Ellipsometry as a Sensitive Technique to Probe film -Substrate Interfaces: Al2O3 on Si(100)

An attempt has been made to study the film-substrate interface by using a sensitive, non- conventional tool. Because of the prospective use of gate oxide in MOSFET devices, we have chosen to study alumina films grown on silicon. Film-substrate interface of alumina grown by MOCVD on Si(100) was studied systematically using spectroscopic ellipsometry in the range 1.5-5.0 eV, supported by cross-sectional SEM, and SIMS. The (ε1,ε2) versus energy data obtained for films grown at 600°C, 700°C, and 750°C were modeled to fit a substrate/interface/film “sandwich”. The experimental results reveal (as may be expected) that the nature of the substrate -film interface depends strongly on the growth temperature. The simulated (ε1,ε2) patterns are in excellent agreement with observed ellipsometric data. The MOCVD precursors results the presence of carbon in the films. Theoretical simulation was able to account for the ellipsometry data by invoking the presence of “free” carbon in the alumina films.

Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.

Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.

Temperature dependent transport studies in InN quantum dots grown by droplet epitaxy on silicon nitride/Si substrate

InN quantum dots (QDs) were fabricated on silicon nitride/Si (111) substrate by droplet epitaxy. Single-crystalline structure of InN QDs was verified by transmission electron microscopy, and the chemical bonding configurations of InN QDs were examined by x-ray photoelectron spectroscopy. Photoluminescence measurement shows a slight blue shift compared to the bulk InN, arising from size dependent quantum confinement effect. The interdigitated electrode pattern was created and current-voltage (I-V) characteristics of InN QDs were studied in a metal-semiconductor-metal configuration in the temperature range of 80-300K. The I-V characteristics of lateral grown InN QDs were explained by using the trap model. (C) 2011 American Institute of Physics. [doi:10.1063/1.3651762]

Tribological characteristics of A356 Al alloy-SiC(P) composite discs

The dry sliding wear and friction behaviour of A356 Al alloy and its composites containing 10 and 20 vol.% SiC(P) have been studied using pin-on-disc set up. In these tests, A356 Al alloy and its composites are used as disc whereas brake pad was used in the form of pins. Wear tests were carried out at a load of 192 N and the sliding speed was varied from 1 to 5 m/s. Tests were done for a sliding distance of 15 km. The effects of sliding velocity on the wear rate, coefficient of friction and nature of tribolayers formed on discs have been studied. Wear rates of composites as calculated by weight loss method, found to be negative at sliding speed of more than 2 m/s. Worn surfaces of pins and discs have been analyzed using scanning electron microscope. SEM and EDAX analysis of worn surfaces of composite discs showed formation of tribolayers, consisting of mixture of oxides of Al, Si, Cu, Ca, Ba, Mg, and Fe. In these layers, copper and barium content found to be increase with sliding speed in the case of composites. (C) 2011 Elsevier B.V. All rights reserved.

Conformational Basis for Substrate Recruitment in Protein Tyrosine Phosphatase 10D

The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.

Effect of substrate bias voltage on the structure, electric and dielectric properties of TiO(2) thin films by DC magnetron sputtering

Titanium dioxide (TiO(2)) films have been deposited on glass and p-silicon (1 0 0) substrates by DC magnetron sputtering technique to investigate their structural, electrical and optical properties. The surface composition of the TiO(2) films has been analyzed by X-ray photoelectron spectroscopy. The TiO(2) films formed on unbiased substrates were amorphous. Application of negative bias voltage to the substrate transformed the amorphous TiO(2) into polycrystalline as confirmed by Raman spectroscopic studies. Thin film capacitors with configuration of Al/TiO(2)/p-Si have been fabricated. The leakage current density of unbiased films was 1 x10(-6) A/cm(2) at a gate bias voltage of 1.5 V and it was decreased to 1.41 x 10(-7) A/cm(2) with the increase of substrate bias voltage to -150 V owing to the increase in thickness of interfacial layer of SiO(2). Dielectric properties and AC electrical conductivity of the films were studied at various frequencies for unbiased and biased at -150 V. The capacitance at 1 MHz for unbiased films was 2.42 x 10(-10) F and it increased to 5.8 x 10(-10) F in the films formed at substrate bias voltage of -150 V. Dielectric constant of TiO(2) films were calculated from capacitance-voltage measurements at 1 MHz frequency. The dielectric constant of unbiased films was 6.2 while those formed at -150 V it increased to 19. The optical band gap of the films decreased from 3.50 to 3.42 eV with the increase of substrate bias voltage from 0 to -150 V. (C) 2011 Elsevier B. V. All rights reserved.

Substrate nitridation induced modulations in transport properties of wurtzite GaN/p-Si (100) heterojunctions grown by molecular beam epitaxy

Phase pure wurtzite GaN films were grown on Si (100) substrates by introducing a silicon nitride layer followed by low temperature GaN growth as buffer layers. GaN films grown directly on Si (100) were found to be phase mixtured, containing both cubic (beta) and hexagonal (alpha) modifications. The x-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence (PL) spectroscopy studies reveal that the significant enhancement in the structural as well as in the optical properties of GaN films grown with silicon nitride buffer layer grown at 800 degrees C when compared to the samples grown in the absence of silicon nitride buffer layer and with silicon nitride buffer layer grown at 600 degrees C. Core-level photoelectron spectroscopy of Si(x)N(y) layers reveals the sources for superior qualities of GaN epilayers grown with the high temperature substrate nitridation process. The discussion has been carried out on the typical inverted rectification behavior exhibited by n-GaN/p-Si heterojunctions. Considerable modulation in the transport mechanism was observed with the nitridation conditions. The heterojunction fabricated with the sample of substrate nitridation at high temperature exhibited superior rectifying nature with reduced trap concentrations. Lowest ideality factors (similar to 1.5) were observed in the heterojunctions grown with high temperature substrate nitridation which is attributed to the recombination tunneling at the space charge region transport mechanism at lower voltages and at higher voltages space charge limited current conduction is the dominating transport mechanism. Whereas, thermally generated carrier tunneling and recombination tunneling are the dominating transport mechanisms in the heterojunctions grown without substrate nitridation and low temperature substrate nitridation, respectively. (C) 2011 American Institute of Physics. [doi:10.1063/1.3658867]

Influence of substrate temperature on the properties of oxygen‐ion‐assisted deposited CeO2 films

Substrate temperature and ion bombardment during deposition have been observed to modify significantly the optical and structural properties of dielectric thin films. Single‐layer films of CeO2 have been deposited by electron beam evaporation with simultaneous oxygen‐ion bombardment using a Kaufman broad beam ion source and maintaining the substrates at elevated temperature. A systematic study has been made on the influence of (a) substrate temperature in the range ambient to 300 °C, (b) ion energy in the range 300–700 eV, and (c) ion current density 100–220 μA/cm2 on optical properties such as refractive index, extinction coefficient, inhomogeneity, packing density, and structural properties. The refractive index increased with in increase in substrate temperature: ion energy up to 600 eV and ion current density. Homogeneous, absorption free and high index (2.48) films have been obtained at 600 eV, 220 μA/cm2 and at substrate temperature of 300 °C. The packing density of the films was observed to be unity for the same deposition conditions. Substrate temperature with simultaneous ion bombardment modified the structure of the films from highly ordered to fine grain structure.

Dielectric properties of (110) oriented PbZrO3 and La-modified PbZrO3 thin films grown by sol-gel process on Pt(111)/Ti/SiO2/Si substrate

Highly (110) preferred orientated antiferroelectric PbZrO3 (PZ) and La-modified PZ thin films have been fabricated on Pt/Ti/SiO2/Si substrates using sol-gel process. Dielectric properties, electric field induced ferroelectric polarization, and the temperature dependence of the dielectric response have been explored as a function of composition. The Tc has been observed to decrease by ∼ 17 °C per 1 mol % of La doping. Double hysteresis loops were seen with zero remnant polarization and with coercive fields in between 176 and 193 kV/cm at 80 °C for antiferroelectric to ferroelectric phase transformation. These slim loops have been explained by the high orientation of the films along the polar direction of the antiparallel dipoles of a tetragonal primitive cell and by the strong electrostatic interaction between La ions and oxygen ions in an ABO3 perovskite unit cell. High quality films exhibited very low loss factor less than 0.015 at room temperature and pure PZ; 1 and 2 mol % La doped PZs have shown the room temperature dielectric constant of 135, 219, and 142 at the frequency of 10 kHz. The passive layer effects in these films have been explained by Curie constants and Curie temperatures. The ac conductivity and the corresponding Arrhenius plots have been shown and explained in terms of doping effect and electrode resistance.

Indium flux, growth temperature and RF power induced effects in InN layers grown on GaN/Si substrate by plasma-assisted MBE

In the present work, we report the growth of wurtzite InN epilayers on GaN/Si (1 1 1) substrate by plasma-assisted molecular beam epitaxy (PAMBE). The growth parameters such as indium flux, substrate temperature and RF power affect the crystallographic and morphological properties of InN layers, which were evaluated using high resolution X-ray diffraction (HRXRD) analysis and atomic force microscopy (AFM). It is found that excess indium (In) concentrations and surface roughness were increased with increase in In flux and growth temperature. The intensity of HRXRD (0 0 0 2) peak, corresponding to c-axis orientation has been increased and full width at half maxima (FWHM) has decreased with increase in RF power. It was found that highly c-axis oriented InN epilayers can be grown at 450 degrees C growth temperature, 450 W RF power and 1.30 x 10(-7) mbar In beam equivalent pressure (BEP). The energy gap of InN layers grown by optimizing growth conditions was determined by photoluminescence and optical absorption measurement. (C) 2011 Elsevier B.V. All rights reserved.