Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (��20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

Growth evolution of ZnO thin films deposited by RF magnetron sputtering

We study the surface morphology evolution of ZnO thin films grown on glass substrates as a function of thickness by RF magnetron sputtering technique. The surface topography of the samples is measured by atomic force microscopy (AFM). All AFM images of the films are analyzed using scaling concepts. The results show that the surface morphology is initially formed by a small grains structure. The grains increase in size and height with growth time resulting in the formation of a mounds-like structure. The growth exponent, beta, and the exponent defining the evolution of the characteristic wavelength of the surface, p, amounted to beta = 0.76 +/- 0.08 and p = 0.3 +/- 0.05. From these exponents, the surface morphology is determined by the nonlocal shadowing effects, that is the dominant mechanism, due to the incident deposition particles during film growth.

Study of the growth process of in situ polyaniline deposited films

Polyaniline (PAni) thin films were deposited onto BK7 glass substrates using the in situ deposition technique. The control of the time and the aniline concentration in the PAni polymerization reaction on the film deposition allowed us to prepare films with different thickness, down to similar to 25 nm. The film growth process was monitored by measuring the UV-vis spectra and the AFM height profiles of the film surface. The curves of adsorption kinetics were analyzed with the Avrami's model, yielding an exponent it n = 3, thus indicating nucleation of spheroids at the initial stages of polymerization that grow through a diffusion process. AFM images of the surface height profiles corroborate this hypothesis, with spheroids growing with no preferred orientation during the in situ deposition. (C) 2007 Elsevier B.V. All rights reserved.

An improved three-dimensional model for growth of oxide films induced by laser heating

In this paper we consider a three-dimensional heat diffusion model to explain the growth of oxide films which takes place when a laser beam is shined on and heats a metallic layer deposited on a glass substrate in a normal atmospheric environment. In particular, we apply this model to the experimental results obtained for the dependence of the oxide layer thickness on the laser density power for growth of TiO2 films grown on Ti-covered glass slides. We show that there is a very good agreement between the experimental results and the theoretical predictions from our proposed three-dimensional model, improving the results obtained with the one-dimensional heat diffusion model previously reported. Our theoretical results also show the occurrence of surface cooling between consecutive laser pulses, and that the oxide track surface profile closely follows the spatial laser profile indicating that heat diffusive effects can be neglected in the growth of oxide films by laser heating. �� 2001 Elsevier Science B.V.

Crystallization of amorphous GaAs films prepared onto different substrates

This work reports changes in structural properties produced by thermal annealing of flash evaporated amorphous GaAs films using the micro-Raman scattering and the X-ray diffraction (XRD) techniques. Films of about 1 ��m were grown on c-Si and glass substrates. The crystallization process is less effective for samples deposited on c-Si. This could be due to the ordering in the first layers of the film imposed by the oriented Si substrates. We propose that this ordering makes the growth of crystallites in these films more restrained than the growth occurring in the completely amorphous films on glass substrates. �� 2002 Elsevier Science B.V. All rights reserved.

Growth and morphology of eumelanin thin films - A future bioelectronic material?

We present a study on the thin film morphology and the optical properties of eumelanin resulting from different synthesis routes: the oxidation of tyrosine with hydrogen peroxide, the auto-oxidation of dihydroxyphenylanaline in water and its auto-oxidation in dimethyl sulfoxid. Atomic Force Microscopy images indicate that the presence of holes and particles depends on the eumelanin synthesis route and the substrate employed. Smooth films with very few defects could be obtained with eumelanin synthesized in dimethyl sulfoxide deposited on glass substrates. Our study shows that all eumelanin preparations are comparable in terms of thin film morphology on the submicrometer scale and UV-visible transmission properties. ��The Electrochemical Society.

Strain- and electric field-induced band gap modulation in nitride nanomembranes

The hexagonal nanomembranes of the group III-nitrides are a subject of interest due to their novel technological applications. In this paper, we investigate the strain- and electric field-induced modulation of their band gaps in the framework of density functional theory. For AlN, the field-dependent modulation of the bandgap is found to be significant whereas the strain-induced semiconductor-metal transition is predicted for GaN. A relatively flat conduction band in AlN and GaN nanomembranes leads to an enhancement of their electronic mobility compared to that of their bulk counterparts. �� 2013 IOP Publishing Ltd.

Understanding growth mechanisms and tribocorrosion behaviour of porous TiO2 anodic films containing calcium, phosphorous and magnesium

Coordena����o de Aperfei��oamento de Pessoal de N��vel Superior (CAPES)

How population loss through habitat boundaries determines the dynamics of a predator-prey system

Funda����o de Amparo �� Pesquisa do Estado de S��o Paulo (FAPESP)

Monoamine oxidase B layer-by-layer film fabrication and characterization toward dopamine detection

Funda����o de Amparo �� Pesquisa do Estado de S��o Paulo (FAPESP)

Advanced SPM studies on the growth of ultrathin films of organic semiconductors at metal and dielectric interfaces

Many studies on the morphology, molecular orientation, device performance, substrate nature and growth parameter dependence have been carried out since the proposal of Sexithiophene (6T) for organic electronics [ ] However, these studies were mostly performed on films thicker than 20nm and without specifically addressing the relationship between morphology and molecular orientation within the nano and micro structures of ultrathin films of 0-3 monolayers. In 2004, the observation that in OFETs only the first few monolayers at the interface in contact with the gate insulator contribute to the charge transport [ ], underlined the importance to study submonolayer films and their evolution up to a few monolayers of thickness with appropriate experimental techniques. We present here a detailed Non-contact Atomic Force Microscopy and Scanning Tunneling Microscopy study on various substrates aiming at the investigation of growth mechanisms. Most reported similar studies are performed on ideal metals in UHV. However it is important to investigate the details of organic film growth on less ideal and even technological surfaces and device testpatterns. The present work addresses the growth of ultra thin organic films in-situ and quasi real-time by NC-AFM. An organic effusion cell is installed to evaporate the organic material directly onto the SPM sample scanning stage.

Improved GaN-based HEMT performance by nanocrystalline diamond capping

As a wide-bandgap semiconductor, gallium nitride (GaN) is an attractive material for next-generation power devices. To date, the capabilities of GaN-based high electron mobility transistors (HEMTs) have been limited by self-heating effects (drain current decreases due to phonon scattering-induced carrier velocity reductions at high drain fields). Despite awareness of this, attempts to mitigate thermal impairment have been limited due to the difficulties involved with placing high thermal conductivity materials close to heat sources in the device. Heat spreading schemes have involved growth of AIGaN/GaN on single crystal or CVD diamond, or capping of fullyprocessed HEMTs using nanocrystalline diamond (NCD). All approaches have suffered from reduced HEMT performance or limited substrate size. Recently, a "gate after diamond" approach has been successfully demonstrated to improve the thermal budget of the process by depositing NCD before the thermally sensitive Schottky gate and also to enable large-area diamond implementation.

Different Tyrosine Autophosphorylation Requirements in Fibroblast Growth Factor Receptor-1 Mediate Urokinase-Type Plasminogen Activator Induction and Mitogenesis

Among the seven tyrosine autophosphorylation sites identified in the intracellular domain of tyrosine kinase fibroblast growth factor receptor-1 (FGFR1), five of them are dispensable for FGFR1-mediated mitogenic signaling. The possibility of dissociating the mitogenic activity of basic FGF (FGF2) from its urokinase-type plasminogen activator (uPA)-inducing capacity both at pharmacological and structural levels prompted us to evaluate the role of these autophosphorylation sites in transducing FGF2-mediated uPA upregulation. To this purpose, L6 myoblasts transfected with either wild-type (wt) or various FGFR1 mutants were evaluated for the capacity to upregulate uPA production by FGF2. uPA was induced in cells transfected with wt-FGFR1, FGFR1-Y463F, -Y585F, -Y730F, -Y766F, or -Y583/585F mutants. In contrast, uPA upregulation was prevented in L6 cells transfected with FGFR1-Y463/583/585/730F mutant (FGFR1���4F) or with FGFR1-Y463/583/585/730/766F mutant (FGFR1���5F) that retained instead a full mitogenic response to FGF2; however, preservation of residue Y730 in FGFR1-Y463/583/585F mutant (FGFR1���3F) and FGFR1-Y463/583/585/766F mutant (FGFR1���4Fbis) allows the receptor to transduce uPA upregulation. Wild-type FGFR1, FGFR1���3F, and FGFR1���4F similarly bind to a 90-kDa tyrosine-phosphorylated protein and activate Shc, extracellular signal-regulated kinase (ERK)2, and JunD after stimulation with FGF2. These data, together with the capacity of the ERK kinase inhibitor PD 098059 to prevent ERK2 activation and uPA upregulation in wt-FGFR1 cells, suggest that signaling through the Ras/Raf-1/ERK kinase/ERK/JunD pathway is necessary but not sufficient for uPA induction in L6 transfectants. Accordingly, FGF2 was able to stimulate ERK1/2 phosphorylation and cell proliferation, but not uPA upregulation, in L6 cells transfected with the FGFR1-Y463/730F mutant, whereas the FGFR1-Y583/585/730F mutant was fully active. We conclude that different tyrosine autophosphorylation requirements in FGFR1 mediate cell proliferation and uPA upregulation induced by FGF2 in L6 cells. In particular, phosphorylation of either Y463 or Y730, dispensable for mitogenic signaling, represents an absolute requirement for FGF2-mediated uPA induction.

Crosstalk between the Ras2p-controlled Mitogen-activated Protein Kinase and cAMP Pathways during Invasive Growth of Saccharomyces cerevisiae

The two highly conserved RAS genes of the budding yeast Saccharomyces cerevisiae are redundant for viability. Here we show that haploid invasive growth development depends on RAS2 but not RAS1. Ras1p is not sufficiently expressed to induce invasive growth. Ras2p activates invasive growth using either of two downstream signaling pathways, the filamentation MAPK (Cdc42p/Ste20p/MAPK) cascade or the cAMP-dependent protein kinase (Cyr1p/cAMP/PKA) pathway. This signal branch point can be uncoupled in cells expressing Ras2p mutant proteins that carry amino acid substitutions in the adenylyl cyclase interaction domain and therefore activate invasive growth solely dependent on the MAPK cascade. Both Ras2p-controlled signaling pathways stimulate expression of the filamentation response element-driven reporter gene depending on the transcription factors Ste12p and Tec1p, indicating a crosstalk between the MAPK and the cAMP signaling pathways in haploid cells during invasive growth.

Photoconductivity and Electro-Optical Properties of Wide Band Gap Metal Oxides

The PhD activity described in this Thesis was focused on the study of metal-oxide wide-bandgap materials, aiming at fabricating new optoelectronic devices such as solar-blind UV photodetectors, high power electronics, and gas sensors. Photocurrent spectroscopy and DC photocurrent time evolution were used to investigate the performance of prototypes under different atmospheres, temperatures and excitation wavelengths (or dark conditions). Cathodoluminescence, absorption spectroscopy, XRD and SEM were used to assess structural, morphologic, electrical and optical properties of materials. This thesis is divided into two main sections, each describing the work done on a different metal-oxide semiconductor. 1) MOVPE-grown Ga2O3 thin films for UV solar-blind photodetectors and high power devices The semiconducting oxides, among them Ga2O3, have been employed for several decades as transparent conducting oxide (TCO) electrodes for fabrication of solar cells, displays, electronic, and opto-electronic devices. The interest was mainly confined to such applications, as these materials tend to grow intrinsically n-type, and attempts to get an effective p-type doping has consistently failed. The key requirements of TCO electrodes are indeed high electrical conductivity and good transparency, while crystallographic perfection is a minor issue. Furthermore, for a long period no high-quality substrates and epi-layers were available, which in turn impeded the development of a truly full-oxide electronics. Recently, Ga2O3 has attracted renewed interest, as large single crystals and high-quality homo- and hetero-epitaxial layers became available, which paved the way to novel application areas. Our research group spent the last two years in developing a low temperature (500-700��C) MOVPE growth procedure to obtain thin films of Ga2O3 on different substrates (Dept. of Physics and IMEM-CNR at UNIPR). We obtained a significant result growing on oriented sapphire epitaxial films of high crystalline, undoped, pure phase ���-Ga2O3 (hexagonal). The crystallographic properties of this phase were investigated by XRD, in order to clarify the lattice parameters of the hexagonal cell. First design and development of solar blind UV photodetectors based on ���-phase was carried out and the optoelectronic performance is evaluated by means of photocurrent spectroscopy. The UV-response is adequately fast and reliable to render this unusual phase a subject of great interest for future applications. The availability of a hexagonal phase of Ga2O3 stable up to 700��C, belonging to the same space group of gallium nitride, with high crystallinity and tunable electrical properties, is intriguing in view of the development of nitride-based devices, by taking advantage of the more favorable symmetry and epitaxial relationships with respect to the monoclinic ��-phase. In addition, annealing at temperatures higher than 700��C demonstrate that the hexagonal phase converts totally in the monoclinic one. 2) ZnO nano-tetrapods: charge transport mechanisms and time-response in optoelectronic devices and sensors Size and morphology of ZnO at the nanometer scale play a key role in tailoring its physical and chemical properties. Thanks to the possibility of growing zinc oxide in a variety of different nanostructures, there is a great variety of applications, among which gas sensors, light emitting diodes, transparent conducting oxides, solar cells. Even if the operation of ZnO nanostructure-based devices has been recently demonstrated, the mechanisms of charge transport in these assembly is still under debate. The candidate performed an accurate investigation by photocurrent spectroscopy and DC-photocurrent time evolution of electrical response of both single-tetrapod and tetrapod-assembly devices. During the research done for this thesis, a thermal activation energy enables the performance of samples at high temperatures (above about 300��C). The energy barrier is related to the leg-to-leg interconnection in the assembly of nanotetrapods. Percolation mechanisms are responsible for both the very slow photo-response (minutes to hours or days) and the significant persistent photocurrent. Below the bandgap energy, electronic states were investigated but their contribution to the photocurrent are two-three order of magnitude lower than the band edge. Such devices are suitable for employ in photodetectors as well as in gas sensors, provided that the mechanism by which the photo-current is generated and gas adsorption on the surface modify the conductivity of the material are known.