Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

Fast Eigen solution for homogeneous quadratic minimization with at most three constraints

We propose an eigenvalue based technique to solve the Homogeneous Quadratic Constrained Quadratic Programming problem (HQCQP) with at most three constraints which arise in many signal processing problems. Semi-Definite Relaxation (SDR) is the only known approach and is computationally intensive. We study the performance of the proposed fast eigen approach through simulations in the context of MIMO relays and show that the solution converges to the solution obtained using the SDR approach with significant reduction in complexity.

Solution of Time Dependent Joule Heat Equation for a Graphene Sheet Under Thomson Effect

We address a physics-based solution of joule heating phenomenon in a single-layer graphene (SLG) sheet under the presence of Thomson effect. We demonstrate that the temperature in an isotopically pure (containing only C-12) SLG sheet attains its saturation level quicker than when doped with its isotopes (C-13). From the solution of the joule heating equation, we find that the thermal time constant of the SLG sheet is in the order of tenths of a nanosecond for SLG dimensions of a few micrometers. These results have been formulated using the electron interactions with the inplane and flexural phonons to demonstrate a field-dependent Landauer transmission coefficient. We further develop an analytical model of the SLG specific heat using the quadratic (out of plane) phonon band structure over the room temperature. Additionally, we show that a cooling effect in the SLG sheet can be substantially enhanced with the addition of C-13. The methodologies as discussed in this paper can be put forward to analyze the graphene heat spreader theory.

Steric and Electronic Interactions Controlling the cis/trans Isomer Equilibrium at X-Pro Tertiary Amide Motifs in Solution

A systematic understanding of the noncovalent interactions that influence the structures of the cis conformers and the equilibrium between the cis and the trans conformers, of the X-Pro tertiary amide motifs, is presented based on analyses of H-1-, C-13-NMR and FTIR absorption spectra of two sets of homologous peptides, X-Pro-Aib-OMe and X-Pro-NH-Me (where X is acetyl, propionyl, isobutyryl and pivaloyl), in solvents of varying polarities. First, this work shows that the cis conformers of any X-Pro tertiary amide motif, including Piv-Pro, are accessible in the new motifs X-Pro-Aib-OMe, in solution. These conformers are uniquely observable by FTIR spectroscopy at ambient temperatures and by NMR spectroscopy from temperatures as high as 273 K. This is made possible by the persistent presence of n(i-1i)* interactions at Aib, which also influence the disappearance of steric effects at these cis X-Pro rotamers. Second, contrary to conventional understanding, the energy contribution of steric effects to the cis/trans equilibrium at the X-Pro motifs is found to be nonvariant (0.54 +/- 0.02 kcal/mol) with increase in steric bulk on the X group. Third, the current studies provide direct evidence for the weak intramolecular interactions namely the n(i-1i)*, the N-Pro center dot center dot center dot Hi+1 (C(5)a), and the C-7 hydrogen bond that operate and influence the structures, stabilities, and dynamics between different conformational states of X-Pro tertiary amide motifs. NMR and IR spectral data suggest that the cis conformers of X-Pro motifs are ensembles of short-lived rotamers about the C-X-N-Pro bond. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 66-77, 2014.

Production of syngas from steam reforming and CO removal with water gas shift reaction over nanosized Zr0.95Ru0.05O2-delta solid solution

This study presents the synthesis, characterization, and kinetics of steam reforming of methane and water gas shift (WGS) reactions over highly active and coke resistant Zr0.93Ru0.05O2-delta. The catalyst showed high activity at low temperatures for both the reactions. For WGS reaction, 99% conversion of CO with 100% H-2 selectivity was observed below 290 degrees C. The detailed kinetic studies including influence of gas phase product species, effect of temperature and catalyst loading on the reaction rates have been investigated. For the reforming reaction, the rate of reaction is first order in CH4 concentration and independent of CO and H2O concentration. This indicates that the adsorptive dissociation of CH4 is the rate determining step. The catalyst also showed excellent coke resistance even under a stoichiometric steam/carbon ratio. A lack of CO methanation activity is an important finding of present study and this is attributed to the ionic nature of Ru species. The associative mechanism involving the surface formate as an intermediate was used to correlate experimental data. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Upper bound solution for pullout capacity of vertical anchors in sand using finite elements and limit analysis

The horizontal pullout capacity of vertical anchors embedded in sand has been determined by using an upper bound theorem of the limit analysis in combination with finite elements. The numerical results are presented in nondimensional form to determine the pullout resistance for various combinations of embedment ratio of the anchor (H/B), internal friction angle (ϕ) of sand, and the anchor-soil interface friction angle (δ). The pullout resistance increases with increases in the values of embedment ratio, friction angle of sand and anchor-soil interface friction angle. As compared to earlier reported solutions in literature, the present solution provides a better upper bound on the ultimate collapse load.

Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)

Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B-6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5 `-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni-NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 angstrom resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unitcell parameters a = 65.11, b = 72.89, c = 107.52 angstrom. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP4 suite using E. coli pyridoxal kinase (PDB entry 2ddm) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.

Exact Solution of the PPP Model for Correlated Electronic States of Tetracene and Substituted Tetracene

Tetracene is an important conjugated molecule for device applications. We have used the diagrammatic valence bond method to obtain the desired states, in a Hilbert space of about 450 million singlets and 902 million triplets. We have also studied the donor/acceptor (D/A)-substituted tetracenes with D and A groups placed symmetrically about the long axis of the molecule. In these cases, by exploiting a new symmetry, which is a combination of C-2 symmetry and electron-hole symmetry, we are able to obtain their low-lying states. In the case of substituted tetracene, we find that optically allowed one-photon excitation gaps reduce with increasing D/A strength, while the lowest singlet triplet gap is only wealdy affected. In all the systems we have studied, the excited singlet state, S-i, is at more than twice the energy of the lowest triplet state and the second triplet is very close to the S-1 state. Thus, donor-acceptor-substituted tetracene could be a good candidate in photovoltaic device application as it satisfies energy criteria for singlet fission. We have also obtained the model exact second harmonic generation (SHG) coefficients using the correction vector method, and we find that the SHG responses increase with the increase in D/A strength.

Insights into the AIEE of 1,8-Naphthalimides (NPIs): Inverse Effects of Intermolecular Interactions in Solution and Aggregates

Systematic structural perturbation has been used to fine-tune and understand the luminescence properties of three new 1,8-naphthalimides (NPIs) in solution and aggregates. The NPIs show blue emission in the solution state and their fluorescence quantum yields are dependent upon their molecular rigidity. In concentrated solutions of the NPIs, intermolecular interactions were found to quench the fluorescence due to the formation of excimers. In contrast, upon aggregation (in THF/H2O mixtures), the NPIs show aggregation-induced emission enhancement (AIEE). The NPIs also show moderately high solid-state emission quantum yields (ca. 10-12.7 %). The AIEE behaviour of the NPIs depends on their molecular rigidity and the nature of their intermolecular interactions. The NPIs 1-3 show different extents of intermolecular (pi-pi and C-H center dot center dot center dot O) interactions in their solid-state crystal structures depending on their substituents. Detailed photophysical, computational and structural investigations suggest that an optimal balance of structural flexibility and intermolecular communication is necessary for achieving AIEE characteristics in these NPIs.

Frequency Domain Based Solution for Certain Class of Wave Equations: An exhaustive study of Numerical Solutions

The paper discusses the frequency domain based solution for a certain class of wave equations such as: a second order partial differential equation in one variable with constant and varying coefficients (Cantilever beam) and a coupled second order partial differential equation in two variables with constant and varying coefficients (Timoshenko beam). The exact solution of the Cantilever beam with uniform and varying cross-section and the Timoshenko beam with uniform cross-section is available. However, the exact solution for Timoshenko beam with varying cross-section is not available. Laplace spectral methods are used to solve these problems exactly in frequency domain. The numerical solution in frequency domain is done by discretisation in space by approximating the unknown function using spectral functions like Chebyshev polynomials, Legendre polynomials and also Normal polynomials. Different numerical methods such as Galerkin Method, Petrov- Galerkin method, Method of moments and Collocation method or the Pseudo-spectral method in frequency domain are studied and compared with the available exact solution. An approximate solution is also obtained for the Timoshenko beam with varying cross-section using Laplace Spectral Element Method (LSEM). The group speeds are computed exactly for the Cantilever beam and Timoshenko beam with uniform cross-section and is compared with the group speeds obtained numerically. The shear mode and the bending modes of the Timoshenko beam with uniform cross-section are separated numerically by applying a modulated pulse as the shear force and the corresponding group speeds for varying taper parameter in are obtained numerically by varying the frequency of the input pulse. An approximate expression for calculating group speeds corresponding to the shear mode and the bending mode, and also the cut-off frequency is obtained. Finally, we show that the cut-off frequency disappears for large in, for epsilon > 0 and increases for large in, for epsilon < 0.

Microscopic description of the evolution of the local structure and an evaluation of the chemical pressure concept in a solid solution

Extended x-ray absorption fine-structure studies have been performed at the Zn K and Cd K edges for a series of solid solutions of wurtzite Zn1-xCdxS samples with x = 0.0, 0.1, 0.25, 0.5, 0.75, and 1.0, where the lattice parameter as a function of x evolves according to the well-known Vegard's law. In conjunction with extensive, large-scale first-principles electronic structure calculations with full geometry optimizations, these results establish that the percentage variation in the nearest-neighbor bond distances are lower by nearly an order of magnitude compared to what would be expected on the basis of lattice parameter variation, seriously undermining the chemical pressure concept. With experimental results that allow us to probe up to the third coordination shell distances, we provide a direct description of how the local structure, apparently inconsistent with the global structure, evolves very rapidly with interatomic distances to become consistent with it. We show that the basic features of this structural evolution with the composition can be visualized with nearly invariant Zn-S-4 and Cd-S-4 tetrahedral units retaining their structural integrity, while the tilts between these tetrahedral building blocks change with composition to conform to the changing lattice parameters according to the Vegard's law within a relatively short length scale. These results underline the limits of applicability of the chemical pressure concept that has been a favored tool of experimentalists to control physical properties of a large variety of condensed matter systems.

Photocatalytic disassembly of tertiary amine-based dendrimers to monomers and their application to the `catch and release' of a dye in aqueous solution

Photocatalytic disassembly of tertiary amine-based poly(propyl ether imine) dendrimers, in the presence of either 9,10-anthraquinone or riboflavin tetraacetate and O-2(g), leads to di- and tripropanolamine monomers. An application is shown by solubilisation of a water-insoluble dye, Sudan I, in aq. dendrimer solution ('catch'), followed by its `release' upon disassembly of the dendrimer.

Solution Processed Cu2CoSnS4 Thin Films for Photovoltaic Applications

Earth abundant alternative chalcopyrite Cu2CoSnS4 (CCTS) thin films were deposited by a facile sol-gel process onto larger substrates. Temperature dependence of the process control of deposition and desired phase formations was studied in detail. Films were analyzed for complete transformation from amorphous to polycrystalline, with textured structures for stannite phase, as reflected from the X-ray diffraction and with nearly stoichiometric compositions of Cu:Co:Sn:S = 2:0:1:0:1:0:4:0 from EDAX analysis. Morphological investigations revealed that the CCTS films with larger grains, on the order of its thickness, were synthesized at higher temperature of 500 degrees C. The optimal band gap for application in photovoltaics was estimated to be 1.4 eV. Devices with SLG/CCTS/Al geometry were fabricated for real time demonstration of photoconductivity under A.M 1.5 G solar and 1064 rim infrared laser illuminations. A photodetector showed one order current amplification from similar to 1.9 X 10(-6) A in the dark to 2.2 x 10(-5) A and 9.8 X 10(-6) A under A.M 1.5 G illumination and 50 mW cm(-2) IR laser, respectively. Detector sensitivity, responsivity, external quantum efficiency, and gain were estimated as 4.2, 0.12 A/W, 14.74% and 14.77%, respectively, at 50 mW cm(-2) laser illuminations. An ON and OFF ratio of 2.5 proved that CCTS can be considered as a potential absorber in low cost photovoltaics applications.

A napthelene-pyrazol conjugate: Al(III) ion-selective blue shifting chemosensor applicable as biomarker in aqueous solution

A newly synthesized and crystalographically characterized napthelene-pyrazol conjugate, 1-(5-phenyl-1H-pyrazole-3-ylimino)-methyl]-naphthalen-2-ol (HL) behaves as an Al(III) ion-selective chemosensor through internal charge transfer (ICT)-chelation-enhanced fluorescence (CHEF) processes in 100 mM HEPES buffer (water-DMSO 5 : 1, v/v) at biological pH with almost no interference of other competitive ions. This mechanism is readily studied from electronic, fluorimetric and H-1 NMR titration. The probe (HL) behaved as a highly selective fluorescent sensor for Al(III) ions as low as 31.78 nM within a very short response time (15-20 s). The sensor (HL), which has no cytotoxicity, is also efficient in detecting the distribution of Al(III) ions in HeLa cells via image development under fluorescence microscope.

Polymorphic phase transition among the titania crystal structures using a solution-based approach: from precursor chemistry to nucleation process

Nanocrystalline titania are a robust candidate for various functional applications owing to its non-toxicity, cheap availability, ease of preparation and exceptional photochemical as well as thermal stability. The uniqueness in each lattice structure of titania leads to multifaceted physico-chemical and opto-electronic properties, which yield different functionalities and thus influence their performances in various green energy applications. The high temperature treatment for crystallizing titania triggers inevitable particle growth and the destruction of delicate nanostructural features. Thus, the preparation of crystalline titania with tunable phase/particle size/morphology at low to moderate temperatures using a solution-based approach has paved the way for further exciting areas of research. In this focused review, titania synthesis from hydrothermal/solvothermal method, conventional sol-gel method and sol-gel-assisted method via ultrasonication, photoillumination and ILs, thermolysis and microemulsion routes are discussed. These wet chemical methods have broader visibility, since multiple reaction parameters, such as precursor chemistry, surfactants, chelating agents, solvents, mineralizer, pH of the solution, aging time, reaction temperature/time, inorganic electrolytes, can be easily manipulated to tune the final physical structure. This review sheds light on the stabilization/phase transformation pathways of titania polymorphs like anatase, rutile, brookite and TiO2(B) under a variety of reaction conditions. The driving force for crystallization arising from complex species in solution coupled with pH of the solution and ion species facilitating the orientation of octahedral resulting in a crystalline phase are reviewed in detail. In addition to titanium halide/alkoxide, the nucleation of titania from other precursors like peroxo and layered titanates are also discussed. The nonaqueous route and ball milling-induced titania transformation is briefly outlined; moreover, the lacunae in understanding the concepts and future prospects in this exciting field are suggested.