Automatic ultrastructure segmentation of reconstructed cryoEM maps of icosahedral viruses.

We present an automatic algorithm to segment all the local and global asymmetric units of a three-dimensional density map of icosahedral viruses. This approach is readily applicable to the structural analysis of a broad range of virus structures that are reconstructed using cryo-electron microscopy (cryo-EM) technique. Our algorithm includes three major steps operating on the three dimensional density map: the detection of critical points of the volumetric density function, the detection of global and local symmetry axes, and, finally, the boundary segmentation of all the asymmetric units. We demonstrate the efficacy of our algorithm and report our results on several experimental volumetric datasets, consisting of both reconstructed cryo-EM molecular density maps taken from the European Bioinformatics Institute archive, as well our own synthetically generated (blurred) maps calculated from X-ray resolution molecular structural data taken from the Protein Data Bank.     

In memory of Professor Ali H. Nayfeh

Nonlinear Dynamics - In this paper, we propose and numerically study a nonlinear, asymmetric, passive metamaterial that achieves giant non-reciprocity with (i) broadband frequency operation and...     

Decays of the mesons and the singlet photon

In an attempt to explain the recent measurements on the radiative decays of the vector-mesons (V→Pγ), we study the consequences of introducing a small admixture of SU (3) singlet piece in the electromagnetic current. We find that this leads to an excellent fit of the theory with the new measurements on theV→Pγ decays. However, this addition adversely affects the fit of the leptonic decays of the vector mesons (V→e ⁺ e ⁻) and of the radiative decay of the pion (π→2γ). We conclude that the overall fit to the available data does not favour a large (>10%) admixture of the SU(3) singlet. The decay rates have been calculated in the vectormeson dominance model. At the hadronic vertex (VVP), we assume asymptotic nonet symmetry. The electromagnetic couplings (V−γ) are the ones appropriate to vector-mixing.     

On experiments in harmonically excited cantilever plates with 1:2 internal resonance

Nonlinear Dynamics - This work presents some experimental results for resonant nonlinear response of hyperelastic plates for 1:2 internal resonance. Previously developed topology optimization...     

Nanocomposite ZnO/Au formation by pulsed laser irradiation

The ZnO/Au nanocomposite formation involves synthesis of Au and ZnO colloidal solutions by 532 nm pulse laser ablation of metal targets in deionized water followed by laser irradiation of the mixed colloidal solution. The transmission electron microscope (TEM) and high-resolution transmission electron microscope (HRTEM) images show evolution of spherical particles into ZnO/Au nanonetworks with irradiation time. The formation mechanism of the nanonetwork can be explained on the basis of near resonance absorption of 532 nm irradiation by gold nanoparticles which can cause selective melting and fusion of gold nanoparticles to form network. The ZnO/Au nanocomposites show blue shift in the ZnO exciton absorption and red shift in the Au plasmon resonance absorption due to interfacial charge transfer.     

Rate coefficients and products for gas‐phase reactions of chlorine atoms with cyclic unsaturated hydrocarbons at 298 K

Rate coefficients for the reaction of Cl atoms with cycloalkenes have been determined using the relative rate method, at 298 K and atmospheric pressure of N₂. Reference molecule was n‐hexane, and the concentrations of the organics were followed by gas chromatographic analysis. Cl atoms were prepared by photolysis of trichloroacetyl chloride at 254 nm. The relative rates of reactions of Cl atoms with cycloalkenes, with respect to n‐hexane, are measured as 1.12 ± 0.38, 1.31 ± 0.14, and 1.69 ± 0.18 for cyclopentene, cyclohexene, and cycloheptene, respectively. Considering the absolute value of the rate coefficient of the reaction of Cl atom with n‐hexane as 3.03 ± 0.06 × 10^?10 cm³ molecule^?1 s^?1, the rate coefficient values for cyclopentene, cyclohexene, and cycloheptene are calculated to be (3.39 ± 1.08) × 10^?10, (3.97 ± 0.43) × 10^?10, and (5.12 ± 0.55) × 10^?10 cm³ molecule^?1 s^?1, respectively. The experiments for each molecule were repeated six to eight times, and the slopes and the rate coefficients given above are the average values of these measurements, and the quoted error includes 2σ as well as all other uncertainties in the measurement and calculations. The rate coefficient increases linearly with the number of carbon atoms, with an increment per additional CH₂ group being (8.7 ± 1.6) × 10^?12 cm³ molecule^?1 s^?1. Chloroketones and chloroalcohols, along with unsaturated ketones and alcohols, were found to be the major products of Cl‐atom‐initiated oxidation of cycloalkenes in the presence of air. The atmospheric implications of these results are discussed, along with a comparison with the reported structure activity relationships. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 42: 98–105, 2010     

Kinetics and mechanism of ruthenium(III) and ruthenium(III)-EDTA catalyzed oxidation of cyclohexanol by molecular oxygen

The kinetics of the oxidation of cyclohexanol by molecular O₂ catalyzed by Ru(III) and Ru(III)-EDTA complexes has been investigated by oxygen absorption method in the pH range 1.75–3.00 at 30°C (=0.1M KNO₃) in a 11 ethanol-water medium. In both cases the reaction was found to be first order with respect to substrate and catalyst concentration. The rate was found to decrease with the decrease of pH in case of Ru(III)-EDTA complex. Ethanol is not oxidized under the reaction conditions. A possible mechanism for the catalytic oxidation of cyclohexanol is proposed.

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O₂, Ru(III) Ru(III)-EDTA, pH 1,75–3,00 30°C (=0,1M KNO₃) - (11). . pH Ru(III)-EDTA. . .

     

Synthesis of enantiopure β-amino alcohols via AKR/ARO of epoxides using recyclable macrocyclic Cr(III) salen complexes

A series of chiral macrocyclic Cr(III) salen complexes 1-8 were synthesized and characterized. These complexes were found to be highly active, regio-, diastereo-, and enantioselective catalysts in aminolytic kinetic resolution (AKR) of racemic trans-epoxides as well as asymmetric ring opening (ARO) of prochiral meso-epoxides with various anilines as nucleophiles at room temperature in 18-24 h. Excellent yields (>99% with respect to the nucleophile) with high enantioselectivity (ee, >99%) of chiral anti-β-amino alcohols was achieved with concomitant recovery of corresponding epoxides in high ee (up to >99%). The complex 1 also catalyzed the ARO of meso-epoxides to provide corresponding syn-β-amino alcohols in high yield (99%) and ee (up to 91%). Due to built-in basic sites in the catalyst, no external base (as an additive) was required to promote AKR and ARO reactions. The catalyst 1 was conveniently recycled several times with retention of its performance. The AKR of trans-stilbene oxide with aniline was successfully demonstrated at relatively higher scale (10 mmol) using the catalyst 1.     

Synthesis of dypnone by solvent free self condensation of acetophenone over nano-crystalline sulfated zirconia catalyst

Nano-crystalline sulfated zirconia catalyst, prepared by two-step sol–gel method, has been studied for the solvent free self condensation of acetophenone to dypnone. The influence of calcination temperature on the structural, textural and catalytic activity of sulfated zirconia has been analyzed. The surface acidity along with the structural and textural features of the catalyst influenced its activity. The conversion of acetophenone was found to be effected by the variation in the reaction and calcination temperature, however, the dypnone selectivity was not affected much. The catalyst calcined at 650 °C, showed maximum dypnone selectivity of 92% with 68.2% acetophenone conversion at 170 °C after 7 h. The catalyst was reused up to five cycles with marginal decrease in acetophenone conversion, however, without losing its selectivity for dypnone.     

Esterification of caprylic acid with alcohol over nano-crystalline sulfated zirconia

The catalytic activity of nano-crystalline sulfated zirconia catalyst, prepared by sol–gel method and characterized by various analytical tools, was evaluated for the esterification of caprylic acid with different short chain alcohols. The lower concentration of catalyst (0.5 wt%) exhibited 96–98% conversion of caprylic acid with methanol and 100% selectivity for methyl caprylate at 60 °C. The conversion was decreased with increasing carbon chain of alcohols namely with ethanol, n-propanol and n-butanol at 60 °C but increased significantly (91–98%) at higher reaction temperature. The selectivity for respective alkyl caprylate was observed to be 100% irrespective of the alcohol used. The activity of the catalyst was slightly decreased with successive five reaction cycles due to the water formed during the reaction.