the first time frequency distributions of energy imparted in DNA structures by several high-energy ions such as cosmic-ray iron ions. Our comparison with results from Monte Carlo simulations at low energies indicates the accuracy of the method.     

Radial secondary electron dose profiles and biological effects in light-ion beams based on analytical and Monte Carlo calculations using distorted wave cross sections

To speed up dose calculation, an analytical pencil-beam method has been developed to calculate the mean radial dose distributions due to secondary electrons that are set in motion by light ions in water. For comparison, radial dose profiles calculated using a Monte Carlo technique have also been determined. An accurate comparison of the resulting radial dose profiles of the Bragg peak for (1)H(+), (4)He(2+) and (6)Li(3+) ions has been performed. The double differential cross sections for secondary electron production were calculated using the continuous distorted wave-eikonal initial state method (CDW-EIS). For the secondary electrons that are generated, the radial dose distribution for the analytical case is based on the generalized Gaussian pencil-beam method and the central axis depth-dose distributions are calculated using the Monte Carlo code PENELOPE. In the Monte Carlo case, the PENELOPE code was used to calculate the whole radial dose profile based on CDW data. The present pencil-beam and Monte Carlo calculations agree well at all radii. A radial dose profile that is shallower at small radii and steeper at large radii than the conventional 1/r(2) is clearly seen with both the Monte Carlo and pencil-beam methods. As expected, since the projectile velocities are the same, the dose profiles of Bragg-peak ions of 0.5 MeV (1)H(+), 2 MeV (4)He(2+) and 3 MeV (6)Li(3+) are almost the same, with about 30% more delta electrons in the sub keV range from (4)He(2+)and (6)Li(3+) compared to (1)H(+). A similar behavior is also seen for 1 MeV (1)H(+), 4 MeV (4)He(2+) and 6 MeV (6)Li(3+), all classically expected to have the same secondary electron cross sections. The results are promising and indicate a fast and accurate way of calculating the mean radial dose profile.     

Applications of amorphous track models in radiation biology

The average or amorphous track model uses the response of a system to gamma-rays and the radial distribution of dose about an ion’s path to describe survival and other cellular endpoints from proton, heavy ion, and neutron irradiation. This model has been used for over 30 years to successfully fit many radiobiology data sets. We review several extensions of this approach that address objections to the original model, and consider applications of interest in radiobiology and space radiation risk assessment. In the light of present views of important cellular targets, the role of target size as manifested through the relative contributions from ion-kill (intra-track) and gamma-kill (inter-track) remains a critical question in understanding the success of the amorphous track model. Several variations of the amorphous model are discussed, including ones that consider the radial distribution of event-sizes rather than average electron dose, damage clusters rather than multiple targets, and a role for repair or damage processing. Received: 30 October 1998 / Accepted in revised form: 6 April 1999     

Tumor therapy and track structure

The elevated relative biological effectiveness (RBE) of heavy ions like carbon is the main reason for their use in radiotherapy and is due to the microscopic distribution of dose inside each particle track. High local doses produce lesions that are expected to have a diminished possibility of repair. Thus, RBE depends on track structure and on the biological repair capacity of the tissue that is affected by the irradiation. For tumor treatment planning with heavy ions, the beam quality and the tissue sensitivity have to be taken into account. Using the dependence of radial dose distribution on particle energy and atomic number on the physical side and x-ray dose response for the repair capacity on the biological side, the response to particle irradiation can be calculated in the local effect model (LEM) and used for treatment planning. This article traces the route from electron emission as the basis of track structure to the RBE calculation and the application in treatment planning. Received: 21 April 1999 / Accepted in revised form: 1 September 1999     

Microdosimetry near the trajectory of high-energy heavy ions

Single-event energy distributions were measured in a 1.3-micron-diameter site as a function of radial distance from the trajectory of high-energy iron ions having an energy of about 600 MeV/amu. It was found that beyond distances of a few micrometers the average lineal energy of the (mostly single) secondary electrons (delta rays) is of the order of 3 keV/micron. This is similar to the value found in a medium irradiated by 170-keV photons. The frequency-mean specific energy for delta rays occurring at large distances from the path of the primary ion exceeds the calculated (radial) absorbed dose by two orders of magnitude.     

Nonisothermal theory of the positive column of an electric discharge in the axial magnetic field

A nonisothermal model of the positive column allowing for electron energy balance is analyzed. The influence of the axial magnetic field on the characteristics of the cylindrical positive column of a low-pressure discharge is investigated in the hydrodynamic approximation. It is shown that the magnetic field affects the plasma density distribution, plasma velocity, and electron energies. The radial dependences of the plasma density, electron energy, and plasma velocity, as well as the azimuthal velocities of electrons and ions, are calculated for helium at different values of the magnetic field strength. It is established that inertia should be taken into account in the equations for the azimuthal motion of electrons and ions. The results obtained in the hydrodynamic approximation differ significantly from those obtained in the framework of the common diffusion model of the positive column in the axial magnetic field. It is shown that the distributions of the plasma density and radial plasma velocity in the greater part of the positive column tend to those obtained in the diffusion approximation at higher values of the axial magnetic field and gas density, although substantial differences remain in the near-wall region.     

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 fractal analysis of the radial distribution of bronchial capillaries around large airways.

We analyzed published measurements of the bronchial circulation and airway wall (Anderson JC, Bernard SL, Luchtel DL, Babb AL, and Hlastala MP. Respir Physiol Neurobiol 132: 329-339, 2002) and determined that the radial distribution of bronchial capillary cross-sectional area was fractal. We limited our analysis to bronchial capillaries, diameter < or =10 mum, that resided between the epithelial basement membrane and adventitia-alveolar boundary, the airway wall tissue. Thirteen different radial distributions of capillary-to-tissue area were constructed simply by changing the number of annuli (i.e., the annular size) used to form each distribution. For the 13 distributions created, these annuli ranged in size from to of the size of the airway wall area. Radial distributions were excluded from the fractal analysis if the sectioning procedure resulted in an annulus with a radial thickness less than the diameter of a capillary. To determine the fractal dimension for a given airway, the coefficient of variation (CV) for each distribution was calculated, and ln(CV) was plotted against the logarithm of the relative piece area. For airways with diameter >2.4 mm, this relationship was linear, which indicated the radial distribution of bronchial capillary cross-sectional area was fractal with an average fractal dimension of 1.27. The radial distribution of bronchial capillary cross-sectional area was not fractal around airways with diameter <1.5 mm. We speculated on how the fractal nature of this circulation impacts the distribution of bronchial blood flow and the efficiency of mass transport during health and disease. A fractal analysis can be used as a tool to quantify and summarize investigations of the bronchial circulation.     

Biophysical modeling of fragment length distributions of DNA plasmids after X and heavy-ion irradiation analyzed by atomic force microscopy

The investigation of fragment length distributions of plasmid DNA gives insight into the influence of localized energy distribution on the induction of DNA damage, particularly the clustering of double-strand breaks. We present an approach that determines the fragment length distributions of plasmid DNA after heavy-ion irradiation by using the Local Effect Model. We find a good agreement of our simulations with experimental fragment distributions derived from atomic force microscopy (AFM) studies by including experimental constraints typical for AFM. Our calculations reveal that by comparing the fragmentation in terms of fluence, we can uniquely distinguish the effect of different radiation qualities. For very high-LET irradiation using nickel or uranium ions, no difference between their fragment distributions can be expected for the same dose level. However, for carbon ions with an intermediate LET, the fragmentation pattern differs from the distribution for very high-LET particles. The results of the model calculations can be used to determine the optimal experimental parameters for a demonstration of the influence of track structure on primary radiation damage. Additionally, we compare the results of our model for two different plasmid geometries.     

Investigation of the Edge Plasma Parameters and Measurements of the Plasma Longitudinal Rotation Velocity by a Mach Probe in a Lithium Experiment on the T-11M Tokamak

The edge plasma parameters were measured by means of a Mach probe in a lithium experiment on the T-11M tokamak. The angular and radial distributions of the ion saturation current, along with the radial distribution of the electron temperature, were obtained in different modes of tokamak operation. The radial distributions of the electron temperature and ion saturation current in the main operating mode (L-mode) revealed a peak in the scrape-off-layer of the vertical limiter (lithium emitter), which can indicate the formation of a magnetic island in this region. The measured plasma flow velocity along the magnetic field was found to be close to one-half of the ion sound velocity for Li⁺ ions.     

Microdosimetry of electron microbeams

Track structures of 25, 50 and 80 keV primary electrons, simulated by the detailed-history Monte Carlo method, were analyzed for the frequency distributions of energy deposited in spheres with a diameter of 1 microm, placed in a cylindrically symmetrical array around the projected initial direction of the primary electron. The frequency mean of specific energy, the dose mean of lineal energy, and the parameters of lognormal functions fit to the dose distributions were calculated as a function of beam penetration and radial distance from the projected beam axis. Given these data, the stochastics of dose and radiation quality for micrometer-scale sites targeted by a medium-energy electron microbeam can be predicted as a function of the site's location relative to the beam entry point.     

Cluster effects within the local effect model

The local effect model predicts the relative biological effectiveness (RBE) for different ions and cell lines starting from the corresponding experimental photon data and an amorphous track structure model. Here we present an extension of the model that takes cluster effects of single-strand breaks (SSBs) at the nanometer scale into account. In line with the main idea of the local effect model, we take the yields of SSBs and double-strand breaks (DSBs) from experimental photon data and use a Monte Carlo method to distribute them onto the DNA. We score clusters of SSBs where individual SSBs are separated by less than 25 bp as additional DSBs. Assuming that the number of DSBs is a measure of cell lethality, we derive a modified cell survival curve for photons that takes these cluster effects into account. In combination with an improved radial dose distribution, we find that the extended local effect model including cluster effects reproduces most experimental data better than the original local effect model and thus enhances the accuracy of the local effect model.     

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations

The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg²⁺ distributions are still at significant variances for shorter distances.     

Properties of average score distributions of SEQUEST: the probability ratio method

High throughput identification of peptides in databases from tandem mass spectrometry data is a key technique in modern proteomics. Common approaches to interpret large scale peptide identification results are based on the statistical analysis of average score distributions, which are constructed from the set of best scores produced by large collections of MS/MS spectra by using searching engines such as SEQUEST. Other approaches calculate individual peptide identification probabilities on the basis of theoretical models or from single-spectrum score distributions constructed by the set of scores produced by each MS/MS spectrum. In this work, we study the mathematical properties of average SEQUEST score distributions by introducing the concept of spectrum quality and expressing these average distributions as compositions of single-spectrum distributions. We predict and demonstrate in the practice that average score distributions are dominated by the quality distribution in the spectra collection, except in the low probability region, where it is possible to predict the dependence of average probability on database size. Our analysis leads to a novel indicator, the probability ratio, which takes optimally into account the statistical information provided by the first and second best scores. The probability ratio is a non-parametric and robust indicator that makes spectra classification according to parameters such as charge state unnecessary and allows a peptide identification performance, on the basis of false discovery rates, that is better than that obtained by other empirical statistical approaches. The probability ratio also compares favorably with statistical probability indicators obtained by the construction of single-spectrum SEQUEST score distributions. These results make the robustness, conceptual simplicity, and ease of automation of the probability ratio algorithm a very attractive alternative to determine peptide identification confidences and error rates in high throughput experiments.     

Spectral vs. compartmental averaging of VA/Q distributions: confidence limits

We have investigated the method of statistical averaging as a nonparametric approach to obtain a representative ventilation-perfusion (VA/Q) distribution that exemplifies the family of compatible solutions for multiple inert gas elimination data. The variability of the compatible solutions was examined by determining the standard deviation of the statistical average. For six inert gases, it can be predicted that a distribution with up to seven contiguous nonzero VA/Q compartments can be uniquely recovered, whereas the compatible family becomes more diverse, the broader the distribution. For a given compatible family consisting of multimodal distributions with various phase relationships, the average distribution was found to display an uncharacteristically unimodal shape as a result of modal smoothing. To avoid this possible artifact, an alternative approach was adopted in which statistical averaging was performed in the frequency domain. For both deterministic and empirical data, the energy spectra of all feasible VA/Q distributions displayed a well-defined low-frequency band that was invariant within the compatible family and with a bandwidth that approximated the predicted sampling cutoff frequency. The nonuniqueness of the result was ascribable to a variable high-frequency band that was due to an aliasing effect. For a wide range of clinical data, the representative distributions resulting from compartmental and spectral averaging were indistinguishable from each other and had little variability both in the VA/Q and frequency domains. For these cases, therefore, the resolving power of the recovery algorithm was not critical. Finally, an efficient method of finding the average distribution was proposed.     

Radiation quality of tritium beta-rays: microdosimetric distributions for nanometer-size targets in a medium containing tritiated water

To elucidate the characteristics of the action of tritium beta-rays, the following parameters are derived: electron slowing down spectra of primary electrons (beta-rays) and delta-rays in a medium containing tritiated water; and frequency distributions for the microdosimetric quantity j (number of effective primary events per track per target), fj, for nanometer-size targets exposed to tritiated water. Features of the radiation quality of tritium beta-rays are discussed by comparing the present results with those for 60Co gamma-rays and 7 MeV electrons. It is concluded that, although tritium beta-rays, 60Co gamma-rays, and 7 MeV electrons are classified as the same low l.e.t. radiation, the radiation quality of tritium beta-rays is considerably different from those of 60Co gamma-rays and 7 MeV electrons, and has specific features such as a high average l.e.t., a small total electron fluence per unit absorbed dose, and a different microdosimetric distribution, fj, for nanometer-size targets.     

Composite cylinder models of DNA: application to the electrostatics of the B-Z transition.

We develop and test a Poisson-Boltzmann model of the electrostatics of the B-Z transition of DNA. Starting from the detailed geometries of the two forms, we compute at each radius the fractions of DNA matter, of volume forbidden (for nonpoint-like ions), and of volume accessible to the center of ions. These radial distributions are incorporated in a composite cylinder model; availability to ions (porosity) and the dielectric constant at each radial distance are then obtained. The phosphate charge is distributed with cylindrical symmetry on two layers at the appropriate radial distances. The porous sheath, between the axis and the charge distribution, provides much more room for ions in B-DNA than in Z-DNA. By using previously developed methods, the Poisson-Boltzmann problem of such cylinders is easily solved. The computational load is small, so that results can be obtained for a large set of salt concentrations and for a number of ionic radii. The variation of the electrostatic free energy difference with salt concentration compares favorably with the experimental value (it is half as large). There is also qualitative agreement with experiments on supercoiled DNA, including a maximum of the free energy difference at submolar salt concentrations. The results for this cylinder with porous sheath are in line with those of the earlier simple planar model and of a plain cylinder with sheath, which is also presented here. They are thus insensitive to details of the model. They support the proposition that the main electrostatic feature of the B-Z transition is the better immersion of the B-DNA phosphates into the solution. They also give confidence in the validity of the Poisson-Boltzmann approach, despite the large salt concentrations involved. Prior studies using an approach based on the potential of mean force are discussed.     

Monte Carlo simulation of the spatial distribution of energy deposition for an electron microbeam

Dosimetry calculations characterizing the spatial variation of the energy deposited by the slowing and stopping of energetic electrons are reported and compared with experimental measurements from an electron microbeam facility. The computations involve event-by-event, detailed-histories Monte Carlo simulations of low-energy electrons interacting in water vapor. Simulations of electron tracks with starting energies from 30 to 80 keV are used to determine energy deposition distributions in thin cylindrical rings as a function of penetration and radial distance from a beam source. Experimental measurements of the spatial distribution of an electron microbeam in air show general agreement with the density-scaled simulation results for water vapor at these energies, yielding increased confidence in the predictions of Monte Carlo track-structure simulations for applications of the microbeam as a single-cell irradiator.     

On pathlength and energy straggling of megavoltage electrons slowing down

Purposeto elucidate the effects of multiple scattering and energy-loss straggling on electron beams slowing down in materials.MethodsEGSnrc Monte Carlo simulations are done using a purpose-written user-code.ResultsPlots are presented of the primary electron’s energy as a function of pathlength for 20 MeV electrons incident on water and tantalum as are plots of the overall distribution of pathlengths as the 20 MeV electrons slow down under various Monte Carlo scenarios in water and tantalum. The distributions range from 1 % to 135 % of the CSDA range in water and from 1 % to 186 % in tantalum. The effects of energy-loss straggling on energy spectra at depth and electron fluence at depth are also presented.ConclusionsThe role of energy-loss straggling and multiple scattering are shown to play a significant role in the range straggling which determines the dose fall-off region in electron beam dose vs depth curves and a significant role in the energy distributions as a function of depth.