Analysis and use of fragment-occurrence data in similarity-based virtual screening

Current systems for similarity-based virtual screening use similarity measures in which all the fragments in a fingerprint contribute equally to the calculation of structural similarity. This paper discusses the weighting of fragments on the basis of their frequencies of occurrence in molecules. Extensive experiments with sets of active molecules from the MDL Drug Data Report and the World of Molecular Bioactivity databases, using fingerprints encoding Tripos holograms, Pipeline Pilot ECFC_4 circular substructures and Sunset Molecular keys, demonstrate clearly that frequency-based screening is generally more effective than conventional, unweighted screening. The results suggest that standardising the raw occurrence frequencies by taking the square root of the frequencies will maximise the effectiveness of virtual screening. An upper-bound analysis shows the complex interactions that can take place between representations, weighting schemes and similarity coefficients when similarity measures are computed, and provides a rationalisation of the relative performance of the various weighting schemes.     

On k-uniformly close-to-convex functions of complex order

In this paper, we define and study some subclasses of analytic functions by using fractional derivative operator. Some interesting properties, coefficients problems and inclusion results of these classes are investigated. It is also shown that these classes are closed under convolution with convex functions and some applications are given.     

Fractal analysis of time series in oil and gas production

The peculiarities of fractal characteristics’ calculations for time series are described in this article. An algorithm for calculation of fractal dimension is suggested. It has been proved that the suggested method possesses high accuracy and the rapidity of convergence on the limited number of measurements compared to the methods of covering.The criteria of early diagnosis for changes in the condition of hydrodynamic processes, which do not vary by fractal dimension, have been recommended.The presented method is applicable for practical engineering calculations with self-affine, chaotic data, usually with relatively limited number of measurements. It is quite a simple method for calculation of fractal dimension, algorithm can be easily realized and it should be useful for engineers.The applicability of the proposed algorithm for fractal dimension calculation and early diagnosis criteria of qualitative changes in the behaviour of various dynamic systems has been tested both on simulated as well as practical examples of oil and gas production.     

Primary pulse transmission in coupled steel granular chains embedded in PDMS matrix: Experiment and modeling

We present an experimental study of primary pulse transmission in coupled ordered steel granular chains embedded in poly-di-methyl-siloxane (PDMS) elastic matrix. Two granular one-dimensional chains are considered (an ‘excited’ and an ‘absorbing’ one), each composed of 11 identical steel beads of 9.5 mm diameter with the centerline of the chain spaced at fixed distances of 0.5, 1.5 or 2.5 mm apart. We directly force one of the chains (the excited one) by a transient pulse and measure, by means of laser vibrometry, the primary transmitted pulses at the end beads of both chains and at the first bead of the absorbing chain. It is well known that the dynamics of this type of ordered granular media is strongly nonlinear due, (i) to Hertzian interactions between adjacent beads, and (ii) to possible bead separations in the absence of compressive forces and ensuing collisions between neighboring beads. Accordingly, we develop a strongly nonlinear theoretical model that takes into account the coupling of the granular chains due to the PDMS matrix, with the aim to model primary pulse transmission in this system. After validating the model with experimental measurements, we employ it in a predictive fashion to estimate energy transfer between chains as a function of the interspatial distance between chains. Furthermore, based on this model we perform predictive matrix design to achieve maximum energy transfer from the excited to the absorbing chain, and provide a theoretical explanation of the nonlinear dynamics governing energy transfer (including energy equi-partition) in this system.     

Mathematical Characterization of Thermo-reversible Phase Transitions of Agarose Gels

The thermal phase transition temperatures of high (HMP) and low melting point (LMP) agarose gels were investigated by using UV–vis spectroscopy techniques. Transmitted light intensities from the gel samples with different agarose concentrations were monitored during the heating (gel-sol) and cooling (sol–gel) processes. It was observed that the transition temperatures, T_m, defined as the location of the maximum of the first derivative of the sigmoidal transition paths obtained from the UV–vis technique, slightly increased by increasing the agarose concentration in both the HMP and LMP samples. Here, we express the phase transitions of the agar-water system, as a representative of reversible physical gels, in terms of a modified Susceptible-Infected-Susceptible epidemic model whose solutions are the well-known 5-point sigmoidal curves. The gel point is hard to determine experimentally and various computational techniques are used for its characterization. Based on previous work, we locate the gel point, T₀, of sol-gel and gel-sol transitions in terms of the horizontal shift in the sigmoidal transition curve. For the gel-sol transition (heating), T₀ is greater than T_m, i.e. later in time, and the difference between T₀ and T_m is reduced as the agarose content increases. For the sol-gel transition (cooling), T₀ is again greater than T_m, but it is earlier in time for all agarose contents and moves forward in time and gets closer to T_m as the agarose content increases.     

A correlation for crystallite size of undoped ZnO thin film with the band gap energy – precursor molarity – substrate temperature

Transparent conducting undoped zinc oxide thin films were deposited on glass substrate by ultrasonic spray and spray pyrolysis techniques. The thin films were deposited at different substrate temperatures ranging between 300 and 450 °C with various precursor molarities. The correlation between the structural and optical properties suggests that the crystallites sizes of the films are predominantly influenced by the band gap energy of the thin films. The data of the correlation is suspected of involving some experimental measurement errors and therefore discarded in the development of the present correlation. The coefficient of correction is equal to 0.01, indicating high quality representation of data based on Eq. (1). The correlation also indicates that the crystallites sizes of the films are predominantly influenced by the band gap energy and the precursor molarity of the thin films. The model proposed of undoped ZnO thin film with substrate temperature was investigated.     

Laser bending of AISI 304 steel sheets: Thermal stress analysis

Laser induced bending of steel sheet is carried out and thermal stress developed in the heated region is examined. Temperature and stress fields are predicted using the finite element model. The microstructural changes in the melted region are investigated through scanning electron microscope, energy dispersive spectroscopy and X-ray diffraction. The residual stress developed at the surface vicinity of the laser treated region is measured using the X-ray diffraction technique, which is then compared with its counterpart predicted from the simulations. It is found that the residual stress at the surface vicinity is compressive and the prediction of the residual stress agrees well with that obtained from the X-ray diffraction technique. In addition, surface temperature predictions are in good agreement with the thermocouple data. The laser treated region is free from major cracks and large cavities.     

Design, synthesis, and biological activities of some branched carbasugars: construction of a substituted 6-oxabicyclo[3.2.1]nonane skeleton

Transformation of cyclohexa-2,4-diene-1,2-diylbis(methylene) diacetate to various carbasugars is described. Photooxygenation of a cyclohexadiene derivative gave a bicyclicendoperoxide, which was reduced with thiourea to [2-[(acetyloxy)methyl]cyclohexa-2,4-dien-1-yl]methyl acetate. Epoxidation of the remaining double bond followed by epoxide ring-opening and hydrolysis of the acetate groups gave one of the target hexols. The bicyclic endoperoxide was rearranged to a diepoxide with CoTPP. The diepoxide was reacted with sulfamic acid in acetic anhydride, resulting in the formation of a new branched carbasugar as well as in the formation of cyclitols with a 6-oxabicyclo[3.2.1]nonane skeleton. The mechanism of the formation of the products is discussed. The inhibition activity of six cyclitol derivatives was tested against α-glycosidase.     

Size-fractionated airborne particulate matter characterization of a residential area near Islamabad airport by IBA methods

Size fractionated PM_2.5 and PM_2.5?C10 airborne particulates collected from the airport housing society site in Rawalpindi were characterized using the non destructive ion beam analysis method. Proton induced X-ray emission and Proton induced gamma ray emission were employed to quantify 28 trace elements in fine and coarse filter samples. The average PM_2.5 and PM_2.5?C10 masses were found to be 15.7 and 144???g/m³, respectively which, when combined exceed the Pakistani limit for PM₁₀ of 100???g/m³. The average black carbon (BC) content was found to be 3.49 and 5.95???g/m³ corresponding to 23.8 and 4.30% of the fine and coarse masses, respectively. The reconstructed mass (RCM) was calculated for both particle modes using 5 pseudo sources, namely soil, sulfate, smoke, sea salt and BC. It was found that 5 sources could account for 80.6 and 49.0% of the fine and coarse masses, respectively. The low value of RCM for the coarse mode may imply a much higher organic content. The major sources contributing to the fine mode were soil, sulfate and BC. Similarly for the coarse mass fraction it was found that soil was the major source whereas the sulfate and BC sources did not contribute as much.