The weighted Grammar constraint

We introduce the WeightedGrammar constraint and propose propagation algorithms based on the CYK parser and the Earley parser. We show that the traces of these algorithms can be encoded as a weighted negation normal form (WNNF), a generalization of NNF that allows nodes to carry weights. Based on this connection, we prove the correctness and complexity of these algorithms. Specifically, these algorithms enforce domain consistency on the WeightedGrammar constraint in time O(n ³). Further, we propose that the WNNF constraint can be decomposed into a set of primitive arithmetic constraint without hindering propagation.     

Univariate hyperbolic tangent neural network approximation

Here we study the univariate quantitative approximation of real and complex valued continuous functions on a compact interval or all the real line by quasi-interpolation hyperbolic tangent neural network operators. This approximation is derived by establishing Jackson type inequalities involving the modulus of continuity of the engaged function or its high order derivative. Our operators are defined by using a density function induced by the hyperbolic tangent function. The approximations are pointwise and with respect to the uniform norm. The related feed-forward neural network is with one hidden layer.     

Forcing operators on MTL‐algebras

We study the forcing operators on MTL‐algebras, an algebraic notion inspired by the Kripke semantics of the monoidal t ‐norm based logic (MTL). At logical level, they provide the notion of the forcing value of an MTL‐formula. We characterize the forcing operators in terms of some MTL‐algebras morphisms. From this result we derive the equality of the forcing value and the truth value of an MTL‐formula (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Tunneling currents that increase with molecular elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.     

Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).     

Wettability control and patterning of PDMS using UV-ozone and water immersion

We demonstrate a simple method to tune and pattern the wettability of polydimethylsiloxane (PDMS) to generate microfluidic mimics of heterogeneous porous media. This technique allows one to tailor the capillary forces at different regions within the PDMS channel to mimic multi-phase flow in oil reservoirs. In this method, UV-ozone treatment is utilized to oxidize and hydrophilize the surface of PDMS. To maintain a stable surface wettability, the oxidized surfaces are immersed in water. Additionally, the use of a photomask makes it convenient to pattern the wettability in the porous media. A one-dimensional diffusive reaction model is established to understand the UV-ozone oxidation as well as hydrophobic recovery of oxidized PDMS surfaces. The modeling results show that during UV-ozone, surface oxidation dominates over diffusion of low-molecular-weight (LMW) species. However, the diffusivity of LMW species plays an important role in wettability control of PDMS surfaces.     

Synthesis and anion-exchange reactions of a new anionic clay, α-magnesium hydroxide

A new anionic clay, α-magnesium hydroxide, was synthesized by hydrolysis of magnesium acetate in propylene glycol. The structure of this α-hydroxide is similar to that of hydrotalcites. It consists of positively charged magnesium hydroxide layers arising out of partial protonation of the hydroxyl groups of the [Mg(OH)(2)] layers and loosely held anions in the interlayer region. As expected it ages readily in water to give β-magnesium hydroxide, brucite. While anion-exchange reactions of α-magnesium hydroxide could not be carried out in aqueous medium a number of anion-exchange reactions could be carried out successfully in ethanol medium.     

Dissociation and fractionation of heavy and light chains from IgG monoclonal antibodies

A basic method for dissociation and fractionation of monoclonal IgG heavy and light chain is described. It employs less noxious and hazardous reagents than the classical mercaptoethanol/propionic acid process and replaces size exclusion chromatography with cation exchange on a monolith to improve productivity. Significant scope remains to refine the conditions. The method can be applied to other disulfide bonded proteins with significant affinity for cation exchangers.     

Electrokinetic properties of wavellite and its floatability with cationic and anionic collectors

The reverse apatite flotation with fatty acids has been widely used for the reduction of phosphorus content of magmatic origin iron ores. However, the occurrence of phosphorus intensely disseminated as secondary minerals such as wavellite renders the anionic reverse flotation a challenge. Zeta potential measurements and microflotation tests of wavellite with the use of anionic and cationic collectors were carried out in this work. The wavellite's IEP value was achieved at pH 4.5. Below the IEP value, the surface positively charged sites are made up of aluminum ions. The species H(+), Al(OH)(2)(+), Al(OH)(2+), Al(3+), OH(-), H(2)PO(4)(-), HPO(4)(2-), and PO(4)(3-) play a role in the protonation and deprotonation reactions that will determine the wavellite-solution interface properties. The highest values of wavellite's floatability under basic pH conditions were achieved in the presence of cationic collectors (1 × 10(-4) mol L(-1)). The formation of surface complexes and the precipitation of insoluble salt of aluminum onto wavellite surface seems to be the most likely hypothesis for the chemical nature interactions between amines and wavellite. The surface formation of aluminum oleate on the wavellite's surface seems to be the most probable hypothesis for the adsorption mechanism and the resultant high floatability of wavellite between pH 7.5 and pH 10.0 in the presence of sodium oleate (1 × 10(-4) mol L(-1)). The results showed that the cationic reverse flotation of secondary phosphates is a promising route to reduce the phosphorus content of iron ores from deposits that underwent a supergene enrichment process, since wavellite floatability in the alkaline pH range, using amine as collector, was not significantly affected by the presence of corn starch.     

Molybdenum site structure of Escherichia coli YedY, a novel bacterial oxidoreductase

We report a structural characterization using X-ray absorption spectroscopy of the molybdenum site of Escherichia coli YedY, a novel oxidoreductase related to be the sulfite oxidase family of molybdenum enzymes. We find that the enzyme can exist in Mo(V) and Mo(IV) oxidation states but cannot be readily oxidized to the Mo(VI) form. Mo(V) YedY has molybdenum coordination similar to that of sulfite oxidase, with one Mo═O at 1.71 ?, three Mo-S at 2.39 ?, and one Mo-OH at 2.09 ?, which elongates to 2.20 ? upon reduction to Mo(IV), indicating Mo-OH(2) coordination. The Mo(V) enzyme also possesses a long Mo-O coordination at 2.64 ?, which may be due to oxygen coordination by Asn-45 O(δ), with Mo-O(δ) approximately trans to the Mo═O group. A comparison with sulfite oxidase indicates that YedY possesses a much more uniform Mo-S coordination, with a maximum permitted deviation of less than 0.05 ?. Our results indicate that the YedY active site shows considerable similarity to but also important differences from that of reduced forms of sulfite oxidase.