Surface modifications in single crystal surfaces of YBa2Cu3O7-delta upon high energy ion irradiation

Atomic force microscopy investigations on swift heavy ion (200 MeV An) irradiated surfaces of a high T-c single crystal YBa2Cu3O7-delta are presented. Results obtained revealed an ion-induced erosion/sputtering clearly confirming our earlier observation on grain boundary dominated thin films. Apart from sputtering, notable effects were seen with many defect structures like dikes/hillocks surrounded by craters, dikes, holes, pearl like structures and ripple formation of sub-micron undulations, all in one crystal. Results are discussed in the light of co-operative phenomena of material re-distribution mechanism related to mass transfer and crater formations.

Darcian mixed convection plumes along vertical adiabatic surfaces in a saturated porous medium

The mixed convection flow due to a line thermal source embedded at the leading edge of an adiabatic vertical plane surface immersed in a saturated porous medium has been studied. Both weakly and strongly buoyant plume regimes have been considered. The cases of buoyancy assisting and buoyancy opposing flow conditions have been incorporated in the analysis. The results are presented for the entire range of buoyancy parameter from the pure forced convection (xgr=0) to the pure free convection (xgr rarr infin@#@) regimes. For buoyancy-assisting flow, the wall temperature and the velocity at the wall increase as the plume strength increases. However, they all decrease as the free-stream velocity increases. For buoyancyopposing flow, the temperature at the wall increases as the strength of the plume increases but velocity at the wall decreases.

Laser Surface Alloying of a Creep Resistant Magnesium Alloy MRI 230D with Al and Al2O3

A creep resistant permanent mould cast Mg alloy MRI 230D was laser surface alloyed with Al and a mixture of Al and Al2O3 using pulsed Nd:YAG laser irradiation at four different scan speeds in order to improve the corrosion and wear resistance. The microstructure, corrosion and wear behavior of the laser surface alloyed material is reported in this manuscript. The coating comprised of a featureless microstructure with cellular-dendritic microstructure near the interface and exhibited good interfacial bonding. A few solidification cracks reaching down to substrate were also observed. The two step coating with Al followed by a mixture of Al and Al2O3 exhibited a slightly better corrosion resistance than the single step coating with Al. In the long run, however, corrosion resistance of both the coatings became comparable to the as-cast alloy. The corroded surface of the laser surface alloyed specimens revealed a highly localized corrosion. The laser surface alloyed specimens exhibited an improvement in wear resistance. The laser scan speed did not exhibit a monotonic trend either in corrosion or wear resistance.

Functional Surfaces for Microfluidics in Proteomic Analysis

Microchips for use in biomolecular analysis show a lot of promise for medical diagnostics and biomedical basic research. Among the potential advantages are more sensitive and faster analyses as well as reduced cost and sample consumption. Due to scaling laws, the surface are to volume ratios of microfluidic chips is very high. Because of this, tailoring the surface properties and surface functionalization are very important technical issues for microchip development. This thesis studies two different types of functional surfaces, surfaces for open surface capillary microfluidics and surfaces for surface assisted laser desorption ionization mass spectrometry, and combinations thereof. Open surface capillary microfluidics can be used to transport and control liquid samples on easily accessible open surfaces simply based on surface forces, without any connections to pumps or electrical power sources. Capillary filling of open partially wetting grooves is shown to be possible with certain geometries, aspect ratios and contact angles, and a theoretical model is developed to identify complete channel filling domains, as well as partial filling domains. On the other hand, partially wetting surfaces with triangular microstructures can be used for achieving directional wetting, where the water droplets do not spread isotropically, but instead only spread to a predetermined sector. Furthermore, by patterning completely wetting and superhydrophobic areas on the same surface, complex droplet shapes are achieved, as the water stretches to make contact with the wetting surface, but does not enter into the superhydrophobic domains. Surfaces for surface assisted laser desorption ionization mass spectrometry are developed by applying various active thin film coatings on multiple substrates, in order to separate surface and bulk effects. Clear differences are observed between both surface and substrate layers. The best performance surfaces consisted of amorphous silicon coating and an inorganic-organic hybrid substrate, with nanopillars and nanopores. These surfaces are used for matrix-free ionization of drugs, peptides and proteins, and for some analytes, the detection limits were in the high attomoles. Microfluidics and laser desorption ionization surfaces are combined on a functionalized drying platforms, where the surface is used to control the shape of the deposited analyte droplet, and the shape of the initial analyte droplet affects the dried droplet solute deposition pattern. The deposited droplets can then directly detected by mass spectrometry. Utilizing this approach, results of analyte concentration, splitting and separation are demonstrated.

Plasmid DNA mediated transfer of the herpes simplex virus thymidine kinase gene to a new bromodeoxyuridine resistant variant of human primary lung carcinoma cells

A human primary lung carcinoma cell line (HPL-R1) established from the tumor biopsy of a lung cancer patient, lacking in cytochrome P1-450 [aryl hydrocarbon (benzo[a]pyrene) hydroxylase (AHH)], was cloned and used to obtain variants deficient in the expression of thymidine-kinase via treatment with 5-bromo-2'-deoxyuridine, and selection for drug resistance phenotype. The variant cell line, precharacterized for thymidine kinase negative phenotype, was transfected with the thymidine kinase gene bearing p R-tk and px1-tk plasmids. Transfections from both the plasmids, demonstrated a frequency of 5.5 X 10(-5). The transfectants showed a 76-100% retention of the transferred phenotype. These data suggest that transfection in variant human cells can approach significant levels of stability observed with rodent cell recipients.

Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model

Nevirapine forms the mainstay of our efforts to curtail the pediatric AIDS epidemic through prevention of mother-to-child transmission of HIV-1. A key limitation, however, is the rapid selection of HIV-1 strains resistant to nevirapine following the administration of a single dose. This rapid selection of resistance suggests that nevirapine-resistant strains preexist in HIV-1 patients and may adversely affect outcomes of treatment. The frequencies of nevirapine-resistant strains in vivo, however, remain poorly estimated, possibly because they exist as a minority below current assay detection limits. Here, we employ stochastic simulations and a mathematical model to estimate the frequencies of strains carrying different combinations of the common nevirapine resistance mutations K103N, V106A, Y181C, Y188C, and G190A in chronically infected HIV-1 patients naive to nevirapine. We estimate the relative fitness of mutant strains from an independent analysis of previous competitive growth assays. We predict that single mutants are likely to preexist in patients at frequencies (similar to 0.01% to 0.001%) near or below current assay detection limits (>0.01%), emphasizing the need for more-sensitive assays. The existence of double mutants is subject to large stochastic variations. Triple and higher mutants are predicted not to exist. Our estimates are robust to variations in the recombination rate, cellular superinfection frequency, and the effective population size. Thus, with 10(7) to 10(8) infected cells in HIV-1 patients, even when undetected, nevirapine-resistant genomes may exist in substantial numbers and compromise efforts to prevent mother-to-child transmission of HIV-1, accelerate the failure of subsequent antiretroviral treatments, and facilitate the transmission of drug resistance.

Nanomechanical properties of silicon surfaces nanostructured by excimer laser

Excimer laser irradiation at ambient temperature has been employed to produce nanostructured silicon surfaces. Nanoindentation was used to investigate the nanomechanical properties of the deformed surfaces as a function of laser parameters, such as the angle of incidence and number of laser pulses at a fixed laser fluence of 5 J cm(-2). A single-crystal silicon 311] surface was severely damaged by laser irradiation and became nanocrystalline with an enhanced porosity. The resulting laser-treated surface consisted of nanometer-sized particles. The pore size was controlled by adjusting the angle of incidence and the number of laser pulses, and varied from nanometers to microns. The extent of nanocrystallinity was large for the surfaces irradiated at a small angle of incidence and by a high number of pulses, as confirmed by x-ray diffraction and Raman spectroscopy. The angle of incidence had a stronger effect on the structure and nanomechanical properties than the number of laser pulses.

Nature of nitrogen adsorbed on transition metal surfaces as revealed by electron spectroscopy and cognate techniques

The nature of the chemisorbed states of nitrogen on various transition metal surfaces is discussed comprehensively on the basis of the results of electron spectroscopic investigations augmented by those from other techniques such as LEED and thermal desorption. A brief discussion of the photoemission spectra of free N2, a comparison of adsorbed N2 and CO as well as of physisorption of N2 on metal surfaces is also presented. We discuss the chemisorption of N2 on the surfaces of certain metals (e.g. Ni, Fe, Ru and W) in some detail, paying considerable attention to the effect of electropositive and electronegative surface modifiers. Features of the various chemisorbed states (one or more weakly chemisorbed gamma-states, strongly chemisorbed alpha-states with bond orders between 1 and 2. and dissociative chemisorbed beta-states) on different surfaces are described and relations between them indicated. While the gamma-state could be a precursor of the alpha-state, the alpha-state could be the precursor of the beta-state and this kind of information is of direct relevance to ammonia synthesis. The nature of adsorption of N2 on the surfaces of some metals (e.g. Cr, Co) deserves further study and such investigations might as well suggest alternative catalysts for ammonia synthesis.

Interior Medial Axis Transform computation of 3D objects bound by free-form surfaces

This paper presents an algorithm for generating the Interior Medial Axis Transform (iMAT) of 3D objects with free-form boundaries. The algorithm proposed uses the exact representation of the part and generates an approximate rational spline description of the iMAT. The algorithm generates the iMAT by a tracing technique that marches along the object's boundary. The level of approximation is controlled by the choice of the step size in the tracing procedure. Criteria based on distance and local curvature of boundary entities are used to identify the junction points and the search for these junction points is done in an efficient way. The algorithm works for multiply-connected objects as well. Results of the implementation are provided. (C) 2010 Elsevier Ltd. All rights reserved.

Segmenting point-sampled surfaces

Extracting features from point-based representations of geometric surface models is becoming increasingly important for purposes such as model classification, matching, and exploration. In an earlier paper, we proposed a multiphase segmentation process to identify elongated features in point-sampled surface models without the explicit construction of a mesh or other surface representation. The preliminary results demonstrated the strength and potential of the segmentation process, but the resulting segmentations were still of low quality, and the segmentation process could be slow. In this paper, we describe several algorithmic improvements to overcome the shortcomings of the segmentation process. To demonstrate the improved quality of the segmentation and the superior time efficiency of the new segmentation process, we present segmentation results obtained for various point-sampled surface models. We also discuss an application of our segmentation process to extract ridge-separated features in point-sampled surfaces of CAD models.

Direct Growth of Gold Nanorods on Gold and Indium Tin Oxide Surfaces: Spectral, Electrochemical, and Electrocatalytic Studies

The surfactant-assisted seed-mediated growth method was used for the formation of gold nanorods (GNRs) directly on gold (Au) and indium tin oxide (ITO) surfaces. Citrate-stabilized similar to 2.6 nm spherical gold nanoparticles (AuNPs) were first self-assembled on ITO or Au surfaces modified with (3-mercaptopropyl)-trimethoxysilane (MPTS) sol-gel film and then immersed in a cationic surfactant growth solution to form GNRs. The growth of GNRs on the MPTS sol gel film modified ITO surface was monitored by UV-visible spectroscopy. The ITO surface with the attached spherical AuNPs shows a surface plasmon resonance band at 550 nm. The intensity of this absorption band increases while increasing the immersion time of the AuNP-modified ITO surface into the growth solution, and after 5 h, an additional shoulder band around 680 nm was observed. The intensity of this shoulder band increases, and it was shifted to longer wavelength as the immersion time of the AuNP-modified ITO surface into the growth solution increases. After 20 h, a predominant wave at 720 nm was observed along with a band at 550 nm. Further immersion of the modified ITO surface into the growth solution did not change the absorption characteristics. The bands observed at 550 and 720 nm were characteristics of GNRs, corresponding to transverse and longitudinal waves, respectively. The AFM images showed the presence of GNRs on the surface of the MPTS sol gel modified ITO surface with a typical length of similar to 100-120 nm and a width of similar to 20-22 nm in addition to a few spherical AuNPs, indicating that seeded spherical AuNPs were not completely involved in the GNRs' formation. Finally, the electrocatalytic activity of the surface-grown GNRs on the MPTS sol gel film modified Au electrode toward the oxidation of ascorbic acid (AA) was studied. Unlike a polycrystalline Au electrode, the surface-grown GNR-modified electrode shows two well-defined voltammetric peaks for AA at 0.01 and 0.35 V in alkaline, neutral, and acidic pHs. The cause for the observed two oxidation peaks for AA was due to the presence of both nanorods and spherical nanoparticles on the electrode surface. The presence of spherical AuNPs on the MPTS sol gel film oxidized AA at more positive potential, whereas the GNRs oxidized AA at less positive potential. The observed 340 mV less positive potential shift in the oxidation of AA suggested that GNRs are better electrocatalysts for the oxidation of AA than the spherical AuNPs.

Molecular methods for the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae

Methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae are major health problems worldwide, both found in symptomless carriage but also causing even life-threatening infections. The aim of this thesis was to characterise MRSA and S. pneumoniae in detail by using several molecular typing methods for various epidemiological purposes: clonality analysis, epidemiological surveillance, outbreak investigation, and virulence factor analysis. The characteristics of MRSA isolates from the strain collection of the Finnish National Infectious Disease Register (NIDR) and pneumococcal isolates collected from military recruits and children with acute otitis media (AOM) were analysed using various typing techniques. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), spa typing, staphylococcal cassette chromosome mec (SCCmec) typing, and the detection of Panton-Valentine leukocidin (PVL) genes were performed for MRSA isolates. Pneumococcal isolates were analysed using antimicrobial susceptibility testing, serotyping, MLST, and by detecting pilus islet 1 (PI-1) and 2 (PI-2) genes. Several international community- and hospital-associated MRSA clones were recognised in Finland. The genetic diversity among MRSA FIN-4 isolates and among FIN-16 isolates was low. Overall, MRSA blood isolates from 1997 to 2006 were genetically diverse. spa typing was found to be a highly discriminatory, rapid and accurate typing method and it also qualifies as the primary typing method in countries with a long history of PFGE-based MRSA strain nomenclature. However, additional typing by another method, e.g. PFGE, is needed in certain situations to be able to provide adequate discrimination for epidemiological surveillance and outbreak investigation. An outbreak of pneumonia was associated with one pneumococcal strain among military recruits, previously healthy young men living in a crowded setting. The pneumococcal carriage rate after the outbreak was found to be exceptionally high. PI-1 genes were detected at a rather low prevalence among pneumococcal isolates from children with AOM. However, the study demonstrated that PI-1 has existed among pneumococcal isolates prior to pneumococcal conjugate vaccine and the increased antimicrobial resistance era. Moreover, PI-1 was found to associate with the serotype rather than the genotype. This study adds to our understanding of the molecular epidemiology of MRSA strains in Finland and the importance of an appropriate genotyping method to be able to perform high-level laboratory-based surveillance of MRSA. Epidemiological and molecular analyses of S. pneumoniae add to our knowledge of the characteristics of pneumococcal strains in Finland.

Surface Chemistry of Thiobacillus ferrooxidans Relevant to Adhesion on Mineral Surfaces

Thiobacillus ferrooxidans cells grown on sulfur, pyrite, and chalcopyrite exhibit greater hydrophobicity than ferrous ion-grown cells. The isoelectric points of sulfur-, pyrite-, and chalcopyrite-grown cells were observed to be at a pH higher than that for ferrous ion-grown cells. Microbe-mineral interactions result in change in the surface chemistry of the organism as well as that of the minerals with which it has interacted. Sulfur, pyrite, and chalcopyrite after interaction with T. ferrooxidans exhibited a significant shift in their isoelectric points from the initial values exhibited by uninteracted minerals. With antibodies raised against sulfur-grown T. ferrooxidans, pyrite- and chalcopyrite-grown cells showed immunoreactivity, whereas ferrous ion-grown cells failed to do so. Fourier transform infrared spectroscopy of sulfur-grown cells suggested that a proteinaceous new cell surface appendage synthesized in mineral-grown cells brings about adhesion to the solid mineral substrates. Such an appendage was found to be absent in ferrous ion-grown cells as it is not required during growth in liquid substrates.