Kholmirzo Kholmurodov

A Smooth-Particle Mesh Ewald Method for DL_POLY Molecular Dynamics Simulation Package on the Fujitsu VPP700

An N⋅ log (N) smooth‐particle mesh Ewald method has been incorporated into the DL_POLY molecular dynamics simulation package. The performance of the new code has been tested on a Fujitsu VPP700 for several DL_POLY‐specific benchmark systems. The new method is highly vectorizable, and makes use of the extremely efficient Fast Fourier Transforms on the Fujitsu vector machine. In calculations of the coulombic forces in periodic systems requiring large reciprocal space vectors, the new code was found to be considerably faster than the conventional Ewald method.

Calcium and Zinc Differentially Affect the Structure of Lipid Membranes

Interactions of calcium (Ca2+) and zinc (Zn2+) cations with biomimetic membranes made of dipalmitoylphosphatidylcholine (DPPC) were studied by small angle neutron diffraction (SAND). Experiments show that the structure of these lipid bilayers is differentially affected by the two divalent cations. Initially, both Ca2+ and Zn2+ cause DPPC bilayers to thicken, while further increases in Ca2+ concentration result in the bilayer thinning, eventually reverting to having the same thickness as pure DPPC. The binding of Zn2+, on the other hand, causes the bilayers to swell to a maximum thickness, and the addition of more Zn2+ does not result in a further thickening of the membrane. Agreement between our results obtained using oriented planar membranes and those from vesicular samples implies that the effect of cations on bilayer thickness is the result of electrostatic interactions, rather than geometrical constraints due to bilayer curvature. This notion is further reinforced by MD simulations. Finally, the radial distribution functions reveal a strong interaction between Ca2+ and the phosphate oxygens, while Zn2+ shows a much weaker binding specificity.

A highly vectorised "link-cell" FORTRAN code for the DL_POLY molecular dynamics simulation package

Abstract Highly vectorised FORTRAN subroutines, based on the link-cell algorithm for DL_POLY molecular dynamics simulation package, are developed. For several specific benchmark systems the efficiency of the proposed codes on a Fujitsu VPP700/128E vector computer has been tested. It is shown that in constructing the neighbor list and in calculating atomic forces our link-cell method is significantly faster than the original code.

Model of Abnormal Chromophore-Protein Interaction for Е181К Rhodopsin Mutation: Computer Molecular Dynamics Study

The interaction of the 11-cis-retinal chromophore with the surrounding amino acid residues in the chromophore center of the rhodopsin protein has been investigated for the Е181К mutant form using molecular dynamics simulation. A comparative analysis of the arrangement of the amino acid residues in the chromophore center has been performed for both wild (native) and mutant rhodopsins. It is shown that for the Е181К mutant rhodopsin there is no proper binding of 11-cis-retinal with the surrounding amino acid residues. The distortion of the conformation states in the mutant rhodopsin molecule takes place in both the chromophore center and cytoplasmic domain. Our simulations suggest that a stable covalent linkage of 11-cis-retinal with the protein part (viz. opsin) of the rhodopsin molecule will not form. This, on the other hand, implies that the protein’s active site in the cytoplasmic domain, which is responsible for the G-protein binding (so-called transducin), may not be completely blocked. Based on our molecular simulation data, we discuss the possible correlation between retinitis pigmentosa pathogenesis and the structural and functional properties of the rhodopsin protein.

Density functional theory calculations of the water interactions with ZrO2 nanoparticles Y2O3 doped

Development of a new electricity generation techniques is one of the most relevant tasks, especially nowadays under conditions of extreme growth in energy consumption. The exothermic heterogeneous electrochemical energy conversion to the electric energy through interaction of the ZrO2 based nanopowder system with atmospheric moisture is one of the ways of electric energy obtaining. The questions of conversion into the electric form of the energy of water molecules adsorption in 3 mol% Y2O3 doped ZrO2 nanopowder systems were investigated using the density functional theory calculations. The density functional theory calculations has been realized as in the Kohn-Sham formulation, where the exchange-correlation potential is approximated by a functional of the electronic density. The electronic density, total energy and band structure calculations are carried out using the all-electron, full potential, linear augmented plane wave method of the electronic density and related approximations, i.e. the local density, the generalized gradient and their hybrid approximations.

Water permeation through the internal water pathway in activated GPCR rhodopsin

Rhodopsin is a light-driven G-protein-coupled receptor that mediates signal transduction in eyes. Internal water molecules mediate activation of the receptor in a rhodopsin cascade reaction and contribute to conformational stability of the receptor. However, it remains unclear how internal water molecules exchange between the bulk and protein inside, in particular through a putative solvent pore on the cytoplasmic. Using all-atom molecular dynamics simulations, we identified the solvent pore on cytoplasmic side in both the Meta II state and the Opsin. On the other hand, the solvent pore does not exist in the dark-adapted rhodopsin. We revealed two characteristic narrow regions located within the solvent pore in the Meta II state. The narrow regions distinguish bulk and the internal hydration sites, one of which is adjacent to the conserved structural motif “NPxxY”. Water molecules in the solvent pore diffuse by pushing or sometimes jumping a preceding water molecule due to the geometry of the solvent pore. These findings revealed a total water flux between the bulk and the protein inside in the Meta II state, and suggested that these pathways provide water molecules to the crucial sites of the activated rhodopsin.

Cation-containing lipid membranes – experiment and md simulations

Abstract Using small angle neutron diffraction and molecular dynamics simulations we studied the interactions between calcium (Ca2+) or zinc (Zn2+) cations, and oriented gel phase dipalmitoyl-phosphatidylcholine (DPPC) bilayers. For both cations studied at ~1:7 divalent metal ion to lipid molar ratio (Me2+:DPPC), bilayer thickness increased. Simulation results helped reveal subtle differences in the effects of the two cations on gel phase membranes.

Computer Molecular Dynamics Studies on Protein Structures (Visual Pigment Rhodopsin and Cyclin‐Dependent Kinases)

Based on the computer molecular dynamics (MD) calculations we have simulated for the visual pigment rhodopsin and cyclin‐dependent kinase proteins the dynamical and structural properties at reliable physiological temperatures and conditions. MD simulations are carried out on the rhodopsin protein to investigate the conformational changes of the protein in relation to the inclusion of the 11‐cis chromophore retinal into consideration. It was demonstrated that the adaptation of the chromophore retinal in the opsin site causes a considerable influence on its protein binding pocket, as well as on conformations of the cytoplasmic part, but the extracelluar part of the protein shows a comparably small changes. On the basis of the simulaton results we discuss some molecular mechanisms for the rhodopsin protein function as a G‐protein‐coupled receptor in the dark state, i.e. for the chromophore retinal as a ligand‐agonist stabilizaing the inactive conformation. The central role that cyclin‐dependent kinases (CDK)...

Molecular Dynamics Simulations of the Droplet Spreading Process for Metallic Phases: The Low Energy Cluster-Substrate Impacts

The many-body Finnis-Sinclair potential has been used to perform a MD simulation of the impact of an A1 cluster on an A1 surface. We have used an optimised version of the DL_POLY molecular dynamics simulation code [1] to study the cluster-surface impact processes. Based on the density and temperature distribution data the low energy cluster-surface interactions has been analyzed in detail and a novel interpretation of droplet spreading process is given.