Isogeometric analysis of free-form Timoshenko curved beams including the nonlinear effects of large deformations

In the present paper, the isogeometric analysis (IGA) of free-form planar curved beams is formulated based on the nonlinear Timoshenko beam theory to investigate the large deformation of beams with variable curvature. Based on the isoparametric concept, the shape functions of the field variables (displacement and rotation) in a finite element analysis are considered to be the same as the non-uniform rational basis spline (NURBS) basis functions defining the geometry. The validity of the presented formulation is tested in five case studies covering a wide range of engineering curved structures including from straight and constant curvature to variable curvature beams. The nonlinear deformation results obtained by the presented method are compared to well-established benchmark examples and also compared to the results of linear and nonlinear finite element analyses. As the nonlinear load-deflection behavior of Timoshenko beams is the main topic of this article, the results strongly show the applicability of the IGA method to the large deformation analysis of free-form curved beams. Finally, it is interesting to notice that, until very recently, the large deformations analysis of free-form Timoshenko curved beams has not been considered in IGA by researchers.     

Optimizing Image Reconstruction in SENSE Using GPU

Parallel magnetic resonance imaging (MRI) (pMRI) uses multiple receiver coils to reduce the MRI scan time. To accelerate the data acquisition process in MRI, less amount of data is acquired from the scanner which leads to artifacts in the reconstructed images. SENSitivity Encoding (SENSE) is a reconstruction algorithm in pMRI to remove aliasing artifacts from the undersampled multi coil data and recovers fully sampled images. The main limitation of SENSE is computing inverse of the encoding matrix. This work proposes the inversion of encoding matrix using Jacobi singular value decomposition (SVD) algorithm for image reconstruction on GPUs to accelerate the reconstruction process. The performance of Jacobi SVD is compared with Gauss–Jordan algorithm. The simulations are performed on two datasets (brain and cardiac) with acceleration factors 2, 4, 6 and 8. The results show that the graphics processing unit (GPU) provides a speed up to 21.6 times as compared to CPU reconstruction. Jacobi SVD algorithm performs better in terms of acceleration in reconstructions on GPUs as compared to Gauss–Jordan method. The proposed algorithm is suitable for any number of coils and acceleration factors for SENSE reconstruction on real time processing systems.     

Design of a surface plasmon resonance biosensor based on photonic crystal fiber with elliptical holes

In this paper, a photonic-crystal fiber based plasmonic biosensor in which gold is used as the plasmonic material is proposed. The introduced sensor is designed in such a way that the plasmonic metal layer and the sensing layer are placed outside the fiber structure so that the fabrication process and the numerical analysis has become comparatively much easier. The proposed plasmonic biosensor properties are calculated numerically using the finite element method. Amongst the parameters affecting the performance of the biosensor are the thickness of the gold layer and the diameter of the central cavity. By applying the wavelength interrogation method, the maximum sensitivity and the resolution of the proposed biosensor are computed as 5723.5 nm/RIU and 1.74?×?10^?5 RIU, respectively. The proposed structure with the above properties is suitable for detecting biological molecules, organic chemicals and analytes.     

High-temperature dynamic behavior in bulk liquid water: A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

Classical molecular dynamics simulations were performed to study the high-temperature (above 300 K) dynamic behavior of bulk water, specifically the behavior of the diffusion coefficient, hydrogen bond, and nearest-neighbor lifetimes. Two water potentials were compared: the recently proposed “globally optimal” point charge (OPC) model and the well-known TIP4P-Ew model. By considering the Arrhenius plots of the computed inverse diffusion coefficient and rotational relaxation constants, a crossover from Vogel–Fulcher–Tammann behavior to a linear trend with increasing temperature was detected at T* ≈ 309 and T* ≈ 285 K for the OPC and TIP4P-Ew models, respectively. Experimentally, the crossover point was previously observed at T* ± 315–5 K. We also verified that for the coefficient of thermal expansion α _P (T, P), the isobaric α _P (T) curves cross at about the same T* as in the experiment. The lifetimes of water hydrogen bonds and of the nearest neighbors were evaluated and were found to cross near T*, where the lifetimes are about 1 ps. For T < T*, hydrogen bonds persist longer than nearest neighbors, suggesting that the hydrogen bonding network dominates the water structure at T < T*, whereas for T > T*, water behaves more like a simple liquid. The fact that T* falls within the biologically relevant temperature range is a strong motivation for further analysis of the phenomenon and its possible consequences for biomolecular systems.     

Molecular Dynamics Simulations of Adsorption of Polymer Chains on the Surface of B<Subscript>m</Subscript>N<Subscript>n</Subscript> Graphyne-Like Monolayers

Molecular dynamics simulations are used here to study the interactions between B_mN_n graphyne-like monolayers and four different polymer chains. BN, B₁N₉, and B₂N₈ graphyne-like monolayers are selected from the family of B_mN_n graphyne-like monolayers. It is observed that increasing the number of B atoms in the structure of B_mN_n graphyne-like monolayers results in larger interaction energies of nanosheet/polymer systems. It is also shown that the polymer chains with the linear adsorbed configurations on the nanosheets have larger interaction energies with the nanosheets. Investigating the effect of number of polymer repeat units on the polymer/nanosheet interaction energy, it is observed that increasing the number of repeat units of polymers leads to enhancing the polymer/nanosheet interaction energy.     

PIV Measurements in the Near and Intermediate Field Regions of Jets Issuing from Eight Different Nozzle Geometries

An experimental study was conducted to investigate the effect of nozzle geometry on the mixing characteristics and turbulent transport phenomena in turbulent jets. The nozzle geometry examined were round, square, cross, eight-corner star, six-lobe daisy, equilateral triangle as well as ellipse and rectangle each with aspect ratio of 2. The jets were produced from sharp linear contoured nozzles which may be considered intermediate to the more widely studied smooth contraction and orifice nozzles. A high resolution particle image velocimetry was used to conduct detailed velocity measurements in the near and intermediate regions. It was observed that the lengths of the potential cores and the growth rates of turbulence intensities on the jet centerline are comparable with those of the orifice jets. The results indicate that the decay and spreading rates are lower than reported for orifice jets but higher than results for smooth contoured jets. The jets issuing from the elliptic and rectangular nozzles have the best mixing performance while the least effective mixing was observed in the star jet. The distributions of the Reynolds stresses and turbulent diffusion clearly showed that turbulent transport phenomena are quite sensitive to nozzle geometry. Due to the specific shape of triangular and daisy jets, the profiles of mean velocity and turbulent quantities are close to each other in their minor and major planes while in the elliptic and rectangular jets are considerably different. They also exhibit more isotropic behavior compared to the elliptic and rectangular jets. In spite of significant effects of nozzle geometry on mean velocity and turbulent quantities, the integral length scales are independent of changes in nozzle geometry.     

Isolation of PHA–Producing Bacteria from Date Syrup Waste

Since the major problem associated with the industrial production of Polyhydroxyalkanoates (PHAs) is their high production cost, this study was carried out using date syrup as the major carbon source to decrease the production cost and also help to supply other nutrient requirements. To isolate PHA–producing bacteria for this purpose, microorganisms were isolated from the syrup waste of a local date factory. These purified colonies were screened for intracellular granules by staining with Sudan Black. The positive-staining strains were grown for production of PHAs in 5% date syrup as carbon source supplemented with mineral salt medium. The culture was incubated at 30 °C with shaking at 140 rpm for 60 h. Among positively stained bacteria, the best PHA producers were selected on the basis of cell growth, cell dry weight, PHA content and the monomer composition of PHA. One of them could utilize date syrup for growth and produce the homopolymer of Polyhydroxybutyrate (PHB) with a cell density of about 5.1 g/L and maximum concentration of PHB equal to 3.6 g/L which is 71% of cell dry weight. Another one produces copolymer of Poly (hydroxybutyrate-hydroxyvalerate) in date syrup media with a maximum concentration of 2.2 g/L containing 10 wt % valerate in shake flask cultivation.     

Diammonium hydrogen phosphate as a versatile and efficient catalyst for the one-pot synthesis of pyrano[2,3-<Emphasis Type="Italic">d</Emphasis>]pyrimidinone derivatives in aqueous media

Diammonium hydrogen phosphate, (NH(4))(2)HPO(4), was used as a catalyst for one-pot, three-component condensation reactions consisting of aromatic aldehydes, malononitrile and barbituric/thiobarbituric acid in aqueous ethanol at room temperature. This method has the advantages of a simple operation, mild reaction conditions, high yields, by using a less toxic and low cost chemical as a catalyst.     

Characterization of partially transesterified poly(beta-hydroxyalkanoate)s using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was used for the characterization of a partially transesterified poly(beta-hydroxyalkanoate), PHA, polymer produced by the bacterial strain Alcaligenes eutrophus using saponified vegetable oils as the sole carbon sources. The transesterification was carried out separately under acidic and basic conditions to obtain PHA oligomers weighing less than 10 kDa. The intact oligomers were detected in their cationized [M + Na](+) and [M + K](+) forms by MALDI-TOFMS. A composition analysis, using the MALDI-TOF spectra, indicate that the oligomers obtained via acid catalysis were terminated with a methyl 3-hydroxybutyrate end group, and those obtained by base catalysis had a methyl crotonate (olefinic) termination. In addition to HB (hydroxy butyrate), the oligomers were found to contain a small percentage of HV (hydroxy valerate). This was independently confirmed using gas chromatography/mass spectrometry (GC/MS). In comparison, the analysis of a commercial PHA polymer, transesterified under identical conditions, only showed the presence of HB, i.e. a pure PHB homopolymer. Copyright 1999 John Wiley & Sons, Ltd.     

Computational Screening of Natural Compounds for Identification of Potential Anti-Cancer Agents Targeting MCM7 Protein

Minichromosome maintenance complex component 7 (MCM7) is involved in replicative licensing and the synthesis of DNA, and its overexpression is a fascinating biomarker for various cancer types. There is currently no effective agent that can prevent the development of cancer caused by the MCM7 protein. However, on the molecular level, inhibiting MCM7 lowers cancer-related cellular growth. With this purpose, this study screened 452 biogenic compounds extracted from the UEFS Natural Products dataset against MCM protein by using the in silico art of technique. The hit compounds UEFS99, UEFS137, and UEFS428 showed good binding with the MCM7 protein with binding energy values of −9.95, −8.92, and −8.71 kcal/mol, which was comparatively higher than that of the control compound ciprofloxacin (−6.50). The hit (UEFS99) with the minimum binding energy was picked for molecular dynamics (MD) simulation investigation, and it demonstrated stability at 30 ns. Computational prediction of physicochemical property evaluation revealed that these hits are non-toxic and have good drug-likeness features. It is suggested that hit compounds UEFS99, UEFS137, and UEFS428 pave the way for further bench work validation in novel inhibitor development against MCM7 to fight the cancers.