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Microstructural properties of liquid and amorphous SiO 2 nanoparticles have been investigated via molecular dynamics (MD) simulations with the interatomic potentials that have weak Coulomb interaction and Morse-type short-range interaction under non-periodic boundary conditions. Structural properties of spherical nanoparticles with different sizes of 2, 4 and 6 nm obtained at 3500 K have been studied through partial radial distribution functions (PRDFs), coordination number and bond-angle distributions, and compared with those observed in the bulk. The core and surface structures of liquid SiO 2 nanoparticles have been studied in detail. We found significant size effects on structure of nanoparticles. Calculations also show that if the size is larger than 4 nm, liquid SiO 2 nanoparticles at the temperature of 3500 K have a lightly distorted tetrahedral network structure with the mean coordination number Z Si–O ≈4.0 and Z O–Si ≈2.0 like those observed in the bulk. Moreover, temperature dependence of structural defects and SiO x stoichiometry in nanoparticles on cooling from the melt has been found and presented.

Structural properties of amorphous GeO2 nanoparticles have been studied by using molecular dynamics (MD) simulations. Four models with different sizes of 2, 3, 4 and 5 nm have been obtained by cooling from the melt via the MD method under nonperiodic boundary conditions. We used the interatomic potentials that have a weak Coulomb interaction and Morse-type short-range interaction. Structural properties of amorphous nanoparticles obtained at 300 K have been analyzed in detail through the partial radial distribution functions (PRDFs), mean interatomic distances, coordination number and bond-angle distributions compared with those observed for the bulk counterpart. Moreover, the radial density profile in nanoparticles was found and discussed. Calculations showed that size effects on structure of amorphous GeO2 nanoparticles are significant in that if the size is larger than 3 nm amorphous GeO2 nanoparticle has a distorted tetrahedral network structure with the mean coordination number ZGe–O ≈ 4.0 and ZO–Ge ≈ 2.0 like those observed in the bulk counterpart. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Diffusion in simulated liquid GeO2 under pressure at different temperatures has been studied via isochore molecular dynamics (MD) simulation in a model containing 3000 particles with interatomic potentials that have weak Coulomb interaction and Morse-type short-range interaction. Calculations were done in models at three different densities of 3.65, 5.90 and 7.90 g/cm3. After intensive testing we found that the temperature dependence of the diffusion constant of atomic species in liquid GeO2 shows an Arrhenius law at relatively low temperatures, and at higher temperatures it shows a power law, D∼(T–Tc)γ, with an exception for models at a very high density of 7.90 g/cm3. Specific features of diffusion in liquid GeO2 compared with those observed in other strong liquids such as SiO2 or in other GeO2 models have been observed and discussed.

We perform molecular dynamics (MD) simulation of diffusion in liquid GeO2 at the temperatures ranged from 3000 to 5000 K and densities ranged from 3.65 to 7.90 g/cm3. Simulations were done in a model containing 3000 particles with the new interatomic potentials for liquid and amorphous GeO2, which have weak Coulomb interaction and Morse-type short-range interaction. We found a liquid–liquid phase transition in simulated liquid GeO2 from a tetrahedral to an octahedral network structure upon compression. Moreover, such phase transition accompanied with an anomalous diffusion of particles in liquid GeO2 that the diffusion constant of both Ge and O particles strongly increases with increasing density (e.g. with increasing pressure) and it shows a maximum at the density around 4.95 g/cm3. The possible relation between anomalous diffusion of particles and structural phase transition in the system has been discussed.

By using molecular dynamics (MD) simulations we found a transition from a tetrahedral to an octahedral network structure in an amorphous SiO2 model under compression from 2.20 to 5.35 g/cm3. And on heating of a high density amorphous (hda) model of 5.35 g/cm3 at zero pressure, the structure transforms to a low density amorphous (lda) form. Simulations were done in a model containing 3000 particles under periodic boundary conditions with interatomic potentials which have a weak Coulomb interaction and a Morse type short-range interaction.

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. © 2013 Sandal et al.

Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

Equations of state of a frustrated two-sublattice Ising ferrimagnet are derived in the mean-field approximation. The H - T phase diagram is studied. It is pointed out that the intrasublattice frustration strongly affects the reentrant transition temperature T g ( H ). For certain parameters of the model T g ( H ) increases with the field. The influence of frustration on the compensation point is investigated. It is shown that the magnetization of the frustrated ferrimagnetic is continuous at the transition from a ferrimagnetic state to a state of coexistence of ferrimagnetism and spin glass. The temperature dependence of the susceptibility in the ergodic phase is obtained for various degrees of frustration.

We model s-wave and d-wave disordered granular superconductors with a three-dimensional lattice of randomly distributed Josephson junctions. The nonlinear ac resistivity rho(2) of these systems was calculated using Langevin dynamical equations. The current amplitude dependence of rho(2) at the peak position is found to be a power law characterized by exponent alpha, which 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 alpha = 0.5+/-0.1 for both s- and d-wave materials. In accord with experiments, we find alpha approximately 1 for some interval of inductance in the strong current regime.

We model s-wave and d-wave disordered granular superconductors with a three-dimensional lattice of randomly distributed Josephson junctions. The nonlinear ac resistivity rho(2) of these systems was calculated using Langevin dynamical equations. The current amplitude dependence of rho(2) at the peak position is found to be a power law characterized by exponent alpha, which 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 alpha = 0.5+/-0.1 for both s- and d-wave materials. In accord with experiments, we find alpha approximately 1 for some interval of inductance in the strong current regime.

The current–voltage characteristics of the three-dimensional anisotropic vortex glass model of disordered type-II superconductors with a uniformly field threading the system are studied by the Lagevin dynamics technique. Using the finite size scaling analysis, we show that in the presence of screening the correlation length exponent ν=2.6±0.35 which is compatible with recent results of the static Monte-Carlo simulations but it is considerably higher than that for the standard gauge glass model.

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., 27 pages, 15 figures

Diffusion of Si and O ions in simulated liquid SiO2 under high pressure (or high density) have been studied in a model containing 3000 ions under periodic boundary conditions with pairwise interatomic potentials which have a weak electrostatic interaction and Morse-type short-range interaction. In order to observe diffusion in the liquid state, amorphous models at fixed densities of 2.20, 4.30 and 5.35 g cm−3 have been heated up from 350 to 7000 K via molecular dynamics (MD) simulation and the diffusion constant has been calculated at temperatures ranging from above the melting point to 7000 K. Calculations show that the temperature dependence of the diffusion constant D of components in the system shows an Arrhenius law at relatively low temperatures above the melting point and shows a power law, , at higher temperatures. Dynamical heterogeneities under high pressure have been observed and discussed.