Effect of interface friction on the mechanics of indentation of a finite layer resting on a rigid substrate

Copper strips of 2.5 mm thickness resting on stainless steel anvils were normally indented by wedges under nominal plane strain conditions. Inflections in the hardness-penetration characteristics were identified. Inflections separate stages where each stage has typical mechanics of deformation. These are arrived at by studying the distortion of 0.125 mm spaced grids inscribed on the deformation plane of the strip. The sensitivity of hardness and deformation mechanics to wedge angle and the interfacial friction between strip and anvil were investigated within the framework of existing slip line field models of indentation of semi-infinite and finite blocks.

Selective-Area Atomic Layer Deposition

Atomic layer deposition (ALD) is a method to deposit thin films from gaseous precursors to the substrate layer-by-layer so that the film thickness can be tailored with atomic layer accuracy. Film tailoring is even further emphasized with selective-area ALD which enables the film growth to be controlled also on the substrate surface. Selective-area ALD allows the decrease of a process steps in preparing thin film devices. This can be of a great technological importance when the ALD films become into wider use in different applications. Selective-area ALD can be achieved by passivation or activation of a surface. In this work ALD growth was prevented by octadecyltrimethoxysilane, octadecyltrichlorosilane and 1-dodecanethiol SAMs, and by PMMA (polymethyl methacrylate) and PVP (poly(vinyl pyrrolidone) polymer films. SAMs were prepared from vapor phase and by microcontact printing, and polymer films were spin coated. Microcontact printing created patterned SAMs at once. The SAMs prepared from vapor phase and the polymer mask layers were patterned by UV lithography or lift-off process so that after preparation of a continuous mask layer selected areas of them were removed. On these areas the ALD film was deposited selectively. SAMs and polymer films prevented the growth in several ALD processes such as iridium, ruthenium, platinum, TiO2 and polyimide so that the ALD films did grow only on areas without SAM or polymer mask layer. PMMA and PVP films also protected the surface against Al2O3 and ZrO2 growth. Activation of the surface for ALD of ruthenium was achieved by preparing a RuOX layer by microcontact printing. At low temperatures the RuCp2-O2 process nucleated only on this oxidative activation layer but not on bare silicon.

Substrate-mediated purification and characterization of a 3-hydroxybenzoic acid-6-hydroxylase from Micrococcus

3-Hydroxybenzoic acid-6-hydroxylase from Micrococcus sp. was purified to homogeneity in a single step using the substrate-mediated interaction of the enzyme with blue-Sepharose. The enzyme was bound to the affinity matrix in the presence of 3-hydroxybenzoic acid and was eluted in its absence. The molecular weight of the purified enzyme is 70,000 with no subunit structure. The flavoenzyme required the exogenous addition of FAD for its complete activity and had a strict preference for NADH over NADPH. The activity of the enzyme was drastically inhibited by Cu2+ and Hg2+ and the inhibition was reversed by thiol reagents.

Detection of a CpA methylase in an insect system: characterization and substrate specificity

A cytosine-specific DNA methyltransferase (EC 2.1.1.37) has been purified to near homogeneity from a mealybug (Planococcus lilacinus). The enzyme can methylate cytosine residues in CpG sequences as well as CpA sequences. The apparent molecular weight of the enzyme was estimated as 135,000 daltons by FPLC. The enzyme exhibits a processive mode of action and a salt dependance similar to mammalian methylases. Mealybug methylase exhibits a preference for denatured DNA substrates.

Effect of substrate temperature on the properties of ZrO2 films prepared by d.c. reactive magnetron sputtering

Studies of ZrO2 films prepared by d.c. reactive magnetron sputtering are described. The effects of substrate temperature on the packing density, refractive index, extinction coefficient and crystallinity phase have been investigated in the temperature range 25–450 °C. The refractive index varied from 1.84 to 1.95 and extinction coefficient from 2 × 10−3 to 9.6 × 10−3. This was explained on the basis of an increase in packing density from 0.686 to 0.813. The change in packing density has been attributed to a decrease in the oxygen condensation at higher temperatures. Annealing results in a decrease in refractive index and increase in extinction coefficient. The films deposited at 150 °C showed a monoclinic phase which transforms to a tetragonal phase at higher substrate temperatures.

Effect of Substrate and Annealing Temperatures on Mechanical Properties of Ti-rich NiTi Films

The effect of substrate and annealing temperatures on mechanical properties of Ti-rich NiTi films deposited on Si (100) substrates by DC magnetron sputtering was studied by nanoindentation. NiTi films were deposited at two substrate temperatures viz. 300 and 400 degrees C. NiTi films deposited at 300 degrees C were annealed for 4 h at four different temperatures, i.e. 300, 400, 500 and 600 degrees C whereas films deposited at 400 degrees C were annealed for 4 h at three different temperatures, i.e. 400, 500 and 600 degrees C. The elastic modulus and hardness of the films were found to be the same in the as-deposited as well as annealed conditions for both substrate temperatures. For a given substrate temperature, the hardness and elastic modulus were found to remain unchanged as long as the films were amorphous. However, both elastic modulus and hardness showed an increase with increasing annealing temperature as the films become crystalline. The results were explained on the basis of the change in microstructure of the film with change in annealing temperature.

Computer modeling studies on the binding of 2',5'-linked dinucleoside phosphates to ribonuclease T1-influence of subsite interactions on the substrate specificity

The modes of binding of Gp(2',5')A, Gp(2',5')C, Gp(2',5')G and Gp(2',5')U to RNase T1 have been determined by computer modelling studies. All these dinucleoside phosphates assume extended conformations in the active site leading to better interactions with the enzyme. The 5'-terminal guanine of all these ligands is placed in the primary base binding site of the enzyme in an orientation similar to that of 2'-GMP in the RNase T1-2'-GMP complex. The 2'-terminal purines are placed close to the hydrophobic pocket formed by the residues Gly71, Ser72, Pro73 and Gly74 which occur in a loop region. However, the orientation of the 2'-terminal pyrimidines is different from that of 2'-terminal purines. This perhaps explains the higher binding affinity of the 2',5'-linked guanine dinucleoside phosphates with 2'-terminal purines than those with 2'-terminal pyrimidines. A comparison of the binding of the guanine dinucleoside phosphates with 2',5'- and 3',5'-linkages suggests significant differences in the ribose pucker and hydrogen bonding interactions between the catalytic residues and the bound nucleoside phosphate implying that 2',5'-linked dinucleoside phosphates may not be the ideal ligands to probe the role of the catalytic amino acid residues. A change in the amino acid sequence in the surface loop region formed by the residues Gly71 to Gly74 drastically affects the conformation of the base binding subsite, and this may account for the inactivity of the enzyme with altered sequence i.e., with Pro, Gly and Ser at positions 71 to 73 respectively. These results thus suggest that in addition to recognition and catalytic sites, interactions at the loop regions which constitute the subsite for base binding are also crucial in determining the substrate specificity.

Random sequential multilayer deposition of different‐sized k mers on a one dimensional infinite substrate

Kinetics of random sequential, irreversible multilayer deposition of macromolecules of two different sizes on a one dimensional infinite lattice is analyzed at the mean field level. A formal solution for the corresponding rate equation is obtained. The Jamming limits and the distribution of gaps of exact sizes are discussed. In the absence of screening, the jamming limits are shown to be the same for all the layers. A detailed analysis for the components differing by one monomer unit is presented. The small and large time behaviors and the dependence of the individual jamming limits of the k mers and (k−1) mers on k and the rate parameters are analyzed.

Growth temperature induced effects in non-polar a-plane GaN on r-plane sapphire substrate by RF-MBE

Non-polar a-plane GaN films were grown on an r-plane sapphire substrate by plasma assisted molecular beam epitaxy (PAMBE). The effect of growth temperature on structural, morphological and optical properties has been studied. The growth of non-polar a-plane (1 1 - 2 0) orientation of the GaN epilayers were confirmed by high resolution X-ray diffraction (HRXRD) study. The X-ray rocking curve (XRC) full width at half maximum of the (1 1 - 2 0) reflection shows in-plane anisotropic behavior and found to decrease with increase in growth temperature. The atomic force micrograph (AFM) shows island-like growth for the film grown at a lower temperature. Surface roughness has been decreased with increase in growth temperature. Room temperature photoluminescence shows near band edge emission at 3.434-3.442 eV. The film grown at 800 degrees C shows emission at 2.2 eV, which is attributed to yellow luminescence along with near band edge emission. (C) 2010 Elsevier B.V. All rights reserved.

Influence of Substrate Temperature and Deposition Rate on Structural and Mechanical Properties of Shape Memory NiTi Films

NiTi thin films deposited by DC magnetron sputtering of an alloy (Ni/Ti:45/55) target at different deposition rates and substrate temperatures were analyzed for their structure and mechanical properties. The crystalline structure, phase-transformation and mechanical response were characterized by X-ray diffraction (XRD), Differential Scanning Calorimetry (DSC) and Nano-indentation techniques, respectively. The films were deposited on silicon substrates maintained at temperatures in the range 300 to 500 degrees C and post-annealed at 600 degrees C for four hours to ensure film crystallinity. Films deposited at 300 degrees C and annealed for 600 degrees C have exhibited crystalline behavior with Austenite phase as the prominent phase. Deposition onto substrates held at higher deposition temperatures (400 and 500 degrees C) resulted in the co-existence of Austenite phase along with Martensite phase. The increase in deposition rates corresponding to increase in cathode current from 250 to 350 mA has also resulted in the appearance of Martensite phase as well as improvement in crystallinity. XRD analysis revealed that the crystalline film structure is strongly influenced by process parameters such as substrate temperature and deposition rate. DSC results indicate that the film deposited at 300 degrees C had its crystallization temperature at 445 degrees C in the first thermal cycle, which is further confirmed by stress temperature response. In the second thermal cycle the Austenite and Martensite transitions were observed at 75 and 60 degrees C respectively. However, the films deposited at 500 degrees C had the Austenite and Martensite transitions at 73 and 58 degrees C, respectively. Elastic modulus and hardness values increased from 93 to 145 GPa and 7.2 to 12.6 GPa, respectively, with increase in deposition rates. These results are explained on the basis of change in film composition and crystallization. (C) 2010 Published by Elsevier Ltd

Instability and dewetting of ultrathin solid viscoelastic films on homogeneous and heterogeneous substrates

Instability and dewetting engendered by the van der Waals force in soft thin (<100 nm) linear viscoelastic solid (e. g., elastomeric gel) films on uniform and patterned surfaces are explored. Linear stability analysis shows that, although the elasticity of the film controls the onset of instability and the corresponding critical wavelength, the dominant length-scale remains invariant with the elastic modulus of the film. The unstable modes are found to be long-wave, for which a nonlinear long-wave analysis and simulations are performed to uncover the dynamics and morphology of dewetting. The stored elastic energy slows down the temporal growth of instability significantly. The simulations also show that a thermodynamically stable film with zero-frequency elasticity can be made unstable in the presence of physico-chemical defects on the substrate and can follow an entirely different pathway with far fewer holes as compared to the viscous films. Further, the elastic restoring force can retard the growth of a depression adjacent to the hole-rim and thus suppress the formation of satellite holes bordering the primary holes. These findings are in contrast to the dewetting of viscoelastic liquid films where nonzero frequency elasticity accelerates the film rupture and promotes the secondary instabilities. Thus, the zero-frequency elasticity can play a major role in imposing a better-defined long-range order to the dewetted structures by arresting the secondary instabilities. (C) 2011 American Institute of Physics. doi: 10.1063/1.3554748]

Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach.

In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the second base binding (B2) site is insufficient. Further, the nature of ligand-protein interaction is elucidated generally by studies on RNase A-substrate analog complexes (mainly with the help of X-ray crystallography). Hence, the details of interactions at atomic level arising due to substrates are inferred indirectly. In the present paper, the dinucleotide substrate UpA is fitted into the active site of RNase A Several possible substrate conformations are investigated and the binding modes have been selected based on Contact Criteria. Thus identified RNase A-UpA complexes are energy minimized in coordinate space and are analysed in terms of conformations, energetics and interactions. The best possible ligand conformations for binding to RNase A are identified by experimentally known interactions and by the energetics. Upon binding of UpA to RNase A the changes associated,with protein back bone, Side chains in general and at the binding sites in particular are described. Further, the detailed interactions between UpA and RNase A are characterized in terms of hydrogen bonds and energetics. An extensive study has helped in interpreting the diverse results obtained from a number of experiments and also in evaluating the extent of changes the protein and the substrate undergo in order to maximize their interactions.

Substrate-dependent structure, microstructure, composition and properties of nanostructured TiN films

Titanium nitride films of a thickness of similar to 1.5 mu m were deposited on amorphous and crystalline substrates by DC reactive magnetron sputtering at ambient temperature with 100% nitrogen in the sputter gas. The growth of nanostructured, i.e. crystalline nano-grain sized, films at ambient temperature is demonstrated. The microstructure of the films grown on crystalline substrates reveals a larger grain size/crystallite size than that of the films deposited on amorphous substrates. Specular reflectance measurements on films deposited on different substrates indicate that the position of the Ti-N 2s band at 2.33 eV is substrate-dependent, indicating substrate-mediated stoichiometry. This clearly demonstrates that not only structure and microstructure, but also chemical composition of the films is substrate-influenced. The films deposited on amorphous substrates display lower hardness and modulus values than the films deposited on crystalline substrates, with the highest value of hardness being 19 GPa on a lanthanum aluminate substrate. (C) 2011 Elsevier Ltd. All rights reserved.

Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity

2-Methylcitric acid (2-MCA) cycle is one of the well studied pathways for the utilization of propionate as a source of carbon and energy in bacteria such as Salmonella typhimurium and Escherichia coli. 2-Methylcitrate synthase (2-MCS) catalyzes the conversion of oxaloacetate and propionyl-CoA to 2-methylcitrate and CoA in the second step of 2-MCA cycle. Here, we report the X-ray crystal structure of S. typhimurium 2-MCS (StPrpC) at 2.4 A resolution and its functional characterization. StPrpC was found to utilize propionyl-CoA more efficiently than acetyl-CoA or butyryl-CoA. The polypeptide fold and the catalytic residues of StPrpC are conserved in citrate synthases (CSs) suggesting similarities in their functional mechanisms. In the triclinic P1 cell, StPrpC molecules were organized as decamers composed of five identical dimer units. In solution, StPrpC was in a dimeric form at low concentrations and was converted to larger oligomers at higher concentrations. CSs are usually dimeric proteins. In Gram-negative bacteria, a hexameric form, believed to be important for regulation of activity by NADH, is also observed. Structural comparisons with hexameric E. coil CS suggested that the key residues involved in NADH binding are not conserved in StPrpC. Structural comparison with the ligand free and bound states of CSs showed that StPrpC is in a nearly closed conformation despite the absence of bound ligands. It was found that the Tyr197 and Leu324 of StPrpC are structurally equivalent to the ligand binding residues His and Val, respectively, of CSs. These substitutions might determine the specificities for acyl-CoAs of these enzymes. (C) 2010 Elsevier Inc. All rights reserved.