On molecular topological properties of hex‐derived networks

Topological indices are numerical parameters of a molecular graph, which characterize its topology and are usually graph invariant. In quantitative structure–activity relationship/quantitative structure–property relationship study, physico‐chemical properties and topological indices such as Randić, atom–bond connectivity (ABC), and geometric–arithmetic (GA) index are used to predict the bioactivity of chemical compounds. Graph theory has found a considerable use in this area of research. In this paper, we study hex‐derived networks HDN1(n) and HDN2(n), which are generated by hexagonal network of dimension n and derive analytical closed results of general Randić index R_α(G) for different values of α, for these networks of dimension n. We also compute the general first Zagreb, ABC, GA, ABC₄, and GA₅ indices for these hex‐derived networks for the first time and give closed formulae of these degree‐based indices for hex‐derived networks. Copyright © 2016 John Wiley & Sons, Ltd.     

Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology

BackgroundIn this study, the network pharmacological methods were used to predict the target of effective components of compounds in Zisheng Shenqi Decoction (ZSD, or Nourishing Kidney Qi Decoction) in the treatment of gouty arthritis (GA).MethodThe main effective components and corresponding key targets of herbs in the ZSD were discerned through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP), Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) database. UniProt database and Swiss Target Prediction (STP) database was used to rectify and unify the target names and supply the target information. The targets related to GA were obtained by using GeneCards database. After we discovered the potential common targets between ZSD and GA, the interaction network diagram of “ZSD-component-GA-target” was constructed by Cytoscape software (Version 3.7.1). Subsequently, the Protein-protein interaction (PPI) network of ZSD effective components-targets and GA-related targets was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING). Bioconductor package “org.Hs.eg.db” and “cluster profiler” package were installed in R software (Version 3.6.0) which used for Gene Ontology analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis.Results146 components and 613 targets of 11 herbal medicines in the ZSD were got from TCMSP database and BATMAN-TCM database. 987 targets of GA were obtained from GeneCards database. After intersected and removed duplications, 132 common targets between ZSD and GA were screened out by Cytoscape software (Version 3.7.1). These common targets derived from 81 effective components of 146 components, such as quercetin, stigmasterol and kaempferol. They were closely related to anti-inflammatory, analgesic and anti oxidative stress and the principal targets comprised of Purinergic receptor P2X, ligand-gated ion channel 7 (P2x7R), Nod-like receptor protein 3 (NLRP3) and IL-1β. GO enrichment analysis and KEGG pathway enrichment analysis by R software (Version 3.6.0) showed that the key target genes had close relationship with oxidative stress, reactive oxygen species (ROS) metabolic process and leukocyte migration in aspects of biological process, cell components and molecular function. It also indicated that ZSD could decrease inflammatory reaction, alleviate ROS accumulation and attenuate pain by regulating P2 × 7R and NOD like receptor signaling pathway of inflammatory reaction.ConclusionA total of 81 effective components and 132 common target genes between ZSD and GA were screened by network pharmacology. The PPI network, GO enrichment analysis and KEGG pathway enrichment analysis suggested that ZSD can exerte anti-inflammatory and analgesic effects on the treatment of GA by reducing decreasing inflammatory reaction, alleviating ROS accumulation, and attenuating pain. The possible molecular mechanism of it mainly involved multiple components, multiple targets and multiple signaling pathways, which provided a comprehensive understanding for further study. In general, the network pharmacological method applied in this study provides an alternative strategy for the mechanism of ZSD in the treatment of GA.     

Numerical solution of Navier–Stokes equations using multiquadric radial basis function networks

A numerical method based on radial basis function networks (RBFNs) for solving steady incompressible viscous flow problems (including Boussinesq materials) is presented in this paper. The method uses a ‘universal approximator’ based on neural network methodology to represent the solutions. The method is easy to implement and does not require any kind of ‘finite element‐type’ discretization of the domain and its boundary. Instead, two sets of random points distributed throughout the domain and on the boundary are required. The first set defines the centres of the RBFNs and the second defines the collocation points. The two sets of points can be different; however, experience shows that if the two sets are the same better results are obtained. In this work the two sets are identical and hence commonly referred to as the set of centres. Planar Poiseuille, driven cavity and natural convection flows are simulated to verify the method. The numerical solutions obtained using only relatively low densities of centres are in good agreement with analytical and benchmark solutions available in the literature. With uniformly distributed centres, the method achieves Reynolds number Re = 100 000 for the Poiseuille flow (assuming that laminar flow can be maintained) using the density of , Re = 400 for the driven cavity flow with a density of and Rayleigh number Ra = 1 000 000 for the natural convection flow with a density of . Copyright © 2001 John Wiley & Sons, Ltd.     

Reduced‐order modelling of an adaptive mesh ocean model

A novel proper orthogonal decomposition (POD) model has been developed for use with an advanced unstructured mesh finite‐element ocean model, the Imperial College Ocean Model (ICOM, described in detail below), which includes many recent developments in ocean modelling and numerical analysis. The advantages of the POD model developed here over existing POD approaches are the ability:

• 1. To increase accuracy when representing geostrophic balance (the balance between the Coriolis terms and the pressure gradient). This is achieved through the use of two sets of geostrophic basis functions where each one is calculated by basis functions for velocities u and v.
• 2. To speed up the POD simulation. To achieve this a new numerical technique is introduced, whereby a time‐dependent matrix in the discretized equation is rapidly constructed from a series of time‐independent matrices. This development imparts considerable efficiency gains over the often‐used alternative of calculating each finite element over the computational domain at each time level.
• 3. To use dynamically adaptive meshes in the above POD model.

Copyright © 2008 John Wiley & Sons, Ltd.     

Stopping a Viscous Fluid by a Feedback Dissipative Field: I. The Stationary Stokes Problem

We consider a planar stationary flow of an incompressible viscous fluid in a semiinfinite strip governed by the Stokes system with a body forces field. We show how this fluid can be stopped at a finite distance of the entrance of the semi-infinite strip by means of a feedback field depending in a sub-linear way on the velocity field. This localization effect is proved reducing the problem to a non-linear bi-harmonic type one for which the localization of solutions is obtained by means of the application of a suitable energy method. Since the presence of the non-linear terms defined through the body forces field is not standard in the fluid mechanics literature, we establish also some results about the existence and uniqueness of weak solutions for this problem.     

Optical and Electronic Properties of Different Kinds of Water‐Soluble Porphyrin Films

Water‐soluble porphyrin‐porphyrin and porphyrin‐CdSe nanoparticle monolayer films were self‐assembled on different substrates. The influence of substrates, types of films, and heat treatment temperature on fluorescence of different kinds of porphyrin films was investigated. The SEM images showed the formation of monolayer films on porous alumina foil. The films assembled on porous alumina foil possessed higher fluorescence intensity and thermal stability. The result of conductance measurement indicated that the interaction of trimethylamidophenylporphyrin iodide (TAPPI) molecules with hydroxyl groups on porous alumina foil was weakened after CdSe nanoparticles assembled with TAPPI.     

Metallomicellar Catalysis: Hydrolysis of Phosphodiester with Cu(II) and Zn(II) Complexes in Micellar Solution

Abstract

The effects of two metal complexes of 2,2′‐dipyridylamine (bpya) ligand, [(bpya)Cu]Cl₂ and [(bpya)Zn]Cl₂, in promoting the hydrolysis of bis(4‐nitrophenyl) phosphate (BNPP) have been kinetically investigated in Brij35 micellar solution and at 298 K, pH ranging from 6.41 to 8.6. In neutral micellar solution at 298 K, pH 7.02, the rate constants for the catalytic hydrolysis of BNPP by [(bpya)Cu]Cl₂ and [(bpya)Zn]Cl₂ are 1.2 × 10⁶ times and 1.5 × 10⁵ times higher than those for the spontaneous hydrolysis, respectively. Kinetic studies show that the active species in the catalytic hydrolysis of BNPP is the aquo‐hydroxy form, and the relative kinetic and thermodynamic parameters indicate that the mechanism of the reaction involves intramolecular nucleophilic attack on the metal center‐bound diester.     

An Efficient One-Pot Synthesis of Nitriles from Carboxylic Acids Without Solvent Under Microwave Irradiation

Nitriles were prepared from alkyl and aryl carboxylic acids in dry media conditions, under microwave irradiation. Heating of the carboxylic acid, urea and amidosulfonic acid adsorbed on alumina support in a microwave oven affords nitriles in 20–93% yields.     

Synthesis and Characterization of N‐methylenephenyl Phosphonic Chitosan

Chitosan is a natural based polymer obtained by alkaline deacetylation of chitin, exhibiting excellent properties such as non‐toxicity, biocompatibility and biodegradability. N‐Methylenephenyl phosphonic chitosan (NMPPC) is synthesized from chitosan by reacting with phenyl phosphonic acid using formaldehyde. The NMPPC was characterized by FTIR, ³¹P‐NMR, X‐ray diffraction, scanning electron microscopy, thermogravimeteric analysis and solubility studies. A significant decrease of molecular weight was observed in the NMPPC. The TGA studies suggested that NMPPC has less thermal stability than chitosan. The X‐ray diffraction analysis showed that NMPPC was amorphous in nature. The solubility property of the polymer was improved after the incorporation of a phenyl phosphonic group.