Related papers: Conformational properties of neutral and charged a…
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…
We have investigated the potential energy surfaces for alanine 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…
In interfaces between inorganic and biological materials relevant for technological applications, the general challenge of structure determination is exacerbated by the high flexibility of bioorganic components, chemical bonding, and charge…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
We studied the electronic and the structural properties of amino acids (alanine, glycine, and histidine) attached to graphene oxide (GO) by peptide bonding, via plane wave pseudopotential total-energy calculations within the local spin…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
A polycrystalline graphene consists of perfect domains tilted at angle {\alpha} to each other and separated by the grain boundaries (GB). These nearly one-dimensional regions consist in turn of elementary topological defects, 5-pentagons…
Encoding the complex features of an energy landscape is a challenging task, and often chemists pursue the most salient features (minima and barriers) along a highly reduced space, i.e. 2- or 3-dimensions. Even though disconnectivity graphs…
In this paper, we analyze the effect of geometrical constraint on the conformational properties of an infinitely long linear semiflexible polymer chain confined in-between two constraints under good solvent condition in two dimensions. The…
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…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
We study the potential and the charge distribution across the interface of a plasma and a dielectric wall. For this purpose, the charge bound to the wall is modelled as a quasi-stationary electron surface layer which satisfies Poisson's…
We investigate the structure of the potential energy surfaces of the superheavy nuclei 258Fm, 264Hs, (Z=112,N=166), (Z=114,N=184), and (Z=120,N=172) within the framework of self-consistent nuclear models, i.e. the Skyrme-Hartree-Fock…
First-principles full-potential linearized augmented plane wave (FLAPW) calculations are performed to clarify the role of the interface geometry on piezoelectric fields and on potential line-ups at the [0001]-wurtzite and [111]-zincblende…
First-principles density functional calculations reveal that aluminum can form planar chains in zigzag and ladder structures. The most stable one has equilateral triangular geometry with four nearest neighbors; the other stable zigzag…
Grain boundaries (GBs), an important constituent of polycrystalline materials, have a wide range of manifestion and significantly affect the properties of materials. Fully understanding the effects of GBs is stalemated due to lack of…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
The distribution of net electric charge in graphene is investigated, using both a constitutive atomic charge-dipole interaction model and an approximate analytical solution to Laplace's equation. We demonstrate a strong size dependence of…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…