Fabrication, characterization, and measurement of viscosity of α-Fe2O3-glycerol nanofluids

Magnetic nanofluids, ferrofluids, are a special category of smart nanomaterials, consisting of stable dispersion of magnetic nanoparticles in different fluids. In this study, magnetic nanoparticles of hematite, α-Fe₂O₃, were prepared by solvothermal method using Fe(NO₃)₃ as a starting material. The nanoparticles were characterized by X-ray diffraction (XRD) and transmission electronic microscope (TEM).To the best of our knowledge, this is the first research on the rheological properties of nanofluids of α-Fe₂O₃ nanoparticles and glycerol. The experimental results showed that the viscosity of α-Fe₂O₃-glycerol nanofluids increases with increasing the particle volume fraction and decreases with increasing temperature. Our results clearly showed that the α-Fe₂O₃-glycerol nanofluids are non-Newtonian shear-thinning and their shear viscosity depends strongly on temperature. The experimental data were compared with some theoretical models. The measured values of the effective viscosity of nanofluids are underestimated by the theoretical models.     

Estimation of mutual information by the fuzzy histogram

Mutual Information (MI) is an important dependency measure between random variables, due to its tight connection with information theory. It has numerous applications, both in theory and practice. However, when employed in practice, it is often necessary to estimate the MI from available data. There are several methods to approximate the MI, but arguably one of the simplest and most widespread techniques is the histogram-based approach. This paper suggests the use of fuzzy partitioning for the histogram-based MI estimation. It uses a general form of fuzzy membership functions, which includes the class of crisp membership functions as a special case. It is accordingly shown that the average absolute error of the fuzzy-histogram method is less than that of the naïve histogram method. Moreover, the accuracy of our technique is comparable, and in some cases superior to the accuracy of the Kernel density estimation (KDE) method, which is one of the best MI estimation methods. Furthermore, the computational cost of our technique is significantly less than that of the KDE. The new estimation method is investigated from different aspects, such as average error, bias and variance. Moreover, we explore the usefulness of the fuzzy-histogram MI estimator in a real-world bioinformatics application. Our experiments show that, in contrast to the naïve histogram MI estimator, the fuzzy-histogram MI estimator is able to reveal all dependencies between the gene-expression data.     

Ethynyl and Propynylpyrene Inhibitors of Cytochrome P450

Abstract  

The single-crystal X-ray structures and in vivo activities of three aryl acetylenic inhibitors of cytochromes P450 1A1, 1A2, 2A6, and 2B1 have been determined and are reported herein. These are 1-ethynylpyrene, 1-propynylpyrene, and 4-propynylpyrene. To investigate electronic influences on the mechanism of enzyme inhibition, the experimental electron density distribution of 1-ethynylpyrene has been determined using low-temperature X-ray diffraction measurements, and the resulting net atomic charges compared with various theoretical calculations. A total of 82,390 reflections were measured with Mo Kα radiation to a (sinθ/λ)_max = 0.985 Å⁻¹. Averaging symmetry equivalent reflections yielded 8,889 unique reflections. A least squares refinement procedure was used in which multipole parameters were added to describe the distortions of the atomic electron distributions from spherical symmetry. A map of the model electron density distribution of 1-ethynylpyrene was obtained. Net atomic charges calculated from refined monopole population parameters yielded charges that showed that the terminal acetylenic carbon atom (C18) is more negative than the internal carbon (C17). Net atomic charges calculated by ab initio, density functional theory, and semi-empirical methods are consistent with this trend suggesting that the terminal acetylenic carbon atom is more likely to be the site of oxidation. This is consistent with the inhibition mechanism pathway that results in the formation of a reactive ketene intermediate. This is also consistent with assay results that determined that 1-ethynylpyrene acts as a mechanism-based inhibitor of P450s 1A1 and 1A2 and as a reversible inhibitor of P450 2B1. Crystallographic data: 1-ethynylpyrene, C₁₈H₁₀, P2₁/c, a = 14.571(2) Å, b = 3.9094(5) Å, c = 20.242(3) Å, β = 105.042(2)°, V = 1,113.5(2) Å³; 1-propynylpyrene, C₁₉H₁₂, P2₁/n, a = 8.970(2) Å, b = 10.136(1) Å, c = 14.080(3) Å, β = 99.77(2)°, V = 1,261.5(4) Å³; 4-propynylpyrene, C₁₉H₁₂, Pbca, a = 9.904(1) Å, b = 13.174(2) Å, c = 19.401(1) Å, V = 2,531.4(5) Å³.     

Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides

Deamidation plays an important role in biochemical phenomena such as aging. The role of the n + 1 residue on the deamidation of asparagine (asparagine being the nth residue) in three pentapeptide chains (GGNGG, GGNMG and GGNIG) has been analysed with hybrid computational tools. Potentials of mean force at 300 K were calculated from the MD/replica exchange simulations using weighted histogram analysis (WHAM) in explicit water. The snapshots were clustered taking into account the requirements of the plausible deamidation mechanisms, as such the tautomerisation of the asparagine side chain as initial step has been confirmed, based on the proximity of water to the deamidation site. The ultimate goal being to gain an insight on the peptide backbone N-H acidity, quantum mechanical calculations have been carried out. For this purpose, the distribution of Φ/Ψ, Φ₂/Ψ and end-to-end distances deduced from the WHAM diagrams have been considered and a total of 110 structures have been sampled. These neutral pentapeptides as well as their corresponding anions have been optimised (B3LYP/6-31++G(d,p)) in implicit water in order to gain an insight on the peptide backbone N-H acidity. In this study, we have shown that the open conformations of the neutrals and the anions, which display a β sheet like structure are well populated and their pK_as rank in the same order as the deamidating half-lives, that is the peptides that deaminate fastest can more readily access conformations that are more acidic.     

Palladium nanoparticles immobilized on sepiolite–cyclodextrin nanosponge hybrid: Efficient heterogeneous catalyst for ligand‐ and copper‐free C─C coupling reactions

A novel hybrid system composed of sepiolite clay and cyclodextrin nanosponge (CDNS) was prepared via reaction of Cl‐functionalized sepiolite with amine‐functionalized CDNS. CDNS–sepiolite was then applied for immobilization of Pd(0) nanoparticles. The resulting hybrid system, Pd@CDNS‐sepiolite, was characterized using various techniques and successfully used as an efficient and heterogeneous catalyst for ligand‐ and copper‐free Sonogashira and Heck coupling reactions under mild reaction conditions. Recycling experiments confirmed that Pd@CDNS‐sepiolite was recyclable and could be used for several consecutive reaction runs with slight Pd leaching and loss of catalytic activity.     

Numerical solution of stochastic differential equations by second order Runge–Kutta methods

In this paper we propose the numerical solutions of stochastic initial value problems via random Runge–Kutta methods of the second order and mean square convergence of these methods is proved. A random mean value theorem is required and established. The concept of mean square modulus of continuity is also introduced. Expectation and variance of the approximating process are computed. Numerical examples show that the approximate solutions have a good degree of accuracy.     

Retention of lysozyme activity by physical immobilization in nanocellulose aerogels and antibacterial effects

Aerogels prepared from aqueous dispersions of anionic and cationic cellulose nanofibrils (CNFs) were investigated as solid supports for enzymes and silver nanoparticles and to elicit a sustained antibacterial effect. The imparted stabilization in dry conditions was studied with aerogels that were cast after mixing the enzymes with CNFs followed by dehydration (freeze-drying). The activity of lysozyme immobilized in the given CNF system was analyzed upon storage in liquid and air media. In contrast with aqueous solutions of free, unbound enzyme, which lost activity after the first day, the enzyme immobilized physically in unmodified and cationic CNF presented better stability (activity for a longer time). However, the enzyme activity was reduced in the case of anionic CNF, which was prepared by TEMPO-mediated oxidation (TO-CNF). Both humidity and temperature reduced the stability of the enzyme immobilized in the respective CNF aerogel. The antibacterial activity of CNF aerogels carrying lysozyme was also tested against gram-negative and gram-positive bacteria. The results were compared with those obtained from CNF systems loaded with silver nanoparticles (AgNP) after in situ synthesis via UV reduction. Storage in cold or dry conditions preserved the activity and antibacterial performance of enzyme-loaded CNF aerogels. As expected, the lysozyme-containing aerogels showed lower inhibition than the AgNP-containing aerogel. In this latter case, the antibacterial activity depended on the concentration and size of the nanoparticles. Compared to unmodified CNF and TO-CNF, the aerogels prepared with cationic CNF, loaded with either lysozyme or AgNPs, showed remarkably better antibacterial activity. Similar experiments were conducted with horseradish peroxidase, which confirmed, to different degrees, the observations derived from the lysozyme systems. Overall, the results indicate that non-toxic and biodegradable CNF is a suitable support for bio-active materials and is effective in protecting and retaining enzymatic and antibacterial activities.