Lattice Boltzmann simulation of two-sided lid-driven flow in a staggered cavity

In this article, the lattice Boltzmann method is employed in order to explore incompressible fluid flow inside a two-sided lid-driven staggered cavity. Results of the lattice Boltzmann simulation for antiparallel motion of lids are compared with the data from existing literature. For parallel motion of lids, the characteristics of flow pattern for a variety of Re numbers (50–3200) are presented. An asymmetric steady-state flow pattern for parallel motion of lids is obtained.     

Degradation of azithromycin using Ti/RuO<Subscript>2</Subscript> anode as catalyst followed by DPV,HPLC–UV and MS analysis

The electrodegradation of azithromycin was studied by its indirect oxidation using dimensionally stable Ti/RuO₂ anode as catalyst in the electrolyte containing methanol, 0.05 M NaHCO₃, sodium chloride and deionized water. The optimal conditions for galvanostatic electrodegradation for the azithromycin concentration of 0.472 mg cm^?3 were found to be NaCl concentration of 7 mg cm^?3 and the applied current of 300 mA. The differential pulse voltammetry using glassy carbon electrode was performed for the first time in the above-mentioned content of electrolyte for the nine concentration of azithromycin (0.075–0.675 mg cm^?3) giving the limits of azithromycin detection and of quantification as: LOD 0.044 mg cm^?3 and LOQ 0.145 mg cm^?3. The calibration curve was constructed enabling the electrolyte analysis during its electrodegradation process. The electrolyte was analyzed by high-performance liquid chromatography and electrospray ionization time-of-flight mass spectrometry. The electrooxidation products were identified and after 180 min there was no azithromycin in the electrolyte while TOC analysis showed that 79% of azithromycin was mineralized. The proposed degradation scheme is presented.     

The conformation of epinephrine in polar solvents: an NMR study

Structural Chemistry - Epinephrine (Epi) is a physiologically important catecholamine. Molecular conformation of Epi controls the interactions with other molecules and its biological effects. There...     

Optimization of cubic GaN/AlGaN quantum cascade structures for negative refraction in the THz spectral range

In this work we theoretically investigate a possibility to use cubic nitride based multi-layer periodic nanostructure as a semiconductor metamaterial. The structure design is based on an active region of a quantum cascade laser optimized to achieve optical gain in the Terahertz (THz) spectral range. In particular, we test the GaN/AlGaN quantum well configurations, which should exhibit important advantages compared to GaAs-based structures, namely room temperature operation without the assistance of magnetic field and lower doping densities. Our numerical rate-equations model is solved self-consistently and it takes into account electron-longitudinal optical phonon scattering between all the relevant states among the adjacent periods of the structure. A global optimization routine, specifically genetic algorithm is then used to generate new gain-optimized structures. This work confirms the advantages of cubic GaN designs over GaAs ones, namely feasibility of negative refraction at room temperature without the assistance of magnetic field while keeping the doping densities of the same order of magnitude.     

Parallel Interactions at Large Horizontal Displacement in Pyridine–Pyridine and Benzene–Pyridine Dimers

A study of crystal structures from the Cambridge Structural Database (CSD) and DFT calculations reveals that parallel pyridine–pyridine and benzene–pyridine interactions at large horizontal displacements (offsets) can be important, similar to parallel benzene–benzene interactions. In the crystal structures from the CSD preferred parallel pyridine–pyridine interactions were observed at a large horizontal displacement (4.0–6.0 Å) and not at an offset of 1.5 Å with the lowest calculated energy. The calculated interaction energies for pyridine–pyridine and benzene–pyridine dimers at a large offset (4.5 Å) are about 2.2 and 2.1 kcal mol^?1, respectively. Substantial attraction at large offset values is a consequence of the balance between repulsion and dispersion. That is, dispersion at large offsets is reduced, however, repulsion is also reduced at large offsets, resulting in attractive interactions.     

Differential geometric analysis of alterations in MH α‐helices

Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α‐helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α‐helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α‐helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α‐helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α‐helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α‐helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α‐helices for a broad range of applications. © 2013 Wiley Periodicals, Inc.     

Design,synthesis, and characterization of fullerene–peptide–steroid covalent hybrids

The present study reports the synthesis, spectral characterization, self-assembly properties, and preliminary in vitro study of antioxidant capacity of two triple covalent hybrids consisting of fullerene C₆₀, peptide, and steroidal moiety. Previously synthesized fulleropyrrolidinic acid and pregnenolone were connected by peptide linker using a multistep DCC/DMAP and/or EDC/HOBT esterification/amidation procedure. The hybrids were characterized by comparative analysis of spectroscopic data obtained from FTIR, UV–vis, HRMS, and extensive NMR experiments (¹H, ¹³C, COSY, HSQC, and HMBC). The self-assembling properties and morphology of triads samples prepared by drop-drying method were examined by scanning electron microscopy (SEM). Preliminary in vitro antioxidant activity was studied by Ferrous ion Oxidation-Xylenol orange (FOX) method.     

Fatty acid desaturation index in human plasma: comparison of different analytical methodologies for the evaluation of diet effects

Stearoyl-CoA desaturase 1 (SCD1) plays a role in the development of obesity and related conditions, such as insulin resistance, and potentially also in neurological and heart diseases. The activity of SCD1 can be monitored using the desaturation index (DI), the ratio of product (16:1n-7 and 18:1n-9) to precursor (16:0 and 18:0) fatty acids. Here, different analytical strategies were applied to identify the method which best supports SCD1 biology. A novel effective approach was the use of the SCD1-independent fatty acid (16:1n-10) as a negative control. The first approach was based on a simple extraction followed by neutral loss triglyceride fatty acid analysis. The second approach was based on the saponification of triglycerides followed by fatty acid analysis (specific for the position of the double bond within monounsaturated fatty acids (MUFAs)). In addition to the analytical LC-MS assays, different matrices (plasma total triglyceride fraction and the very low-density lipoprotein (VLDL) fraction) were investigated to identify the best for studying changes in SCD1 activity. Samples from volunteers on a high-carbohydrate diet were analyzed. Both ultra HPLC (UHPLC)-MS-based assays showed acceptable accuracies (75–125 % of nominal) and precisions (<20 %) for the analysis of DI-specific fatty acids in VLDL and plasma. The most specific assay for the analysis of the liver SCD activity was then validated for specificity and selectivity, intra- and interday accuracy and precision, matrix effects, dilution effects, and analyte stability. After 3 days of high-carbohydrate diet, only the specific fatty acids in human plasma VLDL showed a significant increase in DI and associated SCD1 activity.