A numerical experimental study of inverse preconditioning for the parallel iterative solution to 3D finite element flow equations

Integration of the subsurface flow equation by finite elements (FE) in space and finite differences (FD) in time requires the repeated solution to sparse symmetric positive definite systems of linear equations. Iterative techniques based on preconditioned conjugate gradients (PCG) are one of the most attractive tool to solve the problem on sequential computers. A present challenge is to make PCG attractive in a parallel computing environment as well. To this aim a key factor is the development of an efficient parallel preconditioner. FSAI (factorized sparse approximate inverse) and enlarged FSAI relying on the approximate inverse of the coefficient matrix appears to be a most promising parallel preconditioner. In the present paper PCG using FSAI, diagonal and pARMS (parallel algebraic recursive multilevel solvers) preconditioners is implemented on the IBM SP4/512 and CLX/768 supercomputers with up to 32 processors to solve underground flow problems of a large size. The results show that FSAI may allow for a parallel relative efficiency larger than 50% on the largest problems with p=32 processors. Moreover, FSAI turns out to be significantly less expensive and more robust than pARMS. Finally, it is shown that for p in the upper range may be much improved if PCG–FSAI is implemented on CLX.     

The LEM exponential integrator for advection–diffusion–reaction equations

We implement a second-order exponential integrator for semidiscretized advection–diffusion–reaction equations, obtained by coupling exponential-like Euler and Midpoint integrators, and computing the relevant matrix exponentials by polynomial interpolation at Leja points. Numerical tests on 2D models discretized in space by finite differences or finite elements, show that the Leja–Euler–Midpoint (LEM) exponential integrator can be up to 5 times faster than a classical second-order implicit solver.     

Development of a simplified method for the simultaneous determination of retinol, α-tocopherol,and β-carotene in serum by liquid chromatography–tandem mass spectrometry with atmospheric pressure chemical ionization

A new and simple method for the determination of fat-soluble vitamins (retinol, alpha-tocopherol, and beta-carotene) in human serum was developed and validated by using liquid chromatography-tandem mass spectrometry with atmospheric pressure chemical ionization (LC-APCI-MS-MS). Different solvent mixtures were tested to obtain deproteinization and extraction of the analytes from the matrix. As a result, a volume of 240 microL of a 1:1 (v/v) ethanol/ethyl acetate mixture added to 60 microL of serum was found to be suitable for both protein precipitation and antioxidants solubilization, giving the best recovery for all three analytes. Deproteinized samples (20 microL) were injected after dilution, without the need for concentration or evaporation to dryness and reconstruction of the sample. Vitamins were separated on a C-8 column using a 95:5 (v/v) methanol/dichloromethane mixture and ionized in the positive-ion mode; detection was performed in the selected-reaction monitoring mode. Linearity of the LC-APCI-MS-MS method was established over 5 orders of magnitude for retinol and alpha-tocopherol, whereas in the case of beta-carotene it was limited to 4 orders. Lower limits of quantitation were 1.7, 2.3, and 4.1 nM for retinol, alpha-tocopherol, and beta-carotene, respectively. Serum concentrations of retinol, alpha-tocopherol, and alpha+beta-carotene determined in a group of healthy volunteers were 2.48, 38.07, and 0.50 microM, respectively, in samples collected in winter ( n=122) and 2.69, 45.88, and 0.90 microM during summer ( n=66).     

Capillary electrophoresis-diode array detection--electrospray mass spectrometry for the analysis of selected tropane alkaloids in plant extracts

Capillary zone electrophoresis, coupled to UV and interfaced with electrospray ionization mass spectrometry (ESI-MS), is described for the simultaneous analysis of hyoscyamine and scopolamine. On-line UV detection occurred at 22 cm from the inlet of the capillary and ESI-MS monitoring was performed along the entire length of the capillary (85 cm). An alkaline solution of 40 mM ammonium acetate at pH 8.5 was suitable for the analysis of the alkaloids under consideration. Under the optimized conditions, including CE and ESI-MS parameters, the two alkaloids were resolved within a short time and with very high sensitivity. The differentiation of hyoscyamine and its positional isomer littorine, commonly encountered in plant material, is also presented using up-front collision-induced dissociation. Finally, the developed method was applied to the analysis of these alkaloids in Belladonna leaf extract and in Datura candida x D. aurea hairy root extract.     

Green and sustainable chemistry in Latin America: Which type of research is going on? And for what?

Green (and sustainable?) frame around ‘Inverted America’ (adapted from Torres García, 1943, Museo Juan Manuel Blanes, Montevideo, CC BY 4.0).

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An Automatic Molecular Dispenser of Chloride

The combined activity of the 1.1.1‐cryptand and of a dicopper(II) bistren cryptate complex including chloride makes the Cl^? ion be continuously and slowly delivered to the solution, without any external intervention. The 1.1.1‐cryptand slowly releases OH^? ions, according to a defined kinetics, and each OH^? ion displaces a Cl^? ion from the cryptate. Chloride displacement induces a sharp colour change from bright yellow to aquamarine and can be conveniently monitored spectrophotometrically, even in diluted solutions. The 1.1.1‐cryptand is the motor of a molecular dispenser (the dicopper(II) cryptate) delivering chloride ion automatically, from the inside of the solution.     

A Sustainable Freeze‐Drying Route to Porous Polysaccharides with Tailored Hierarchical Meso‐ and Macroporosity

Bio‐derived polysaccharide aerogels are of interest for a broad range of applications. To date, these aerogels have been obtained through the time‐ and solvent‐intensive procedure of hydrogel fomation, solvent exchange, and scCO2 drying, which offers little control over meso/macropore distribution. A simpler and more versatile route is developed, using freeze drying to produce highly mesoporous polysaccharide aerogels with various degrees of macroporosity. The hierarchical pore distribution is controlled by addition of different quantities of t‐butanol (TBA) to hydrogels before drying. Through a systematic study an interesting relationship between the mesoporosity and t‐butanol/water phase diagram is found, linking mesoporosity maxima with eutectic points for all polysaccharides studied (pectin, starch, and alginic acid). Moreover, direct gelation of polysaccharides in aqueous TBA offers additional time savings and the potential for solvent reuse. This finding is a doorway to more accessible polysaccharide aerogels for research and industrial scale production, due to the widespread accessibility of the freeze drying technology and the simplicity of the method.

     

Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self-Assembly

Iodination has long been employed as a successful labelling strategy to gain structural insights into proteins and other biomolecules via several techniques, including Small Angle X-ray Scattering, Inductively Coupled Plasma Mass Spectrometer (ICP-MS), and single-crystal crystallography. However, when dealing with smaller biomolecular systems, interactions driven by iodine may significantly alter their self-assembly behaviour. The engineering of amyloidogenic peptides for the development of ordered nanomaterials has greatly benefitted from this possibility. Still, to date, iodination has exclusively been applied to aromatic residues. In this work, an aliphatic bis-iodinated amino acid was synthesized and included into a custom pentapeptide, which showed enhanced fibrillogenic behaviour. Peptide single crystal X-ray structure and powder X-ray diffraction on its dried water solution demonstrated the key role of iodine atoms in promoting intermolecular interactions that drive the peptide self-assembly into amyloid fibrils. These findings enlarge the library of halogenated moieties available for directing and engineering the self-assembly of amyloidogenic peptides.     

Metabolomics Insights of the Immunomodulatory Activities of Phlorizin and Phloretin on Human THP-1 Macrophages

Dihydrochalcones, phlorizin (PZ) and its aglycone phloretin (PT), have evidenced immunomodulatory effects through several mechanisms. However, the differential metabolic signatures that lead to these properties are largely unknown. Since macrophages play an important role in the immune response, our study aimed to characterise human THP-1 macrophages under PZ and PT exposure. A multiplatform-based untargeted metabolomics approach was used to reveal metabolites associated with the anti-inflammatory mechanisms triggered by the dihydrochalcones in LPS-stimulated macrophages, for the first time. Results showed differential phenotypic response in macrophages for all treatments. Dihydrochalcone treatment in LPS-stimulated macrophages mimics the response under normal conditions, suggesting inhibition of LPS response. Antagonistic effects of dihydrochalcones against LPS was mainly observed in glycerophospholipid and sphingolipid metabolism besides promoting amino acid biosynthesis. Moreover, PT showed greater metabolic activity than PZ. Overall, the findings of this study yielded knowledge about the mechanisms of action PZ and PT at metabolic level in modulating inflammatory response in human cells.     

The harmonic inversion of the field-swept fixed-frequency resonance spectrum

When the spin Hamiltonian is a linear function of the magnetic field intensity the resonance fields can be determined, in principle, by an eigenfield equation. In this report, we show a new technical approach to the resonance field problem where the eigenfield equation leads to a dynamic equation or, more specifically, to a first order differential equation of a variable L(x), where x is associated with the magnetic field h. Such differential equation has the property that: its stationary solution is the eigenfield equation and the spectral information contained in L(x) is directly related to the resonance spectrum. Such procedure, known as the "harmonic inversion problem" (HIP), can be solved by the "filter diagonalization method" (FDM) providing sufficient precision and resolution for the spectral analysis of the dynamic signals. Some examples are shown where the resonance fields are precisely determined in a single procedure, without the need to solve eigenvalue equations.