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

Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes

We present the latest advances of the multiscale approach to radiation damage caused by irradiation of a tissue with energetic ions and report the most recent advances in the calculations of complex DNA damage and the effects of thermal spikes on biomolecules. The multiscale approach aims to quantify the most important physical, chemical, and biological phenomena taking place during and following irradiation with ions and provide a better means for clinically-necessary calculations with adequate accuracy. We suggest a way of quantifying the complex clustered damage, one of the most important features of the radiation damage caused by ions. This method can be used for the calculation of irreparable DNA damage. We include thermal spikes, predicted to occur in tissue for a short time after ion's passage in the vicinity of the ions' tracks in our previous work, into modeling of the thermal environment for molecular dynamics analysis of ubiquitin and discuss the first results of these simulations.Comment: 14 pages, 3 figures, submitted to EPJ

Parameters of the crystalline undulator and its radiation for particular experimental conditions

We report the results of theoretical and numerical analysis of the crystalline undulators planned to be used in the experiments which are the part of the ongoing PECU project [1]. The goal of such an analysis was to define the parameters (different from those pre-set by the experimental setup) of the undulators which ensure the highest yield of photons of specified energies. The calculations were performed for 0.6 and 10 GeV positrons channeling through periodically bent Si and Si$_{1-x}$Ge$_x$ crystals.Comment: 13 pages, 8 figures, submitted to SPI

Dynamical Screening of Atom Confined by Finite-Width Fullerene

This is an investigation on the dynamical screening of an atom confined within a fullerene of finite width. The two surfaces of the fullerene lead to the presence of two surface plasmon eigenmodes. It is shown that, in the vicinity of these two eigenfrequencies, there is a large enhancement of the confined atom's photoabsorption rate.Comment: 10 pages, 4 figures correction of figure 2 and equation 1