Dynamics of Robertson–Walker spacetimes with diffusion

We study the dynamics of spatially homogeneous and isotropic spacetimes containing a fluid undergoing microscopic velocity diffusion in a cosmological scalar field. After deriving a few exact solutions of the equations, we continue by analyzing the qualitative behavior of general solutions. To this purpose we recast the equations in the form of a two dimensional dynamical system and perform a global analysis of the flow. Among the admissible behaviors, we find solutions that are asymptotically de-Sitter both in the past and future time directions and which undergo accelerated expansion at all times.     

Efficient implementation of the analytic second derivatives of Hartree–Fock and hybrid DFT energies: a detailed analysis of different approximations

In this paper, various implementations of the analytic Hartree–Fock and hybrid density functional energy second derivatives are studied. An approximation-free four-centre implementation is presented, and its accuracy is rigorously analysed in terms of self-consistent field (SCF), coupled-perturbed SCF (CP-SCF) convergence and prescreening criteria. The CP-SCF residual norm convergence threshold turns out to be the most important of these. Final choices of convergence thresholds are made such that an accuracy of the vibrational frequencies of better than 5 cm^?1 compared to the numerical noise-free results is obtained, even for the highly sensitive low frequencies (<100–200 cm^?1). The effects of the choice of numerical grid for density functional exchange–correlation integrations are studied and various weight derivative schemes are analysed in detail. In the second step of the work, approximations are introduced in order to speed up the computation without compromising its accuracy. To this end, the accuracy and efficiency of the resolution of identity approximation for the Coulomb terms and the semi-numerical chain of spheres approximation to the exchange terms are carefully analysed. It is shown that the largest performance improvements are realised if either Hartree–Fock exchange is absent (pure density functionals) and otherwise, if the exchange terms in the CP-SCF step of the calculation are approximated by the COSX method in conjunction with a small integration grid. Default values for all the involved truncation parameters are suggested. For vancomycine (176 atoms and 3593 basis functions), the RIJCOSX Hessian calculation with the B3LYP functional and the def2-TZVP basis set takes ～3 days using 16 Intel® Xeon® 2.60GHz processors with the COSX algorithm having a net parallelisation scaling of 11.9 which is at least ～20 times faster than the calculation without the RIJCOSX approximation.     

THE CRYSTAL AND MOLECULAR STRUCTURE OF THE POTENTIAL ANTIBACTERIAL AGENT 2-PYRIDYL-PHENYL SULPHONE

Abstract

Crystals of 2-pyridyl-phenyl sulphone are monoclinic, space group P2₁/c, with eight molecules in the unit cell of dimensions a = 11.781, b = 5.903, c = 29.748 Å and B = 94.13°. The dihedral angles between the best planes of the two aromatic rings are significantly different in two crystallographically independent molecules (88.4° and 71.9° for molecule A and molecule B, respectively), as well as those between the CSC plane and the pyridine ring (59.4° and 67.4°) and between the CSC plane and the phenyl ring (51.7° and 81.8°). The average bond distances of interest include C?S 1.77(1) and S?O 1.44(1) Å; among the bond angles there are CSO = 108.1(7), CSC = 105.0(6) and OSO = 118.7(6)°. The packing of the molecule in the crystal is determined by the van der Waals interactions and by two intermolecular H?O contacts of 2.43 and 2.49 Å. The observed conformation in the solid state agrees well with results of previous investigations, in the solution state, by means of dipole moment method and theoretical M.O. calculations, for the analogous di-2-pyridyl sulphone.     

Site-Specific Differences in Proteasome-Dependent Degradation of Monoubiquitinated α-Synuclein

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Stability analysis of the flow past miniature vortex generators in a Blasius boundary layer

It is shown in the literature that Tollmien−Schlichting waves can be damped and transition delayed by a proper modulation of the streamwise velocity in a boundary layer (BL), which can be obtained using miniature vortex generators (MVGs). Experiments show that the amplitude of TS waves is not always monotonically damped past the MVGs. In this study, direct numerical simulations and local stability analysis have been performed in order to provide an interpretation of the experiments and to characterize further the stabilization mechanism induced by this type of control. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis and Evaluation of Thymol-Based Synthetic Derivatives as Dual-Action Inhibitors against Different Strains of H. pylori and AGS Cell Line

Following a similar approach on carvacrol-based derivatives, we investigated the synthesis and the microbiological screening against eight strains of H. pylori, and the cytotoxic activity against human gastric adenocarcinoma (AGS) cells of a new series of ether compounds based on the structure of thymol. Structural analysis comprehended elemental analysis and ¹H/¹³C/¹⁹F NMR spectra. The analysis of structure–activity relationships within this molecular library of 38 structurally-related compounds reported that some chemical modifications of the OH group of thymol led to broad-spectrum growth inhibition on all isolates. Preferred substitutions were benzyl groups compared to alkyl chains, and the specific presence of functional groups at para position of the benzyl moiety such as 4-CN and 4-Ph endowed the most anti-H. pylori activity toward all the strains with minimum inhibitory concentration (MIC) values up to 4 µg/mL. Poly-substitution on the benzyl ring was not essential. Moreover, several compounds characterized by the lowest minimum inhibitory concentration/minimum bactericidal concentration (MIC/MBC) values against H. pylori were also tested in order to verify a cytotoxic effect against AGS cells with respect to 5-fluorouracil and carvacrol. Three derivatives can be considered as new lead compounds alternative to current therapy to manage H. pylori infection, preventing the occurrence of severe gastric diseases. The present work confirms the possibility to use natural compounds as templates for the medicinal semi-synthesis.     

Inorganic Elements in Mytilus galloprovincialis Shells: Geographic Traceability by Multivariate Analysis of ICP-MS Data

The international seafood trade is based on food safety, quality, sustainability, and traceability. Mussels are bio-accumulative sessile organisms that need regular control to guarantee their safe consumption. However, no well-established and validated methods exist to trace mussel origin, even if several attempts have been made over the years. Recently, an inorganic multi-elemental fingerprint coupled to multivariate statistics has increasingly been applied in food quality control. The mussel shell can be an excellent reservoir of foreign inorganic chemical species, allowing recording long-term environmental changes. The present work investigates the multi-elemental composition of mussel shells, including Al, Cu, Cr, Zn, Mn, Cd, Co, U, Ba, Ni, Pb, Mg, Sr, and Ca, determined by inductively-coupled plasma mass-spectrometry in Mytilus galloprovincialis collected along the Central Adriatic Coast (Marche Region, Italy) at 25 different sampling sites (18 farms and 7 natural banks) located in seven areas. The experimental data, coupled with chemometric approaches (principal components analysis and linear discriminant analysis), were used to create a statistical model able to discriminate samples as a function of their production site. The LDA model is suitable for achieving a correct assignment of >90% of individuals sampled to their respective harvesting locations and for being applied to counteract fraud.     

Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.     

Volatiles and Antifungal-Antibacterial-Antiviral Activity of South African Salvia spp. Essential Oils Cultivated in Uniform Conditions

Spontaneous emissions of S. dentata Aiton and S. scabra Thunb., as well as the essential oil (EO) composition of the cited species, together with S. aurea L., were investigated. The chemical profile of the first two species is reported here for the first time. Moreover, in vitro tests were performed to evaluate the antifungal activity of these EOs on Trichophyton mentagrophytes, Microsporum canis, Aspergillus flavus, Aspergillus niger, and Fusarium solani. Secondly, the EO antibacterial activity against Escherichia coli, Staphylococcus aureus, and Staphylococcus pseudointermedius was examined, and their antiviral efficacy against the H1N1 influenza virus was assessed. Leaf volatile organic compounds (VOCs), as well as the EOs obtained from the arial part of Salvia scabra, were characterized by a high percentage of sesquiterpene hydrocarbons (97.8% and 76.6%, respectively), mostly represented by an equal amount of germacrene D (32.8% and 32.7%, respectively). Both leaf and flower spontaneous emissions of S. dentata, as well as the EO composition, showed a prevalence of monoterpenes divided into a more or less equal amount of hydrocarbon and oxygenated compounds. Interestingly, its EO had a non-negligible percentage of oxygenated sesquiterpenes (29.5%). S. aurea EO, on the contrary, was rich in sesquiterpenes, both hydrocarbons and oxygenated compounds (41.5% and 33.5%, respectively). S. dentata EO showed good efficacy (Minimal Inhibitory Concentration (MIC): 0.5%) against M. canis. The tested EOs were not active against E. coli and S. aureus, whereas a low inhibition of S. dentata EO was observed on S. pseudointermedius (MIC = 10%). Once again, S. dentata EO showed a very good H1N1 inhibition; contrariwise, S. aurea EO was completely inactive against this virus. The low quantity of S. scabra EO made it impossible to test its biological activity. S. dentata EO exhibited interesting new perspectives for medicinal and industrial uses.     

Strategies of karyotype differentiation in Elateridae (Coleoptera, Polyphaga)

The chromosome study of five species of the family Elateridae, belonging to the subfamilies Agrypninae and Elaterinae, and the analysis of the cytogenetic data previously recorded for this family permitted the establishment of the main strategies of karyotypic differentiation that has occurred in the elaterids. In Agrypninae, the three species studied (Conoderus fuscofasciatus, Conoderus rufidens, and Conoderus sp.) showed the male karyotype 2n=16+X0. This karyotypic uniformity detected in these Conoderus species has also been shared with other species of the same genus, differing considerably from chromosomal heterogeneity verified in the subfamily Agrypninae. The use of the C-banding technique in C. fuscofasciatus and Conoderus sp. revealed constitutive heterochromatin in the pericentromeric region of the majority of the chromosomes. In C. fuscofasciatus, additional constitutive heterochromatin were also observed in the long arm terminal region of almost all chromosomes. Among the representatives of Elaterinae, the karyotype 2n=18+Xy(p) of Pomachilius sp.2 was similar to that verified in the majority of the Coleoptera species, contrasting with the chromosomal formula 2n=18+X0 detected in Cardiorhinus rufilateris, which is most common in the species of Elaterinae. In the majority of the elaterids, the chromosomal differentiation has frequently been driven by reduction of the diploid number; but, among the four cytogenetically examined subfamilies, there are some differences in relation to the trends of karyotypic evolution.