Evolution of structure of SiO2 nanoparticles upon cooling from the melt

Evolution of structure of spherical SiO2 nanoparticles upon cooling from the melt has been investigated via molecular-dynamics (MD) simulations under non-periodic boundary conditions (NPBC). We use the pair interatomic potentials which have weak Coulomb interaction and Morse type short-range interaction. The change in structure of SiO2 nanoparticles upon cooling process has been studied through the partial radial distribution functions (PRDFs), coordination number and bond-angle distributions at different temperatures. The core and surface structures of nanoparticles have been studied in details. Our results show significant temperature dependence of structure of nanoparticles. Moreover, temperature dependence of concentration of structural defects in nanoparticles upon cooling from the melt toward glassy state has been found and discussed.Comment: 12 pages, 6 figure

Protein mechanical unfolding: importance of non-native interactions

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension 22 nm in the force-extension curve, is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.Comment: 27 pages, 15 figure

Nonlinear AC resistivity in s-wave and d-wave disordered granular superconductors

We model s-wave and d-wave disordered granular superconductors with a three-dimensional lattice of randomly distributed Josephson junctions with finite self-inductance. The nonlinear ac resistivity of these systems was calculated using Langevin dynamical equations. The current amplitude dependence of the nonlinear resistivity at the peak position is found to be a power law characterized by exponent $\alpha$. The later is not universal but depends on the self-inductance and current regimes. In the weak current regime $\alpha$ is independent of the self-inductance and equal to 0.5 or both of s- and d-wave materials. In the strong current regime this exponent depends on the screening. We find $\alpha \approx 1$ for some interval of inductance which agrees with the experimental finding for d-wave ceramic superconductors.Comment: 4 pages, 5 figures, to appear in Phys. Rev. Let

GOMoDo: A GPCRs Online Modeling and Docking Webserver

G-protein coupled receptors (GPCRs) are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo

Structural properties of amorphous TiO

Structural properties of amorphous TiO2 spherical nanoparticles have been studied in models with different sizes of 2 nm, 3 nm, 4 nm and 5 nm under non-periodic boundary conditions. We use the pairwise interatomic potentials proposed by Matsui and Akaogi. Models have been obtained by cooling from the melt via molecular dynamics (MD) simulation. Structural properties of an amorphous nanoparticle obtained at 350 K have been analyzed in detail through the partial radial distribution functions (PRDFs), coordination number distributions, bond-angle distributions and interatomic distances. Moreover, we show the radial density profile in a nanoparticle. Calculations show that size effects on structure of a model are significant and that if the size is larger than 3 nm, amorphous TiO2 nanoparticles have a distorted octahedral network structure with the mean coordination number ZTi-O ≈6.0 and ZO-Ti ≈3.0 like those observed in the bulk. Surface structure and surface energy of nanoparticles have been obtained and presented

Structural properties of amorphous Fe

We have investigated the microstructure of amorphous Fe2O3 nanoparticles by using molecular dynamics (MD) simulations. Non-periodic boundary conditions with Born-Mayer type pair potentials were used to simulate a spherical model of different diameters of 2, 3, 4 and 5 nm. Structural properties of an amorphous model obtained at 350 K have been analyzed in detail through the partial radial distribution functions (PRPFs), coordination number distributions, bond-angle distributions and interatomic distances. Calculations showed that structural characteristics of the model are in qualitative agreement with the experimental data. The observation of a large amount of structural defects as the particle size is decreased suggested that surface structure strongly depends on the size of nanoparticles. In addition, surface structure of amorphous Fe2O3 nanoparticles have been studied and compared with that observed in the core and in the bulk counterpart. Radial density profiles and stoichiometry in amorphous Fe2O3 nanoparticles were also found and discussed

Socinianism - Part 1

Understanding how ligands bind to G-protein coupled receptors (GPCRs) provides insights into a myriad of cell processes and is crucial for drug development. Here we extend a hybrid molecular mechanics/coarse-grained (MM/CG) approach applied previously to enzymes to GPCR/ligand complexes. The accuracy of this method for structural predictions is established by comparison with recent atomistic molecular dynamics simulations on the human β2 adrenergic receptor, a member of the GPCRs superfamily. The results obtained with the MM/CG methodology show a good agreement with previous all-atom classical dynamics simulations, in particular in the structural description of the ligand binding site. This approach could be used for high-throughput predictions of ligand poses in a variety of GPCRs