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.     

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.     

Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.     

Highly Luminescent Red Phosphorescent OLED with Interfacial Layers for Hole Transport and Electron Injection

Four kinds of red phosphorescent organic light-emitting devices were fabricated and compared to investigate the effect of interfacial layers for hole transport and electron injection. 1 nm-thick LiF in the device A and C and 1 nm-thick Cs₂CO₃ in the device B and D were deposited as an electron injection layer between the anode and the electron transport layer, and 5 nm-thick layer of dipyrazion[2,3-f:2′,2′-h]quinoxaline-2,3,6,7,10,11-hexacarbonitrile[HATCN] was inserted as a hole transport interfacial layer between the hole injection layer and the hole transport layer only in the device C and D. Under a luminance of 1000 cd/m², the power efficiencies were 7.6 lm/W and 8.5 lm/W in the device A and B, and 8.6 lm/W and 13.4 lm/W in the device C and D. The quantum efficiency of the device D was 15.8% under 1000 cd/m² which was somewhat lower than those of the device A and C, but a little higher than that of the device B. The luminance of the device D was much higher than those of the other devices at a given votage. The luminance of the device D at 7 V was 23,710 cd/m², which was 13.0, 3.4, and 4.0 times higher than those of the device A, B, and C at the same voltage, respectively.     

HIRFL–CSR加速器中束流与真空中剩余气体的碰撞损失

研究了重离子加速器中束流与真空中剩余气体的碰撞损失过程和碰撞截面,在依据大量实验数据的基础上,提出了一组计算离子一原子的电荷交换截面的经验公式.以兰州重离子加速器HDRFL及冷却储存环CSR为例,给出了依据碰撞截面的公式计算束流在加速器真空中的传输效率的方法,并计算了在不同真空度下HIRFL的ECR源轴向注入束运线、注入器SFC、前束运线、主加速器SSC和后束运线等不同加速阶段及CSR的传输效率,并提出合理的真空度要求.HIRFL的真空分布测量和束流的损失测量证明了该计算方法的可靠性.     

半导体激光器光束准直系统的功率耦合效率

在长距离无线光通信中，接收点光功率密度与光束发散角平方呈反比关系，为了获得小的发散角和大的功率耦合效率，要求准直系统有较大的数值孔径(NA)，但数值孔径过大会增加像差，因此合理设计功率耦合效率与准直系统的数值孔径就非常重要。该文对半导体激光器光束准直系统中功率耦合效率进行了研究，给出了半导体激光器光束功率耦合效率与k(孔径半径与孔径处等效光束半径之比)的关系表达式，并结合激光器光束准直系统，给出了半导体激光器光束功率耦合效率与准直系统数值孔径的关系表达式。该研究结论对于半导体激光器光束准直系统设计具有参考作用。