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

Cluster growing process and a sequence of magic numbers

We present a new theoretical framework for modelling the cluster growing process. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster sizes of more than 100 atoms. We demonstrate that in this way all known global minimum structures of the Lennard-Jonnes (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic numbers sequence for the clusters of noble gases atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence on cluster size of the second derivative of the binding energy per atom calculated for the chain of LJ-clusters based on the icosahedral symmetry with the peaks in the abundance mass spectra experimentally measured for the clusters of noble gases atoms. Our method serves an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solution of a broad variety of problems in which atomic cluster structure is important.Comment: 10 pages, 3 figure

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

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

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.