Modified Lagrangian vortex method with improved boundary conditions for water waves past a thin bottom‐standing barrier

Herein, the modified Lagrangian vortex method (LVM), a hybrid analytical‐numerical algorithm per se, is devised to simulate the process of vortex formation and shedding from the sharp edge of a zero‐thickness vertical plate under linear water‐wave attack. Application of the Helmholtz decomposition facilitates a convenient switch between the inviscid‐ and viscous‐flow models, thereby enabling easy incorporation of vorticity effects into the potential‐flow calculations for the viscous‐dominated region. In evaluating the potential‐flow component, making good use of the quickly convergent technique with singular basis functions, correctly capturing the singular behavior in velocity fields near the tip of the plate, leads to a considerable reduction of computational burdens and to 12‐decimal‐place accuracy. The viscous correction is carried out via the meshless LVM with improved boundary conditions. Comparisons with previously published results show good agreement. Simulations of vortex generation and evolution illuminate the ability of the present method, and provide a supplement to pertinent experimental works. The hybrid scheme proposed herein allows flexibility for the former LVM and convenience in the code development. Such a compromise fits particularly well for the high‐resolution modeling of sharp‐edged vortex shedding without heavy numerical developments. Copyright © 2014 John Wiley & Sons, Ltd.     

A Bio‐inspired Cu4O4 Cubane: Effective Molecular Catalysts for Electrocatalytic Water Oxidation in Aqueous Solution

Inspired by the cubic Mn₄CaO₅ cluster of natural oxygen‐evolving complex in Photosystem II, tetrametallic molecular water oxidation catalysts, especially M₄O₄ cubane‐like clusters (M=transition metals), have aroused great interest in developing highly active and robust catalysts for water oxidation. Among these M₄O₄ clusters, however, copper‐based molecular catalysts are poorly understood. Now, bio‐inspired Cu₄O₄ cubanes are presented as effective molecular catalysts for electrocatalytic water oxidation in aqueous solution (pH 12). The exceptional catalytic activity is manifested with a turnover frequency (TOF) of 267 s^?1 for [(L_Gly‐Cu)₄] at 1.70 V and 105 s^?1 for [(L_Glu‐Cu)₄] at 1.56 V. Electrochemical and spectroscopic study revealed a successive two‐electron transfer process in the Cu₄O₄ cubanes to form high‐valent Cu^III and Cu^IIIO^. intermediates during the catalysis.     

Undoped amorphous SiNx: H alloy semiconductors: Dependence of electronic properties on composition

The electrical and optical properties of a-SiN_x:H thin films prepared by rf growth-discharge in SiH₄N₂H₂ without B or P doping have been measured for 0 < x ? 0.6. It is observed that the activation energy for extended-state electron conduction as well as the optical gap are unaffected by N content for x ? 0.4. The electron mobility in extended states is improved by as much as a factor of 10 by the N incorporation. There is a rapid conversion from the tetrahedral network to a Si₃N₄ network as x increases above ≈ 0.4.     

A crossed beam and ab initio study of the reaction of atomic boron with ethylene

The reaction of atomic boron, B(2P), with the simplest alkene, C2H4, has been investigated under single collision conditions in crossed beam experiments with mass spectrometric detection. Our experimental data clearly showed that the atomic boron versus hydrogen exchange reaction led to molecule(s) of gross formula C2H3B via bound intermediate(s). According to the experimentally derived fraction of the available energy released as product translational energy, we propose that an important reaction pathways is the one leading to the borirene plus atomic hydrogen and/or the one leading to ethynylborane plus atomic hydrogen. The experimental results are accompanied by electronic structure calculations of the relevant potential energy surface and RRKM estimates of the product branching ratio. According to RRKM calculations, within the limit of complete energy randomization, the three isomers borirene, BH=C=CH2 and BH2-CCH, are all formed, with BH2-CCH being the dominant one. The discrepancies between the trend of the product translational energy distributions and the picture emerging from RRKM estimates are a symptom that a statistical treatment is not warranted for this system.     

Achieving Molecular Recognition of Structural Analogues in Surface-Enhanced Raman Spectroscopy: Inducing Charge and Geometry Complementarity to Mimic Molecular Docking

Molecular recognition of complex isomeric biomolecules remains challenging in surface-enhanced Raman scattering (SERS) spectroscopy due to their small Raman cross-sections and/or poor surface affinities. To date, the use of molecular probes has achieved excellent molecular sensitivities but still suffers from poor spectral specificity. Here, we induce “charge and geometry complementarity” between probe and analyte as a key strategy to achieve high spectral specificity for effective SERS molecular recognition of structural analogues. We employ 4-mercaptopyridine (MPY) as the probe, and chondroitin sulfate (CS) disaccharides with isomeric sulfation patterns as our proof-of-concept study. Our experimental and in silico studies reveal that “charge and geometry complementarity” between MPY's binding pocket and the CS sulfation patterns drives the formation of site-specific, multidentate interactions at the respective CS isomerism sites, which “locks” each CS in its analogue-specific complex geometry, akin to molecular docking events. Leveraging the resultant spectral fingerprints, we achieve > 97 % classification accuracy for 4 CSs and 5 potential structural interferences, as well as attain multiplex CS quantification with < 3 % prediction error. These insights could enable practical SERS differentiation of biologically important isomers to meet the burgeoning demand for fast-responding applications across various fields such as biodiagnostics, food and environmental surveillance.     

Ultrafast quenching of tryptophan fluorescence in proteins: Interresidue and intrahelical electron transfer

Quenching of tryptophan fluorescence in proteins has been critical to the understanding of protein dynamics and enzyme reactions using tryptophan as a molecular optical probe. We report here our systematic examinations of potential quenching residues with more than 40 proteins. With site-directed mutation, we placed tryptophan to desired positions or altered its neighboring residues to screen quenching groups among 20 amino acid residues and of peptide backbones. With femtosecond resolution, we observed the ultrafast quenching dynamics within 100 ps and identified two ultrafast quenching groups, the carbonyl- and sulfur-containing residues. The former is glutamine and glutamate residues and the later is disulfide bond and cysteine residue. The quenching by the peptide-bond carbonyl group as well as other potential residues mostly occurs in longer than 100 ps. These ultrafast quenching dynamics occur at van der Waals distances through intraprotein electron transfer with high directionality. Following optimal molecular orbital overlap, electron jumps from the benzene ring of the indole moiety in a vertical orientation to the LUMO of acceptor quenching residues. Molecular dynamics simulations were invoked to elucidate various correlations of quenching dynamics with separation distances, relative orientations, local fluctuations and reaction heterogeneity. These unique ultrafast quenching pairs, as recently found to extensively occur in high-resolution protein structures, may have significant biological implications.     

Enhanced lithium-ion intercalation and conduction of transparent tantalum oxide films by lithium addition with an atmospheric pressure plasma jet

An investigation is conducted on enhancing lithium-ion intercalation and conduction performance of transparent organo tantalum oxide (TaO _y C _z ) films, by addition of lithium via a fast co-synthesis onto 40 Ω/□ flexible polyethylene terephthalate/indium tin oxide substrates at the short exposed durations of 33–34 s, using an atmospheric pressure plasma jet (APPJ) at various mixed concentrations of tantalum ethoxide [Ta(OC₂H₅)₅] and lithium tert-butoxide [(CH₃)₃COLi] precursors. Transparent organo-lithiated tantalum oxide (Li _x TaO _y C _z ) films expose noteworthy Li⁺ ion intercalation and conduction performance for 200 cycles of reversible Li⁺ ion intercalation and deintercalation in a 1 M LiClO₄-propylene carbonate electrolyte, by switching measurements with a potential sweep from ?1.25 to 1.25 V at a scan rate of 50 mV/s and a potential step at ?1.25 and 1.25 V, even after being bent 360° around a 2.5-cm diameter rod for 1000 cycles. The Li⁺ ionic diffusion coefficient and conductivity of 6.2?×?10^?10 cm²/s and 6.0?×?10^?11 S/cm for TaO _y C _z films are greatly progressed of up to 9.6?×?10^?10 cm²/s and 7.8?×?10^?9 S/cm for Li _x TaO _y C _z films by co-synthesis with an APPJ.     

Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies

Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.