On preconditioning for a parallel solution of the Richards equation

In this paper, we present a class of preconditioning methods for a parallel solution of the three-dimensional Richards equation. The preconditioning methods Jacobi scaling, block-Jacobi, incomplete lower–upper, incomplete Cholesky and algebraic multigrid were applied in combination with a parallel conjugate gradient solver and tested for robustness and convergence using two model scenarios. The first scenario was an infiltration into initially dry, sandy soil discretised in 500,000 nodes. The second scenario comprised spatially distributed soil properties using 275,706 numerical nodes and atmospheric boundary conditions. Computational results showed a high efficiency of the nonlinear parallel solution procedure for both scenarios using up to 64 processors. Using 32 processors for the first scenario reduced the wall clock time to slightly more than 1% of the single processor run. For scenario 2 the use of 64 processors reduces the wall clock time to slightly more than 20% of the 8 processors wall clock time. The difference in the efficiency of the various preconditioning methods is moderate but not negligible. The use of the multigrid preconditioning algorithm is recommended, since on average it performed best for both scenarios.     

Hybrid automata, reachability, and Systems Biology

Hybrid automata are a powerful formalism for the representation of systems evolving according to both discrete and continuous laws. Unfortunately, undecidability soon emerges when one tries to automatically verify hybrid automata properties. An important verification problem is the reachability one that demands to decide whether a set of points is reachable from a starting region.If we focus on semi-algebraic hybrid automata the reachability problem is semi-decidable. However, high computational costs have to be afforded to solve it. We analyse this problem by exploiting some existing tools and we show that even simple examples cannot be efficiently solved. It is necessary to introduce approximations to reduce the number of variables, since this is the main source of runtime requirements. We propose some standard approximation methods based on Taylor polynomials and ad hoc strategies. We implement our methods within the software SAHA-Tool and we show their effectiveness on two biological examples: the Repressilator and the Delta-Notch protein signaling.     

The Effects of Embedded Dipoles in Aromatic Self‐Assembled Monolayers

Using a representative model system, here electronic and structural properties of aromatic self‐assembled monolayers (SAMs) are described that contain an embedded, dipolar group. As polar unit, pyrimidine is used, with its orientation in the molecular backbone and, consequently, the direction of the embedded dipole moment being varied. The electronic and structural properties of these embedded‐dipole SAMs are thoroughly analyzed using a number of complementary characterization techniques combined with quantum‐mechanical modeling. It is shown that such mid‐chain‐substituted monolayers are highly interesting from both fundamental and application viewpoints, as the dipolar groups are found to induce a potential discontinuity inside the monolayer, electrostatically shifting the core‐level energies in the regions above and below the dipoles relative to one another. These SAMs also allow for tuning the substrate work function in a controlled manner independent of the docking chemistry and, most importantly, without modifying the SAM‐ambient interface.     

Filler Wetting in Miscible ESBR/SSBR Blends and Its Effect on Mechanical Properties

The selective wetting behavior of silica in emulsion styrene butadiene rubber (ESBR)/solution styrene butadiene rubber (SSBR) blends is characterized by the wetting concept, which is further developed for filled blends based on miscible rubbers. It is found that not only the chemical rubber–filler affinity but also the topology of the filler surface significantly influences the selective filler wetting in rubber blends. The nanopore structure of the silica surface has been recognized as the main reason for the difference in the wetting behavior of the branched ESBR molecules and linear SSBR molecules. However, the effect of nanopore structure becomes more significant in the presence of silane. It is discussed that the adsorption of silane on silica surface constricts the nanopore to some extent that hinders effectively the space filling of the nanopores by the branched ESBR molecules but not by the linear SSBR molecules. As a result, in silanized ESBR/SSBR blends the dominant wetting of silica surface by the tightly bonded layer of SSBR molecules causes a low‐energy dissipation in the rubber–filler interphase. That imparts the low rolling resistance to the blends similar to that of a silica‐filled SSBR compound, while the ESBR‐rich matrix warrants the good tensile behavior, i.e., good abrasion and wear resistance of the blends.

     

Cross-Omics Analysis of Fenugreek Supplementation Reveals Beneficial Effects Are Caused by Gut Microbiome Changes Not Mammalian Host Physiology

Herbal remedies are increasing in popularity as treatments for metabolic conditions such as obesity and Type 2 Diabetes. One potential therapeutic option is fenugreek seeds (Trigonella foenum-graecum), which have been used for treating high cholesterol and Type 2 diabetes. A proposed mechanism for these benefits is through alterations in the microbiome, which impact mammalian host metabolic function. This study used untargeted metabolomics to investigate the fenugreek-induced alterations in the intestinal, liver, and serum profiles of mice fed either a 60% high-fat or low-fat control diet each with or without fenugreek supplementation (2% w/w) for 14 weeks. Metagenomic analyses of intestinal contents found significant alterations in the relative composition of the gut microbiome resulting from fenugreek supplementation. Specifically, Verrucomicrobia, a phylum containing beneficial bacteria which are correlated with health benefits, increased in relative abundance with fenugreek. Metabolomics partial least squares discriminant analysis revealed substantial fenugreek-induced changes in the large intestines. However, it was observed that while the magnitude of changes was less, significant modifications were present in the liver tissues resulting from fenugreek supplementation. Further analyses revealed metabolic processes affected by fenugreek and showed broad ranging impacts in multiple pathways, including carnitine biosynthesis, cholesterol and bile acid metabolism, and arginine biosynthesis. These pathways may play important roles in the beneficial effects of fenugreek.     

Isolation and characterization of copolymers of beta-lactoglobulin, alpha-lactalbumin, kappa-casein, and alphas1-casein generated by pressurization and thermal treatment of raw milk

Raw skim milk was submitted to high pressure (300 to 600 MPa) and temperature (4 to 70 degrees C) treatments for 2 or 5 min. The combined effects of pressure and temperature on milk proteins induced structural changes and polymer and copolymer formation characterized by anion-exchange and size-exclusion fast protein liquid chromatography and electrophoretic techniques. Approximately half of the beta-lactoglobulin formed polymers, and the other half formed large copolymers, mainly with kappa-casein, alpha-lactalbumin via intermolecular disulfide bond exchange, and alpha(s1)-casein via physicochemical interactions, in proportions of 1.0:0.7:0.3:0.1, respectively. Minor whey proteins (serum albumin, immunoglobulins, and lactoferrin) also participated in the formation of the copolymers but to a lesser extent. Two populations of the copolymers were found with apparent molecular masses ranging from 440 to 2000 kDa for the first and more than 2000 kDa for the second. On the contrary, for heated milks the aggregation kinetics obtained by combination of high pressure and thermal treatment were very fast, as no intermediates such as dimers and small size oligomers were observed after pressurization, whatever the temperature studied. Lactosylation of proteins as well as proteolysis were very limited. A beta-casein amino-terminal peptide of 22 kDa was specifically recovered in milk samples treated under the more drastic conditions (500 MPa/55 degrees C per 5 min and 600 MPa/70 degrees C per 5 min) and might have been generated by neutral proteases such as elastase released from somatic cells present in milk. No casein was released from the micelle whatever the combination of high pressure and temperature studied.     

Computer simulation of consumable melted slabs

A mathematical model has been developed to simulate two-dimensional heat flow for a slab ingot produced as a remelted product. Various heat flow parameters have been studied to determine the influence of changes in them on local solidification time. The parameters which show the greatest influence are the heat transfer coefficient and the thickness of the slab. The rate of addition of material changes the depth of the molten pool, but does not affect local solidification time.     

Luminescent Mononuclear and Dinuclear Iridium(III) Cyclometalated Complexes Immobilized in a Polymeric Matrix as Solid-State Oxygen Sensors

Oxygen quenching of the luminescence of mononuclear and dinuclear Ir(III) cyclometalated complexes immobilized in the pPEGMA matrixes has been studied. Linear Stern-Volmer plots, even when experiments at different emission wavelengths have been performed, were evidenced. Despite the different luminescence lifetimes of the chromophores in the absence of quencher, similar Stern-Volmer slopes have been calculated. This behavior was tentatively interpreted by taking into account the size and charge of the chromophores. Increased sizes and lower charges seem to enhance the sensitivity of the systems. Such findings could be of interest for the design of new solid-state luminescent oxygen sensors with improved performance.