Validation of a novel very large eddy simulation method for simulation of turbulent separated flow

The paper describes the validation of a newly developed very LES (VLES) method for the simulation of turbulent separated flow. The new VLES method is a unified simulation approach that can change seamlessly from Reynolds‐averaged Navier–Stokes to DNS depending on the numerical resolution. Four complex test cases are selected to validate the performance of the new method, that is, the flow past a square cylinder at Re = 3000 confined in a channel (with a blockage ratio of 20%), the turbulent flow over a circular cylinder at Re = 3900 as well as Re = 140,000, and a turbulent backward‐facing step flow with a thick incoming boundary layer at Re = 40,000. The simulation results are compared with available experimental, LES, and detached eddy simulation‐type results. The new VLES model performs well overall, and the predictions are satisfactory compared with previous experimental and numerical results. It is observed that the new VLES method is quite efficient for the turbulent flow simulations; that is, good predictions can be obtained using a quite coarse mesh compared with the previous LES method. Discussions of the implementation of the present VLES modeling are also conducted on the basis of the simulations of turbulent channel flow up to high Reynolds number of Re_τ = 4000. The efficiency of the present VLES modeling is also observed in the channel flow simulation. From a practical point of view, this new method has considerable potential for more complex turbulent flow simulations at relative high Reynolds numbers. Copyright © 2013 John Wiley & Sons, Ltd.     

Non-linear global dynamics of an axially moving plate

In the present study, the geometrically non-linear dynamics of an axially moving plate is examined by constructing the bifurcation diagrams of Poincaré maps for the system in the sub and supercritical regimes. The von Kármán plate theory is employed to model the system by retaining in-plane displacements and inertia. The governing equations of motion of this gyroscopic system are obtained based on an energy method by means of the Lagrange equations which yields a set of second-order non-linear ordinary differential equations with coupled terms. A change of variables is employed to transform this set into a set of first-order non-linear ordinary differential equations. The resulting equations are solved using direct time integration, yielding time-varying generalized coordinates for the in-plane and out-of-plane motions. From these time histories, the bifurcation diagrams of Poincaré maps, phase-plane portraits, and Poincaré sections are constructed at points of interest in the parameter space for both the axial speed regimes.     

Issue Information

Three‐dimensional direct numerical simulation results of flow past a circular cylinder are influenced by numerical aspects, for example the spanwise domain length and the lateral boundary condition adopted for the simulation. It is found that inappropriate numerical set‐up, which restricts the development of intrinsic wake structure, leads to an over‐prediction of the onset point of the secondary wake instability (Re_cr). A best practice of the numerical set‐up is presented for the accurate prediction of Re_cr by direct numerical simulation while minimizing the computational cost. The cylinder span length should be chosen on the basis of the intrinsic wavelength of the wake structure to be simulated, whereas a long span length is not necessary. For the wake transitions above Re_cr, because the wake structures no longer follow particular wavelengths but become disordered and chaotic, a span length of more than 10 cylinder diameters (approximately three times the intrinsic wavelength) is recommended for the simulations to obtain wake structures and hydrodynamic forces that are not strongly restricted by the numerical set‐up. The performances of the periodic and symmetry lateral boundary conditions are compared and discussed. The symmetry boundary condition is recommended for predicting Re_cr, while the periodic boundary condition is recommended for simulating the wake structures above Re_cr. The general conclusions drawn through a circular cylinder are expected to be applicable to other bluff body configurations. Copyright © 2017 John Wiley & Sons, Ltd.     

Monofluoroalkene-Isostere as a 19F NMR Label for the Peptide Backbone: Synthesis and Evaluation in Membrane-Bound PGLa and (KIGAKI)3

Solid-state ¹⁹F NMR is a powerful method to study the interactions of biologically active peptides with membranes. So far, in labelled peptides, the ¹⁹F-reporter group has always been installed on the side chain of an amino acid. Given the fact that monofluoroalkenes are non-hydrolyzable peptide bond mimics, we have synthesized a monofluoroalkene-based dipeptide isostere, Val-Ψ[(Z)-CF=CH]-Gly, and inserted it in the sequence of two well-studied antimicrobial peptides: PGLa and (KIGAKI)₃ are representatives of an α-helix and a β-sheet. The conformations and biological activities of these labeled peptides were studied to assess the suitability of monofluoroalkenes for ¹⁹F NMR structure analysis.     

Amino-Acid-Induced Circular Polarized Luminescence in One-Dimensional Manganese(II) Halide Hybrid

Circular polarized luminescence (CPL)-active materials attract great attentions owing to their widely applications in 3D optical displays and encrypted transmission. Inspired by the strategies adopted in perovskite based CPL materials, herein, CPL-active hybrids (D)- and (L)-(tert-butyl prolinate)MnCl₃ were successfully prepared by assembling chiral D/L tert-butyl prolinate with manganese (II) chloride. Single crystal structures show the as-formed hybrids possess one-dimensional (1D) structure containing linear chains of face-sharing MnCl₆ octahedral surrounded by prolinate cations. The 1D Mn(II) hybrids display strong red emission peaked at 646 nm with PLQY of 67.1 % and 57.2 % for d -type and l -type, respectively, representing the highest PLQY for 1D Mn^II hybrids. Interestingly, the 1D Mn(II) hybrids exhibit prominent circular dichroism (CD) signals and remarkable CPL activity with the dissymmetry factor g of 6.1*10⁻³ and −6.3*10⁻³ from 550 to 800 nm for (D)- and (L)-(tert-butyl prolinate)MnCl₃, respectively, owing to the existence of chiral cations. It is worthy noted the obtained g represents the highest value for non-lead organic–inorganic hybrids.     

A Tunable,Fullerene-Based Molecular Amplifier for Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) studies are reported on a chiral compound in which a fullerene C₆₀ moiety is used as an electron acceptor and local VCD amplifier for an alanine-based peptide chain. Four redox states are investigated in this study, of which three are reduced species that possess low-lying electronic states as confirmed by UV/Vis spectroelectrochemistry. VCD measurements in combination with (TD)DFT calculations are used to investigate (i) how the low-lying electronic states of the reduced species modulate the amplification of VCD signals, (ii) how this amplification depends on the distance between oscillator and amplifier, and (iii) how the spatial extent of the amplifier influences amplification. These results pave the way for further development of tailored molecular VCD amplifiers.     

1,2-Dihydro-1-hydroxy-2,3,1-benzodiazaborine Bearing an Acridine Moiety as a Circular Dichroism Probe for Determination of Absolute Configuration of Mono-Alcohols

A new chiral probe molecule for mono-alcohols is developed by using 1,2-dihydro-1-hydroxy-2,3,1-benzodiazaborine (DAB) bearing an acridine moiety 1 . In the presence of mono-alcohols, DAB 1 forms borate 2 by boronic ester formation, followed by coordination of the acridine moiety to the boron atom. Borate 2 has a chiral center on the boron atom and works as a stereodynamic circular dichroism (CD) probe molecule for chiral mono-alcohols based on the π–π interaction between the acridine moiety and the carbon–carbon unsaturated moiety on mono-alcohols.     

Chiral one‐dimensional hydrogen‐bonded architectures constructed from single‐enantiomer phosphoric triamides

The two single‐enantiomer phosphoric triamides N‐(2,6‐difluorobenzoyl)‐N′,N′′‐bis[(S)‐(−)‐α‐methylbenzyl]phosphoric triamide, [2,6‐F₂‐C₆H₃C(O)NH][(S)‐(−)‐(C₆H₅)CH(CH₃)NH]₂P(O), denoted L‐1 , and N‐(2,6‐difluorobenzoyl)‐N′,N′′‐bis[(R)‐(+)‐α‐methylbenzyl]phosphoric triamide, [2,6‐F₂‐C₆H₃C(O)NH][(R)‐(+)‐(C₆H₅)CH(CH₃)NH]₂P(O), denoted D‐1 , both C₂₃H₂₄F₂N₃O₂P, have been investigated. In their structures, chiral one‐dimensional hydrogen‐bonded architectures are formed along [100], mediated by relatively strong N—H…O(P) and N—H…O(C) hydrogen bonds. Both assemblies include the noncentrosymmetric graph‐set motifs R₂²(10), R₂¹(6) and C₂²(8), and the compounds crystallize in the chiral space group P1. Due to the data collection of L‐1 at 120 K and of D‐1 at 95 K, the unit‐cell dimensions and volume show a slight difference; the contraction in the volume of D‐1 with respect to that in L‐1 is about 0.3%. The asymmetric units of both structures consist of two independent phosphoric triamide molecules, with the main difference being seen in one of the torsion angles in the OPNHCH(CH₃)(C₆H₅) part. The Hirshfeld surface maps of these levo and dextro isomers are very similar; however, they are near mirror images of each other. For both structures, the full fingerprint plot of each symmetry‐independent molecule shows an almost asymmetric shape as a result of its different environment in the crystal packing. It is notable that NMR spectroscopy could distinguish between compounds L‐1 and D‐1 that have different relative stereocentres; however, the differences in chemical shifts between them were found to be about 0.02 to 0.001 ppm under calibrated temperature conditions. In each molecule, the two chiral parts are also different in NMR media, in which chemical shifts and P–H and P–C couplings have been studied.     

Finite deformation swelling of a temperature-sensitive hydrogel cylinder under combined extension-torsion

The swelling behavior of a temperature-sensitive poly-N-isopropylacrylamide(PNIPAM) hydrogel circular cylinder is studied subjected to combined extension-torsion and varied temperature. In this regard, a semi-analytical solution is proposed for general combined loading. A finite element(FE) analysis is conducted, subjecting a hydrogel cylinder to the combined extension-torsion and the varied temperature to evaluate the validity and accuracy of the solution. A user-defined UHYPER subroutine is developed and verified under free and constrained swelling conditions. The FE results illustrate excellent agreement with the semi-analytical solution. Due to the complexity of the problem, some compositions and applied loading factors are analyzed. It is revealed that for larger cross-linked density and larger ending temperature, the cylinder yields higher stresses and smaller radial swelling deformation. Besides, the radial and hoop stresses increase by applying larger twist and axial stretch. The hoop stresses intersect at approximately R/Rout = 0.58, where the hoop stress vanishes. Besides, the axial force has direct and inverse relationships with the axial stretch and the twist, respectively. However, the resultant torsional moment behavior is complex, and the position of the maximum point varies significantly by altering the axial stretch and the twist.     

Complete NMR assignments of bioactive rotameric (3 → 8) biflavonoids from the bark of Garcinia hombroniana

The genus Garcinia is reported to possess antimicrobial, anti‐inflammatory, anticancer, hepatoprotective and anti‐HIV activities. Garcinia hombroniana in Malaysia is used to treat itching and as a protective medicine after child birth. This study was aimed to isolate the chemical constituents from the bark of G. hombroniana and explore their possible pharmacological potential. Ethyl acetate extract afforded one new (1) and six (2–7) known 3 → 8 rotameric biflavonoids. Their structures were elucidated by UV, IR and NMR (1D and 2D) spectroscopy together with electron ionization/ESI mass spectrometric techniques and were identified as (2R, 3S) volkensiflavone‐7‐O‐rhamnopyranoside (1), volkensiflavone (2), 4″‐O‐methyl‐volkensiflavone (3), volkensiflavone‐7‐O‐glucopyranoside (4), morelloflavone (5), 3″‐O‐methyl‐morelloflavone (6) and morelloflavone‐7‐O‐glucopyranoside (7). The absolute configuration of compound 1 was assigned by circular dichroism spectroscopy as 2R, 3S. The coexistence of conformers of isolated biflavonoids in solution at 25 °C in different solvents was confirmed by variable temperature NMR studies. At room temperature (25 °C), compounds 1–7 exhibited duplicate NMR signals, while at elevated temperature (90 °C), a single set of signals was obtained. Compound 5 showed significant in vitro antioxidant activities against 1,1‐diphenyl‐2‐picrylhydrazyl and 2,2′‐azino‐bis‐3‐ethyl benzthiazoline‐6‐sulfonic acid radicals. The antibacterial studies showed that compounds 5 and 6 are the most active against Staphylococcus aureus, Bacillus subtilis and Escherichia coli. Compounds 3 and 6 also showed moderate antituberculosis activity against H₃₈Rv. Based on the research findings, G. hombroniana could be concluded as a rich source of flavanone–flavone (3 → 8) biflavonoids that exhibit rotameric behaviour at room temperature and display significant antioxidant and antibacterial activities. Copyright © 2014 John Wiley & Sons, Ltd.