Transport of secondary electrons and reactive species in ion tracks

The transport of reactive species brought about by ions traversing tissue-like medium is analysed analytically. Secondary electrons ejected by ions are capable of ionizing other molecules; the transport of these generations of electrons is studied using the random walk approximation until these electrons remain ballistic. Then, the distribution of solvated electrons produced as a result of interaction of low-energy electrons with water molecules is obtained. The radial distribution of energy loss by ions and secondary electrons to the medium yields the initial radial dose distribution, which can be used as initial conditions for the predicted shock waves. The formation, diffusion, and chemical evolution of hydroxyl radicals in liquid water are studied as well.Comment: 7 pages 4 figure

Multiscale approach to the physics of radiation damage with ions

The multiscale approach to the assessment of biodamage resulting upon irradiation of biological media with ions is reviewed, explained and compared to other approaches. The processes of ion propagation in the medium concurrent with ionization and excitation of molecules, transport of secondary products, dynamics of the medium, and biological damage take place on a number of different temporal, spatial and energy scales. The multiscale approach, a physical phenomenon-based analysis of the scenario that leads to radiation damage, has been designed to consider all relevant effects on a variety of scales and develop an approach to the quantitative assessment of biological damage as a result of irradiation with ions. This paper explains the scenario of radiation damage with ions, overviews its major parts, and applies the multiscale approach to different experimental conditions. On the basis of this experience, the recipe for application of the multiscale approach is formulated. The recipe leads to the calculation of relative biological effectiveness.Comment: 31 pages, 14 figure

Calculation of survival probabilities for cells exposed to high ion fluences

A methodology of calculations of survival curves with an account for ion paths interference is developed using the multiscale approach to the physics of radiation damage with ions. The method is applied to different targets and shouldered survival curves are obtained. The recipe is designed for both high and low values of linear energy transfer.Comment: 9 pages, 6 figures, submitted to Eur. Phys. J.

Cell survival probability in a spread-out Bragg peak for novel treatment planning

The problem of variable cell survival probability along the spread-out Bragg peak is one of the long standing problems in planning and optimisation of ion-beam therapy. This problem is considered using the multiscale approach to the physics of ion-beam therapy. The physical reasons for this problem are analysed and understood on a quantitative level. A recipe of solution to this problem is suggested using this approach. This recipe can be used in the design of a novel treatment planning and optimisation based on fundamental science.Comment: 6 pages, 3 figures, submitted to EPJ

Conformational changes in glycine tri- and hexapeptide

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for the glycine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.Comment: 23 pages, 9 figure

Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle

The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms and the icosahedral Ni$_{309}$ cluster. An explicit set of constant-temperature simulations is performed in order to cover a broad temperature range from 400 to 1200 K, at which a successful growth of carbon nanotubes has been achieved experimentally by means of chemical vapor deposition. The stability of the system depending on parameters of the involved interatomic interactions is analyzed. It is demonstrated that different scenarios of the nanotube dynamics atop the nanoparticle are possible depending on the parameters of the Ni-C potential. When the interaction is weak the nanotube is stable and resembles its highly symmetric structure, while an increase of the interaction energy leads to the abrupt collapse of the nanotube in the initial stage of simulation. In order to validate the parameters of the Ni-C interaction utilized in the simulations, DFT calculations of the potential energy surface for carbon-nickel compounds are performed. The calculated dissociation energy of the Ni-C bond is in good agreement with the values, which correspond to the case of a stable and not deformed nanotube simulated within the MD approach.Comment: 11 pages, 5 figures; submitted to Eur. Phys. J.

Channeling process in a bent crystal

We have investigated the channeling process of charged particles in a bent crystal. Invoking simple assumptions we derive a criterion, which determines whether channeling occurs or not. We obtain the same criterion using the Dirac equation. It is shown that the centrifugal force acting on the particle in the bent crystal significantly alters the effective transverse potential. The cases of axial and planar channeling are considered. The channeling probability and the dechanneling probability due to tunneling of the particle under the barrier in the effective transverse potential are estimated. These probabilities depend on the specific scaling parameter characterizing the process. Using the quasiclassical theory of synchrotron radiation we have calculated the contribution to the radiation spectrum, which arises due to the curvature of the channel. This contribution becomes significant to TeV electrons or positrons. Some practical consequences of our results are briefly discussed