The Picone identity: A device to get optimal uniqueness results and global dynamics in Population Dynamics

This paper infers from a generalized Picone identity the uniqueness of the stable positive solution for a class of semilinear equations of superlinear indefinite type, as well as the uniqueness and global attractivity of the coexistence state in two generalized diffusive prototypes of the symbiotic and competing species models of Lotka–Volterra. The optimality of these uniqueness theorems reveals the tremendous strength of the Picone identity.     

An efficient edge based data structure for the compressible Reynolds-averaged Navier–Stokes equations on hybrid unstructured meshes

An efficient edge based data structure has been developed in order to implement an unstructured vertex based finite volume algorithm for the Reynolds-averaged Navier–Stokes equations on hybrid meshes. In the present approach, the data structure is tailored to meet the requirements of the vertex based algorithm by considering data access patterns and cache efficiency. The required data are packed and allocated in a way that they are close to each other in the physical memory. Therefore, the proposed data structure increases cache performance and improves computation time. As a result, the explicit flow solver indicates a significant speed up compared to other open-source solvers in terms of CPU time. A fully implicit version has also been implemented based on the PETSc library in order to improve the robustness of the algorithm. The resulting algebraic equations due to the compressible Navier–Stokes and the one equation Spalart–Allmaras turbulence equations are solved in a monolithic manner using the restricted additive Schwarz preconditioner combined with the FGMRES Krylov subspace algorithm. In order to further improve the computational accuracy, the multiscale metric based anisotropic mesh refinement library PyAMG is used for mesh adaptation. The numerical algorithm is validated for the classical benchmark problems such as the transonic turbulent flow around a supercritical RAE2822 airfoil and DLR-F6 wing-body-nacelle-pylon configuration. The efficiency of the data structure is demonstrated by achieving up to an order of magnitude speed up in CPU times.     

Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

Mass distribution and skewness for passive scalar transport in pipes with polygonal and smooth cross sections

We extend our previous results characterizing the loading properties of a diffusing passive scalar advected by a laminar shear flow in ducts and channels to more general cross‐sectional shapes, including regular polygons and smoothed corner ducts originating from deformations of ellipses. For the case of the triangle and localized, cross‐wise uniform initial distributions, short‐time skewness is calculated exactly to be positive, while long‐time asymptotics shows it to be negative. Monte Carlo simulations confirm these predictions, and document the timescale for sign change. The equilateral triangle appears to be the only regular polygon with this property—all others possess positive skewness at all times. Alternatively, closed‐form flow solutions can be constructed for smooth deformations of ellipses, and illustrate how both nonzero short‐time skewness and the possibility of multiple sign switching in time is unrelated to domain corners. Exact conditions relating the median and the skewness to the mean are developed which guarantee when the sign for the skewness implies front (more mass to the right of the mean) or back (more mass to the left of the mean) “loading” properties of the evolving tracer distribution along the pipe. Short‐ and long‐time asymptotics confirm this condition, and Monte Carlo simulations verify this at all times. The simulations are also used to examine the role of corners and boundaries on the distribution for short‐time evolution of point source , as opposed to cross‐wise uniform, initial data.     

Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

Influence of Polarity and Activation Energy in Microwave–Assisted Organic Synthesis (MAOS)

The aim of this work was to determine the parameters that have decisive roles in microwave-assisted reactions and to develop a model, using computational chemistry, to predict a priori the type of reactions that can be improved under microwaves. For this purpose, a computational study was carried out on a variety of reactions, which have been reported to be improved under microwave irradiation. This comprises six types of reactions. The outcomes obtained in this study indicate that the most influential parameters are activation energy, enthalpy, and the polarity of all the species that participate. In addition to this, in most cases, slower reacting systems observe a much greater improvement under microwave irradiation. Furthermore, for these reactions, the presence of a polar component in the reaction (solvent, reagent, susceptor, etc.) is necessary for strong coupling with the electromagnetic radiation. We also quantified that an activation energy of 20–30 kcal mol⁻¹ and a polarity (μ) between 7–20 D of the species involved in the process is required to obtain significant improvements under microwave irradiation.     

An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.     

12β-Acetyloxyperforatin,a New Limonoid from Harrisonia Perforata

A new A, D-seco limonoid, named 12-acetyloxyperforatin (1), along with three known ones, were isolated from the leaves of Harrisonia perforata. Their structures were elucidated on the basis of spectroscopic analysis, including extensive NMR techniques and computational modelling. These compounds showed no inhibitory activity against the 11β-HSD1 enzyme.