SPH modelling of depth‐limited turbulent open channel flows over rough boundaries

A numerical model based on the smoothed particle hydrodynamics method is developed to simulate depth‐limited turbulent open channel flows over hydraulically rough beds. The 2D Lagrangian form of the Navier–Stokes equations is solved, in which a drag‐based formulation is used based on an effective roughness zone near the bed to account for the roughness effect of bed spheres and an improved sub‐particle‐scale model is applied to account for the effect of turbulence. The sub‐particle‐scale model is constructed based on the mixing‐length assumption rather than the standard Smagorinsky approach to compute the eddy‐viscosity. A robust in/out‐flow boundary technique is also proposed to achieve stable uniform flow conditions at the inlet and outlet boundaries where the flow characteristics are unknown. The model is applied to simulate uniform open channel flows over a rough bed composed of regular spheres and validated by experimental velocity data. To investigate the influence of the bed roughness on different flow conditions, data from 12 experimental tests with different bed slopes and uniform water depths are simulated, and a good agreement has been observed between the model and experimental results of the streamwise velocity and turbulent shear stress. This shows that both the roughness effect and flow turbulence should be addressed in order to simulate the correct mechanisms of turbulent flow over a rough bed boundary and that the presented smoothed particle hydrodynamics model accomplishes this successfully. © 2016 The Authors International Journal for Numerical Methods in Fluids Published by John Wiley & Sons Ltd     

Chitosan loaded with silver nanoparticles,CS‐AgNPs,using thymus syriacus,wild mint,and rosemary essential oil extracts as reducing and capping agents

The present study describes the green method for the preparation of chitosan loaded with silver nanoparticles (CS‐AgNPs) in the presence of 3 different extracted essential oils. The essential oils play dual roles as reductant and capping agents. The reducing power and DPPH (2,2‐diphenyl‐1‐picrylhydrazyl) assay for the 3 essential oils—Thymus syriacus (T), wild mint (M), and rosemary (R)—have been reported. The preparation of CS‐AgNPs was performed by 2 steps. The 3 previously extracted essential oils have been used as reducing and capping agent in the first step, while in the second step, silver nanoparticles were integrated in chitosan. The integration of AgNPs in the structure of chitosan was confirmed by ultraviolet‐visible, Fourier transform infrared spectroscopy, scanning electron microscopy techniques, and energy dispersive X‐ray. Surface plasmon resonance confirmed the formation of CS‐AgNPs with maximum absorbance at λ_max between 405 ‐ 410 and 410 ‐ 430 nm for colloidal and films of CS‐AgNPs, respectively. The intensity of bands at 3408 cm^?1 in the fourier transform infrared spectroscopy measurements was decreased substantially and shifted slightly to lower frequency (?υ = 43 cm^?1). Scanning electron microscopy shows a spherical morphology of AgNPs with size of 62 nm for both colloidal and film samples, and energy dispersive X‐ray analysis shows peaks confirming AgNPs formation.     

Enantioselective determination of modafinil in pharmaceutical formulations by capillary electrophoresis, and computational calculation of their inclusion complexes

A fast capillary electrophoretic method is described for the separation and determination of the enantiomers of the novel wake-promoting agent, modafinil. Several parameters affecting the separation were studied, including the type and concentration of chiral selector, buffer pH, buffer concentration, voltage and temperature. Good chiral separation of the racemic mixture was achieved in less than 5 min with resolution factor Rs?=?2.51, using a bare fused-silica capillary and a background electrolyte (BGE) of 25 mM H₃PO₄?1 M tris solution; pH 8.0; containing 30 mg mL^?1 of sulfated-β-cyclodextrin (S-β-CD). The separation was carried out in normal polarity mode at 25 ^?C, 18 kV and using hydrostatic injection. Acceptable validation criteria for selectivity, linearity, precision, and accuracy were included. The developed method was successfully applied to the assay of enantiomers of modafinil in pharmaceutical formulations. The computational calculations for the enantiomeric inclusion complexes rationalized the reasons for the different migration times between the modafinil enantiomers.     

Photochemical functionalization of gallium nitride thin films with molecular and biomolecular layers

We demonstrate that photochemical functionalization can be used to functionalize and photopattern the surface of gallium nitride crystalline thin films with well-defined molecular and biomolecular layers. GaN(0001) surfaces exposed to a hydrogen plasma will react with organic molecules bearing an alkene (C=C) group when illuminated with 254 nm light. Using a bifunctional molecule with an alkene group at one end and a protected amine group at the other, this process can be used to link the alkene group to the surface, leaving the protected amine exposed. Using a simple contact mask, we demonstrate the ability to directly pattern the spatial distribution of these protected amine groups on the surface with a lateral resolution of <12 mum. After deprotection of the amines, single-stranded DNA oligonucleotides were linked to the surface using a bifunctional cross-linker. Measurements using fluorescently labeled complementary and noncomplementary sequences show that the DNA-modified GaN surfaces exhibit excellent selectivity, while repeated cycles of hybridization and denaturation in urea show good stability. These results demonstrate that photochemical functionalization can be used as an attractive starting point for interfacing molecular and biomolecular systems with GaN and other compound semiconductors.     

Lithium Choreography: Intramolecular Arylations of Carbamate‐Stabilised Carbanions and Their Mechanisms Probed by In Situ IR Spectroscopy and DFT Calculations

Deprotonation of O‐allyl, O‐propargyl or O‐benzyl carbamates in the presence of a lithium counterion leads to carbamate‐stabilised organolithium compounds that may be quenched with electrophiles. We now report that when the allylic, propargylic or benzylic carbamate bears an N‐aryl substituent, an aryl migration takes place, leading to stereochemical inversion and C‐arylation of the carbamate α to oxygen. The aryl migration is an intramolecular S_NAr reaction, despite the lack of anion‐stabilising aryl substituents. Our in situ IR studies reveal a number of intermediates along the rearrangement pathway, including a “pre‐lithiation complex,” the deprotonated carbamate, the rearranged anion, and the final arylated carbamate. No evidence was obtained for a dearomatised intermediate during the aryl migration. DFT calculations predict that during the reaction the solvated Li cation moves from the carbanion centre, thus freeing its lone pair for nucleophilic attack on the remote phenyl ring. This charge separation leads to several alternative conformations. The one having Li⁺ bound to the carbamate oxygen gives rise to the lowest‐energy transition structure, and also leads to inversion of the configuration. In agreement with the IR studies, the DFT calculations fail to locate a dearomatised intermediate.     

Mueller matrices in fluorescence scattering

A reappraisal of the 1929 analysis of luminescence by Soleillet reveals the form of the Mueller matrix for fluorescence scattering whose parameters are directly defined in terms of the now-familiar fluorescence anisotropy parameter. If the scattering analyte is optically active, it is further shown how fluorescence detected circular dichroism and circularly polarized luminescence can be recovered, simultaneously and free of artifacts.     

Recent performance improvements to the DFT and TDDFT in GAMESS

The general atomic and molecular electronic structure system (GAMESS) is a quantum chemistry package used in the first-principles modeling of complex molecular systems using density functional theory (DFT) as well as a number of other post-Hartree-Fock methods. Both DFT and time-dependent DFT (TDDFT) are of particular interest to the materials modeling community. Millions of CPU hours per year are expended by GAMESS calculations on high-performance computing systems; any substantial reduction in the time-to-solution for these calculations represents a significant saving in CPU hours. As part of this work, three areas for improvement were identified: (1) the exchange-correlation (XC) integration grid, (2) profiling and optimization of the DFT code, and (3) TDDFT parallelization. We summarize the work performed in these task areas and present the resulting performance improvement. These software enhancements are available in 12JAN2009R3 or later versions of GAMESS.     

Selenium status and cancer mortality in subjects residing in four Canadian provinces

The objective of this study was to measure selenium status in maleand female Canadian subjects relative to cancer mortality in their respectiveprovinces. Toenail specimens from 755 subjects, 377 males and 378 females,living in Vancouver (186), Edmonton (188), Toronto (197) and Montreal (184)were analyzed by instrumental neutron activation analysis giving means of0.968±0.177, 0.950±0.148, 0.932±0.135 and 0.896±0.127ppm Se, respectively. The effect of selenium determinants such as gender,selenium supplementation and smoking on selenium status is presented. Detailsof the observed inverse relationship of selenium status and cancer mortalityare discussed.     

Effect of hydrostatic pressure on the elastic moduli of As2S3 and As2Se3 glasses at 195 and 296 K

Velocities of 30 MHz longitudinal and shear ultrasonic waves have been measured in As₂S₃ and As₂Se₃ glasses as a function of hydrostatic pressure up to 1.5 kbar at 195 K and 3 kbar at 296 K. The elastic stiffness moduli are found to have relatively large, positive, pressure dependences which are about the same at both temperatures for both glasses. This behavior is attributed to the weakness of bonding between layers comprised of AsS₃ and AsS₃ pyramids.Inspection of data for a variety of glasses reveals a correlation between the value of C_L/3C_T and whether the elastic moduli are increased or decreased by pressure. (C_L is the longitudinal modulus and C_T the shear modulus.)Using the pressure dependences of the elastic moduli obtained in the present work, it is found that volume change is responsible for most of the temperature dependences of the moduli. In addition elastic gammas are obtained which are consistent with thermal Grüneisen gammas at 12 K. The pressure dependence of the volume of As₂S₃ glass at 296 K is calculated using the present results in the Murnagham equation. Agreement with volumetric data of Weir is obtained.     

A vending machine for drug-like molecules – automated synthesis of virtual screening hits

As a result of high false positive rates in virtual screening campaigns, prospective hits must be synthesised for validation. When done manually, this is a time consuming and laborious process. Large “on-demand” virtual libraries (>7 × 10¹² members), suitable for preparation using capsule-based automated synthesis and commercial building blocks, were evaluated to determine their structural novelty. One sub-library, constructed from iSnAP capsules, aldehydes and amines, contains unique scaffolds with drug-like physicochemical properties. Virtual screening hits from this iSnAP library were prepared in an automated fashion for evaluation against Aedes aegypti and Phytophthora infestans. In comparison to manual workflows, this approach provided a 10-fold improvement in user efficiency. A streamlined method of relative stereochemical assignment was also devised to augment the rapid synthesis. User efficiency was further improved to 100-fold by downscaling and parallelising capsule-based chemistry on 96-well plates equipped with filter bases. This work demonstrates that automated synthesis consoles can enable the rapid and reliable preparation of attractive virtual screening hits from large virtual libraries.

A compact and operationally simple automation technology can prepare virtual screening hits from a large on-demand library of drug-like molecules.