Ion-induced electron production in tissue-like media and DNA damage mechanisms

We propose an inclusive approach for calculating characteristics of secondary electrons produced by ions/protons in tissue-like media. This approach is based on an analysis of the projectile's interaction with the medium on the microscopic level. It allows us to obtain the energy spectrum and abundance of secondary electrons as functions of the projectile kinetic energy. The physical information obtained in this analysis is related to biological processes responsible for the irrepearable DNA damage induced by the projectile. In particular, we consider double strand breaks of DNA caused by secondary electrons and free radicals, and local heating in the ion's track. The heating may enhance the biological effectiveness of electron/free radical interactions with the DNA and may even be considered as an independent mechanism of DNA damage. Numerical estimates are performed for the case of carbon-ion beams. The obtained dose-depth curves are compared with results of the MCHIT model based on the GEANT4 toolkit.Comment: 9 pages, 7 figures, submitted to EPJD, included class files svepj.clo, svjour.cl

Fragmentation pathways of nanofractal structures on surface

We present a detailed systematical theoretical analysis of the post-growth processes occurring in nanofractals grown on surface. For this study we developed a method which accounts for the internal dynamics of particles in a fractal. We demonstrate that particle diffusion and detachment controls the shape of the emerging stable islands on surface. We consider different scenarios of fractal post-growth relaxation and analyze the time evolution of the island's morphology. The results of our calculations are compared with available experimental observations, and experiments in which the post-growth relaxation of deposited nanostructures can be probed are suggested.Comment: 34 pages, 11 figure

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).Comment: 24 pages, 3 figure

Alpha helix-coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter-free partition function of the polypeptide using the suggested method [1]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.Comment: 34 pages, 12 figure

Hybridization-related correction to the jellium model for fullerenes

We introduce a new type of correction for a more accurate description of fullerenes within the spherically symmetric jellium model. This correction represents a pseudopotential which originates from the comparison between an accurate ab initio calculation and the jellium model calculation. It is shown that such a correction to the jellium model allows one to account, at least partly, for the sp2-hybridization of carbon atomic orbitals. Therefore, it may be considered as a more physically meaningful correction as compared with a structureless square-well pseudopotential which has been widely used earlier.Comment: 16 pages, 10 figure

Photon emission by an ultra-relativistic particle channeling in a periodically bent crystal

This paper is devoted to a detailed analysis of the new type of the undulator radiation generated by an ultra-relativistic charged particle channeling along a crystal plane, which is periodically bent by a transverse acoustic wave, as well as to the conditions limiting the observation of this phenomenon. This mechanism makes feasible the generation of electromagnetic radiation, both spontaneous and stimulated, emitted in a wide range of the photon energies, from X- up to gamma-rays

Stable propagation of a modulated positron beam in a bent crystal channel

The propagation of a modulated positron beam in a planar crystal channel is investigated. It is demonstrated that the beam preserves its modulation at sufficiently large penetration depths which opens the prospect of using a crystalline undulator as a coherent source of hard x-rays. This finding is a crucial milestone in developing a new type of lasers radiating in the hard x-ray and gamma-ray range.Comment: 11 pages, 4 figures, iopar

Electron-based crystalline undulator

We discuss the features of a crystalline undulator of the novel type based on the effect of a planar channeling of ultra-relativistic electrons in a periodically bent crystals. It is demonstrated that an electron-based undulator is feasible in the tens of GeV range of the beam energies, which is noticeably higher than the energy interval allowed in a positron-based undulator. Numerical analysis of the main parameters of the undulator as well as the characteristics of the emitted undulator radiation is carried out for 20 and 50 GeV electrons channeling in diamond and silicon crystals along the (111) crystallographic planes.Comment: 16 pages, 8 figures, Latex, IOP styl

The influence of the dechanneling process on the photon emission by an ultra-relativistc positron channeling in a periodically bent crystal

We investigate, both analytically and numerically, the influence of the dechanneling process on the parameters of undulator radiation generated by ultra-relativistic positron channelling along a crystal plane, which is periodically bent. The bending might be due either to the propagation of a transverse acoustic wave through the crystal, or due to the static strain as it occurs in superlattices. In either case the periodically bent crystal serves as an undulator which allows to generate X-ray and gamma-radiation. We propose the scheme for accurate quantitative treatment of the radiation in presence of the dechanneling. The scheme includes (i) the analytic expression for spectral-angular distribution which contains, as a parameter, the dechanneling length, (ii) the simulation procedure of the dechanneling process of a positron in periodically bent crystals. Using these we calculate the dechanneling lengths of 5 GeV positrons channeling in Si, Ge and W crystals, and the spectral-angular and spectral distributions of the undulator over broad ranges of the photons. The calculations are performed for various parameters of the channel bending.Comment: published in J. Phys. G: Nucl. Part. Phys. 27 (2001) 95-125, http://www.iop.or