Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Evolution of ferroelectric SrBi2Nb2O9 phase in the Li2B4O7-SrO-Bi2O3-Nb2O5 glass system

Glasses of various compositions in the system (100 - x)Li-2 B-4 O-7 - x (SrO-Bi2O3-Nb2O5) (10 less than or equal to x less than or equal to 60) (in molar ratio) were prepared via a conventional melt-quenching technique. The glassy nature of the as-quenched samples was established by Differential Thermal Analyses (DTA). X-ray powder diffraction (XRD) and Transmission Electron Microscopic (TEM) studies confirmed the amorphous nature of the as quenched and crystallinity in the heat-treated samples. The formation of nanocrystalline layered perovskite SrBi2Nb2O9 (SBN) phase, in the samples heat-treated at temperatures higher than 550degreesC, through an intermediate fluorite phase in the LBO glass matrix was confirmed by both the XRD and High Resolution Transmission Electron Microscopy (HRTEM). The samples that were heat-treated at two different temperatures, 550 and 625degreesC, (containing 0.35 and 0.47 mum sized SBN crystallites) exhibited broad dielectric anomalies in the vicinity of ferroelectric to paraelectric transition temperature of the parent SBN ceramics. A downward shift in the phase transition temperature was observed with decreasing crystallite size of SBN. The observation of pyroelectric and ferroelectric properties for the present samples confirmed their polar nature.

Simulation and experimental study on compositional evolution of Li-Co in LiCoO(2) thin films during sputter deposition

The compositional evolution in sputter deposited LiCoO(2) thin films is influenced by process parameters involved during deposition. The electrochemical performance of these films strongly depends on their microstructure, preferential orientation and stoichiometry. The transport process of sputtered Li and Co atoms from the LiCoO(2) target to the substrate, through Ar plasma in a planar magnetron configuration, was investigated based on the Monte Carlo technique. The effect of sputtering gas pressure and the substrate-target distance (d(st)) on Li/Co ratio, as well as, energy and angular distribution of sputtered atoms on the substrate were examined. Stable Li/Co ratios have been obtained at 5 Pa pressure and d(st) in the range 5 11 cm. The kinetic energy and incident angular distribution of Li and Co atoms reaching the substrate have been found to be dependent on sputtering pressure. Simulations were extended to predict compositional variations in films prepared at various process conditions. These results were compared with the composition of films determined experimentally using x-ray photoelectron spectroscopy (XPS). Li/Co ratio calculated using XPS was in moderate agreement with that of the simulated value. The measured film thickness followed the same trend as predicted by simulation. These studies are shown to be useful in understanding the complexities in multicomponent sputtering. (C) 2011 American Institute of Physics. doi:10.1063/1.3597829]

First-principles electronic structure of the delafossites ABO(2) (A=Cu, Ag, Au; B=Al, Ga, Sc, In, Y): evolution of d(10)-d(10) interactions

While bonding between d(10) atoms and ions in molecular systems has been well studied, less attention has been paid to interactions between such seemingly closed shell species in extended inorganic solids. In this contribution, we present visualizations of the electronic structures of the delafossites ABO(2) (A = Cu, Ag, Au) with particular emphasis on the nature of d(10)-d(10) interactions in the close packed plane of the coinage metal ion. We find that on going from Cu to Ag to Au, the extent of bonding between A and A increases. However, the structures (in terms of distances) of these compounds are largely determined by the strongly ionic 13,11 0 interaction and for the larger B ions Sc, In and Y, the A atoms are sufficiently well-separated that A-A bonding is almost negligible. We also analyze some interesting differences between Ag and Au, including the larger A-O covalency of the Au. The trends in electronic structure suggest that the Ag and Au compounds are not good candidate transparent conducting oxides. (C) 2002 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

Kinetics of hydrogen evolution on submicron size Co, Ni, Pd and CoNi alloy powder electrodes by d.c. polarization and a.c. impedance studies

Submicron size Co, Ni and Co-Ni alloy powders have been synthesized by the polyol method using the corresponding metal malonates and Pd powder by reduction of PdOx in methanol. The kinetics of the hydrogen evolution reaction ( HER) in 6 M KOH electrolyte have been studied on electrodes made from the pressed powders. The d.c. polarization measurements have resulted in a value close to 120 mV decade(-1) for the Tafel slope, suggesting that the HER follows the Volmer-Heyrovsky mechanism. The values of exchange current density (i(o)) are in the range 1-10 mA cm(-2) for electrodes fabricated in the study. The a.c. impedance spectra measured at several potentials in the HER region showed a single semicircle in the Nyquist plots. Exchange current density (i(o)) and energy transfer coefficient (alpha) have been calculated by employing a nonlinear least square-fitting program.

Evolution of crystallographic texture during deformation of submicron grain size titanium

Evolution of deformation texture in commercially pure titanium with submicron grain size (SMG) was studied using x-ray diffraction (XRD) and electron back scatter diffraction (EBSD) methods. The material was deformed by rolling at room temperature. The deformation mechanism was found to be slip dominated with a pyramidal slip system facilitating plastic deformation. No evidence of tensile or compressive twinning was detected, as generally seen in the case of titanium with conventional microcrystalline grain size. The absence of twinning and the propensity of the pyramidal slip system in the SMG Ti is attributed to the lack of coordinated motion of zonal partial dislocations that leads to twinning.

Formation of amorphous xenon nanoclusters and microstructure evolution in pulsed laser deposited Ti(62.5)Si(37.5) thin films during Xe ion irradiation

As deposited amorphous and crystallized thin films of Ti 37.5% Si alloy deposited by pulsed laser ablation technique were irradiated with 100 keV Xe(+) ion beam to an ion fluence of about 10(16) ions-cm(-2). Transmission electron microscopy revealed that the implanted Xe formed amorphous nanosized clusters in both cases. The Xe ion-irradiation favors nucleation of a fcc-Ti(Si) phase in amorphous films. However, in crystalline films, irradiation leads to dissolution of the Ti(5)Si(3) intermetallic phase. In both cases, Xe irradiation leads to the evolution of similar microstructures. Our results point to the pivotal role of nucleation in the evolution of the microstructure under the condition of ion implantation.

Microstructural evolution in laser-ablation-deposited Fe–25 at.% Ge thin film

Films with Fe–25 at.% Ge composition are deposited by the process of laser ablation on single crystal NaCl and Cu substrates at room temperature. Both the vapor and liquid droplets generated in this process are quenched on the substrate. The microstructures of the embedded droplets show size as well as composition dependence. The hierarchy of phase evolution from amorphous to body-centered cubic (bcc) to DO3 has been observed as a function of size. Some of the medium-sized droplets also show direct formation of ordered DO19 phase from the starting liquid. The evolution of disordered bcc structure in some of the droplets indicates disorder trapping during liquid to solid transformation. The microstructural evolution is analyzed on the basis of heat transfer mechanisms and continuous growth model in the solidifying droplets.

Evolution of metastable phases during crystallization of pulsed laser deposited amorphous Al–Fe films

Amorphous thin films of different Al–Fe compositions were produced by plasma/vapor quenching during pulsed laser deposition. The chosen compositions Al72Fe28, Al40Fe60, and Al18Fe82 correspond to Al5Fe2 and B2-ordered AlFe intermetallic compounds and α–Fe solid solution, respectively. The films contained fine clusters that increased with iron content. The sequences of phase evolution observed in the heating stage transmission electron microscopy studies of the pulsed laser ablation deposited films of Al72Fe28, Al40Fe60, and Al18Fe82 compositions showed evidence of composition partitioning during crystallization for films of all three compositions. This composition partitioning, in turn, resulted in the evolution of phases of compositions richer in Fe, as well as richer in Al, compared to the overall film composition in each case. The evidence of Fe-rich phases was the B2 phase in Al72Fe28 film, the L12- and DO3-ordered phases in Al40Fe60 film, and the hexagonal ε–Fe in the case of the Al18Fe82 film. On the other hand, the Al-rich phases were Al13Fe4 for both Al72Fe28 and Al40Fe60 films and DO3 and Al5Fe2 phases in the case of Al18Fe82 film. We believe that this tendency of composition partitioning during crystallization from amorphous phase is a consequence of the tendency of clustering of the Fe atoms in the amorphous phase during nucleation. The body-centered cubic phase has a nucleation advantage over other metastable phases for all three compositions. The amorphization of Al18Fe82 composition and the evolution of L12 and ε–Fe phases in the Al–Fe system were new observations of this work.

Time Evolution of the Microstructure of VO2(B) Films Deposited on Glass by MOCVD

Thin films of VO2(B), a metastable polymorph of vanadium dioxide, have been grown on glass by low-pressure metalorganic chemical vapor deposition (MOCVD). The films grown for 90 minutes have atypical microstructure, comprising micrometer-sized, island-like entities made up of numerous small, single-crystalline platelets (≅1 μm) emerging orthogonally from larger ones at the center. Microstructure evolution as a function of deposition time has been examined by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The metastable VO2(B) transforms to the stable rutile (R) phase at 550°C in inert ambient, which on cooling convert reversibly to M phase. Electron microscopy shows that annealing leads to the disintegration of the VO2(B) platelets into small crystallites of the rutile phase VO2(R), although the platelet morphology is retained. The magnitude of the jump in resistance at the semiconductor-to-metal, VO2(M)→VO2(R) phase transition depends on the arrangement of polycrystalline platelets in the films.

Quasicrystalline Coatings Through Laser Processing: A Study on Process Optimisation and Microstructure Evolution

Composite coatings containing quasicrystalline (QC) phases in Al-Cu-Fe alloys were prepared by laser cladding using a mixture of the elemental powders. Two substrates, namely pure aluminum and an Al-Si alloy were used. The clad layers were remelted at different scanning velocities to alter the growth conditions of different phases. The process parameters were optimized to produce quasicrystalline phases. The evolution of the microstructure in the coating layer was characterized by detailed microstructural investigation. The results indicate presence of quasicrystals in the aluminum substrate. However, only approximant phase could be observed in the substrate of Al-Si alloys. It is shown that there is a significant transport of Si atoms from the substrate to the clad layer during the cladding and remelting process. The hardness profiles of coatings on aluminum substrate indicate a very high hardness. The coating on Al-Si alloy, on the other hand, is ductile and soft. The fracture toughness of the hard coating on aluminum was obtained by nano-indentation technique. The K1C value was found to be 1.33 MPa m1/2 which is typical of brittle materials.

Texture evolution in an Al-Cu alloy during equal channel angular pressing: the effect of starting microstructure

In this article, the effect of initial microstructure on the texture evolution in 2014 Al alloy during equal channel angular pressing (ECAP) through route A has been reported. Three heat treatment conditions were chosen to generate the initial microstructures, namely (i) the recrystallization anneal (as-received), (ii) solution treatment at 768 K for 1 h, and (iii) solution treatment (768 K for 1 h) plus aging at 468 K for 5 h. Texture analyses were performed using orientation distribution function (ODF) method. The texture strength after ECAP processing was different for the three samples in the order, solutionised > solutionised plus aged condition > as-received. The prominent texture components were A (E) /(A) over bar (E) and B(E)/(B) over bar (E) in addition to several weaker components for the three materials. The strong texture evolution in solutionised condition has been attributed to higher strain hardening of the matrix due to higher amount of solute. In case of the as-received as well as solutionised plus aged alloy, the weaker texture could be due to the strain scattering from extensive precipitate fragmentation and dissolution during ECAP.

Morphological Evolution and Properties of LPE Grown GaSb, AlGaSb and AlGaAsSb

The nucleation morphologies of LPE grown GaSb, AlGaSb and AlGaAsSb layers on GaSb substrates are presented. The morphology of the GaSb layers grown from Sb-rich melts showed facets on highly terraced surface, whereas those grown from Ga-rich melts exhibited fine terraces without facets. An optimum temperature in the range of 500 – 550°C was found to be suitable for the growth of mirror smooth layers from Ga-melts. The surface morphology of the AlxGa1-xSb layers degrades drastically with increase in Al content beyond x = 0.5. The surface morphology of AlGaAsSb epilayers has been found to depend strongly on the pre-growth melt dissolution sequence.

Formation of amorphous xenon nanoclusters and microstructure evolution in pulsed laser deposited Ti62.5Si37.5 thin films during Xe ion irradiation

As deposited amorphous and crystallized thin films of Ti 37.5% Si alloy deposited by pulsed laser ablation technique were irradiated with 100 keV Xe+ ion beam to an ion fluence of about 1016 ions-cm−2. Transmission electron microscopy revealed that the implanted Xe formed amorphous nanosized clusters in both cases. The Xe ion-irradiation favors nucleation of a fcc-Ti(Si) phase in amorphous films. However, in crystalline films, irradiation leads to dissolution of the Ti5Si3 intermetallic phase. In both cases, Xe irradiation leads to the evolution of similar microstructures. Our results point to the pivotal role of nucleation in the evolution of the microstructure under the condition of ion implantation.