106 research outputs found
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 SiGe 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
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