Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Vacancy mediated clipping of multi-layered graphene: A precursor for 1, 2 and 3D carbon structures

Using first principles calculations, we show that the overlapping defects in bi-layer graphene (both AA-and AB-stacked) interact forming inter-layer covalent bonds, giving rise to two-dimensional (2D) clipped structures, without explicit use of functional groups. These clipped structures can be transformed into one-dimensional (1D) double wall nanotubes (DWCNT) or multi-layered three dimensional (3D) bulk structures. These clipped structures show good mechanical strength due to covalent bonding between multi-layers. Clipping also provides a unique way to simultaneously harness the conductivity of both walls of a double wall nanotube through covalently bonded scattering junctions. With additional conducting channels and improved mechanical stability, these clipped structures can lead to a myriad of applications in novel devices. (C) 2015 Elsevier Ltd. All rights reserved.

ABSOLUTE/CONVECTIVE INSTABILITY TRANSITION IN A BACKWARD FACING STEP COMBUSTOR: FUNDAMENTAL MECHANISM AND INFLUENCE OF DENSITY GRADIENT

Hydrodynamic instabilities of the flow field in lean premixed gas turbine combustors can generate velocity perturbations that wrinkle and distort the flame sheet over length scales that are smaller than the flame length. The resultant heat release oscillations can then potentially result in combustion instability. Thus, it is essential to understand the hydrodynamic instability characteristics of the combustor flow field in order to understand its overall influence on combustion instability characteristics. To this end, this paper elucidates the role of fluctuating vorticity production from a linear hydrodynamic stability analysis as the key mechanism promoting absolute/convective instability transitions in shear layers occurring in the flow behind a backward facing step. These results are obtained within the framework of an inviscid, incompressible, local temporal and spatio-temporal stability analysis. Vorticity fluctuations in this limit result from interaction between two competing mechanisms - (1) production from interaction between velocity perturbations and the base flow vorticity gradient and (2) baroclinic torque in the presence of base flow density gradients. This interaction has a significant effect on hydrodynamic instability characteristics when the base flow density and velocity gradients are co-located. Regions in the space of parameters characterizing the base flow velocity profile, i.e. shear layer thickness and ratio of forward to reverse flow velocity, corresponding to convective and absolute instability are identified. The implications of the present results on prior observations of flow instability in other flows such as heated jets and bluff-body stabilized flames is discussed.

Mononuclear five-coordinate cobalt(II) complexes with N-4-coordinate pyrazole based ligand and pseudohalogens: synthesis, structures, DNA and protein binding study

A series of mononuclear five-coordinate cobalt(II) complexes, Co(dbdmp)(X)]Y, where dbdmp=N,N-diethyl-N,N-bis((3,5-dimethyl-1H-pyrazol-1-yl)methyl)ethane-1, 2-diamine, X=N-3(-)/NCO-/NCS- and Y=PF6-/BF4-/ClO4-, have been synthesized and characterized by microanalyses and spectroscopic techniques. Crystal structures of Co(N-3)(dbdmp)]PF6 (1), Co(N-3)(dbdmp)]ClO4 (3), Co(NCO)(dbdmp)]PF6 (4), Co(NCO)(dbdmp)]ClO4 (6), and Co(NCS)(dbdmp)]ClO4 (9) have been solved by single-crystal X-ray diffraction studies and showed that all the complexes have distorted trigonal bipyramidal geometry; PF6- counter anion containing complexes Co(N-3)(dbdmp)]PF6 and Co(NCO)(dbdmp)]PF6 have chiral space groups. The binding ability of synthesized complexes with CT-DNA and bovine serum albumin (BSA) has been studied by spectroscopic methods and viscosity measurements. The experimental results of absorption titration of cobalt(II) complexes with CT-DNA indicate that the complexes have ability to form adducts and they can stabilize the DNA helix. The cobalt(II) complexes exhibit good binding propensity to BSA protein.

High performance sol-gel spin-coated titanium dioxide dielectric based MOS structures

High-kappa TiO2 thin films have been fabricated using cost effective sol-gel and spin-coating technique on p-Si (100) wafer. Plasma activation process was used for better adhesion between TiO2 films and Si. The influence of annealing temperature on the structure-electrical properties of titania films were investigated in detail. Both XRD and Raman studies indicate that the anatase phase crystallizes at 400 degrees C, retaining its structural integrity up to 1000 degrees C. The thickness of the deposited films did not vary significantly with the annealing temperature, although the refractive index and the RMS roughness enhanced considerably, accompanied by a decrease in porosity. For electrical measurements, the films were integrated in metal-oxide-semiconductor (MOS) structure. The electrical measurements evoke a temperature dependent dielectric constant with low leakage current density. The Capacitance-voltage (C-V) characteristics of the films annealed at 400 degrees C exhibited a high value of dielectric constant (similar to 34). Further, frequency dependent C-V measurements showed a huge dispersion in accumulation capacitance due to the presence of TiO2/Si interface states and dielectric polarization, was found to follow power law dependence on frequency (with exponent `s'=0.85). A low leakage current density of 3.6 x 10(-7) A/cm(2) at 1 V was observed for the films annealed at 600 degrees C. The results of structure-electrical properties suggest that the deposition of titania by wet chemical method is more attractive and cost-effective for production of high-kappa materials compared to other advanced deposition techniques such as sputtering, MBE, MOCVD and AID. The results also suggest that the high value of dielectric constant kappa obtained at low processing temperature expands its scope as a potential dielectric layer in MOS device technology. (C) 2015 Elsevier Ltd. All rights reserved.

In-plane effective shear modulus of generalized circular honeycomb structures and bundled tubes in a diamond array structure

Use of circular hexagonal honeycomb structures and tube assemblies in energy absorption systems has attracted a large number of literature on their characterization under crushing and impact loads. Notwithstanding these, effective shear moduli (G*) required for complete transverse elastic characterization and in analyses of hierarchical structures have received scant attention. In an attempt to fill this void, the present study undertakes to evaluate G* of a generalized circular honeycomb structures and tube assemblies in a diamond array structure (DAS) with no restriction on their thickness. These structures present a potential to realize a spectrum of moduli with minimal modifications, a point of relevance for manufactures and designers. To evaluate G* in this paper, models based on technical theories - thin ring theory and curved beam theory - and rigorous theory of elasticity are investigated and corroborated with FEA employing contact elements. Technical theories which give a good match for thin HCS offer compact expressions for moduli which can be harvested to study sensitivity of moduli on topology. On the other hand, elasticity model offers a very good match over a large range of thickness along with exact analysis of stresses by employing computationally efficient expressions. (C) 2015 Elsevier Ltd. All rights reserved.

Estimation of nonlinearities from pseudodynamic and dynamic responses of bridge structures using the Delay Vector Variance method

Analysis of the variability in the responses of large structural systems and quantification of their linearity or nonlinearity as a potential non-invasive means of structural system assessment from output-only condition remains a challenging problem. In this study, the Delay Vector Variance (DVV) method is used for full scale testing of both pseudo-dynamic and dynamic responses of two bridges, in order to study the degree of nonlinearity of their measured response signals. The DVV detects the presence of determinism and nonlinearity in a time series and is based upon the examination of local predictability of a signal. The pseudo-dynamic data is obtained from a concrete bridge during repair while the dynamic data is obtained from a steel railway bridge traversed by a train. We show that DVV is promising as a marker in establishing the degree to which a change in the signal nonlinearity reflects the change in the real behaviour of a structure. It is also useful in establishing the sensitivity of instruments or sensors deployed to monitor such changes. (C) 2015 Elsevier B.V. All rights reserved.

Effect of absolute pressure on flow through a textured hydrophobic microchannel

The potential of textured hydrophobic surfaces to provide substantial drag reduction has been attributed to the presence of air bubbles trapped on the surface cavities. In this paper, we present results on water flow past a textured hydrophobic surface, while systematically varying the absolute pressure close to the surface. Trapped air bubbles on the surface are directly visualized, along with simultaneous pressure drop measurements across the surface in a microchannel configuration. We find that varying the absolute pressure within the channel greatly influences the trapped air bubble behavior, causing a consequent effect on the pressure drop (drag). When the absolute pressure within the channel is maintained below atmospheric pressure, we find that the air bubbles grow in size, merge and eventually detach from the surface. This growth and subsequent merging of the air bubbles leads to a substantial increase in the pressure drop. On the other hand, a pressure above the atmospheric pressure within the channel leads to gradual shrinkage and eventual disappearance of trapped air bubbles. We find that in this case, air bubbles do cause reduction in the pressure drop with the minimum pressure drop (or maximum drag reduction) occurring when the bubbles are flush with the surface. These results show that the trapped air bubble dynamics and the pressure drop across a textured hydrophobic microchannel are very significantly dependent on the absolute pressure within the channel. The results obtained hold important implications toward achieving sustained drag reduction in microfluidic applications.

Global response sensitivity analysis of uncertain structures

The problem of characterizing global sensitivity indices of structural response when system uncertainties are represented using probabilistic and (or) non-probabilistic modeling frameworks (which include intervals, convex functions, and fuzzy variables) is considered. These indices are characterized in terms of distance measures between a fiducial model in which uncertainties in all the pertinent variables are taken into account and a family of hypothetical models in which uncertainty in one or more selected variables are suppressed. The distance measures considered include various probability distance measures (Hellinger,l(2), and the Kantorovich metrics, and the Kullback-Leibler divergence) and Hausdorff distance measure as applied to intervals and fuzzy variables. Illustrations include studies on an uncertainly parametered building frame carrying uncertain loads. (C) 2015 Elsevier Ltd. All rights reserved.

DLTS analysis of amphoteric interface defects in high-TiO2 MOS structures prepared by sol-gel spin-coating

High-kappa TiO2 thin films have been fabricated from a facile, combined sol-gel spin - coating technique on p and n type silicon substrate. XRD and Raman studies headed the existence of anatase phase of TiO2 with a small grain size of 18 nm. The refractive index `n' quantified from ellipsometry is 2.41. AFM studies suggest a high quality, pore free films with a fairly small surface roughness of 6 angstrom. The presence of Ti in its tetravalent state is confirmed by XPS analysis. The defect parameters observed at the interface of Si/TiO2 were studied by capacitance - voltage (C - V) and deep level transient spectroscopy (DLTS). The flat - band voltage (V-FB) and the density of slow interface states estimated are -0.9, -0.44 V and 5.24x10(10), 1.03x10(11) cm(-2); for the NMOS and PMOS capacitors, respectively. The activation energies, interface state densities and capture cross -sections measured by DLTS are E-V + 0.30, E-C - 0.21 eV; 8.73x10(11), 6.41x10(11) eV(-1) cm(-2) and 5.8x10(-23), 8.11x10(-23) cm(2) for the NMOS and PMOS structures, respectively. A low value of interface state density in both P-and N-MOS structures makes it a suitable alternate dielectric layer for CMOS applications. And also very low value of capture cross section for both the carriers due to the amphoteric nature of defect indicates that the traps are not aggressive recombination centers and possibly can not contribute to the device operation to a large extent. (C) 2015 Author(s).

Uncertainty Quantification in Ultrasonic Wave Based Detection of Delamination in Composite Structures

In this paper we consider the problem of guided wave scattering from delamination in laminated composite and further the problem of estimating delamination size and layer-wise location from the guided wave measurement. Damage location and region/size can be estimated from time of flight and wave packet spread, whereas depth information can be obtained from wavenumber modulation in the carrier packet. The key challenge is that these information are highly sensitive to various uncertainties. Variation in reflected and transmitted wave amplitude in a bar due to boundary/interface uncertainty is studied to illustrate such effect. Effect of uncertainty in material parameters on the time of flight are estimated for longitudinal wave propagation. To evaluate the effect of uncertainty in delamination detection, we employ a time domain spectral finite element (tSFEM) scheme where wave propagation is modeled using higher-order interpolation with shape function have spectral convergence properties. A laminated composite beam with layer-wise placement of delamination is considered in the simulation. Scattering due to the presence of delamination is analyzed. For a single delamination, two identical waveforms are created at the two fronts of the delamination, whereas waves in the two sub-laminates create two independent waveforms with different wavelengths. Scattering due to multiple delaminations in composite beam is studied.

Air microjet system for non-contact force application and the actuation of micro-structures

We demonstrate a non-contact technique to apply calibrated and localized forces in the micro-Newton to milli-Newton range using an air microjet. An electromagnetically actuated diaphragm controlled by a signal generator is used to generate the air microjet. With a nozzle diameter of 150 mu m, the microjet diameter was maintained to a maximum of 1 mm at a distance of 5 mm from the nozzle. The force generated by the microjet was measured using a commercial force sensor to determine the velocity profile of the jet. Axial flow velocities of up to 25 m s(-1) were obtained at distances as long as 6 mm. The microjet exerted a force up to 1 mu N on a poly dimethyl siloxane (PDMS) micropillar (50 mu m in diameter, 157 mu m in height) and 415 mu N on a PDMS membrane (3 mm in diameter, 28 mu m thick). We also demonstrate that from a distance of 6 mm our microjet can exert a peak pressure of 187 Pa with a total force of about 84 mu N on a flat surface with 8 V operating voltage. Out of the cleanroom fabrication and robust design make this system cost effective and durable.

Efficient and practical synthesis of modular chiral beta-organochalcogeno amines, ArYCH2CH(R)NH2, and single crystal structures of (S) - MsOCH2CH(Bz)NH3+ center dot Cl- and (R)-MsOCH2CH(Ph)NH3+ center dot Cl-

Modular chiral I3-organochalcogeno amines, ArYCH2CH(R)NH2 (4a-4g) where R = Me, Bz, Ph; and ArY = PhS, BzSe and 4-MeOC6H4Te respectively have been synthesized and characterized. Compounds 4a-4g were synthesized (Method II) from chiral aminoalkyl 13-methanesulfonate hydrochlorides, MsOCH2CH(R)NH3+ center dot Cl- (2a-2c) through nucleophilic displacement of MsO- with organochalcogenolate (ArY-). In another attempt (Method I) chiral beta-organotelluro amines (4a-4c) were prepared by deprotection of chiral N-boc I3-organotelluro amides, 4-MeOC6H4TeCH2CH(R)NH-Boc (3a-3c), which in turn, 13,-,1 were made from chiral N-boc 13-methanesulfonate amides (la-lc) and ArTeNa. 1H, and FTIR spectra of all the compounds (3a-3c and 4a-4g) were characteristic. The composition of 3a-3c was determined by elemental analysis. The a]TD values of 3b-3c and 4a-4g were determined. The single crystal structures of (S)-2b and (R)-2c were determined by X-Ray diffraction studies. Both (S)-2b and (R)2c were crystallized in orthorhombic system and the Flack parameter x was found 0.08(12) and 0.00(2) respectively. The crystal of (S)-2b contain two asymmetric units with gauche (A) and staggered (B) conformations. There are NH Cl-, NH-O and CH-O intra and intermolecular secondary interactions in (S)-2b and (R)-2c resulting in supramolecular structures. (C) 2015 Elsevier By. All rights reserved.

Optimal input cross-power spectra in shake table testing of asymmetric structures

The study considers earthquake shake table testing of bending-torsion coupled structures under multi-component stationary random earthquake excitations. An experimental procedure to arrive at the optimal excitation cross-power spectral density (psd) functions which maximize/minimize the steady state variance of a chosen response variable is proposed. These optimal functions are shown to be derivable in terms of a set of system frequency response functions which could be measured experimentally without necessitating an idealized mathematical model to be postulated for the structure under study. The relationship between these optimized cross-psd functions to the most favourable/least favourable angle of incidence of seismic waves on the structure is noted. The optimal functions are also shown to be system dependent, mathematically the sharpest, and correspond to neither fully correlated motions nor independent motions. The proposed experimental procedure is demonstrated through shake table studies on two laboratory scale building frame models.