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Sample records for afm analysis showed

  1. Vibration signature analysis of AFM images

    SciTech Connect

    Joshi, G.A.; Fu, J.; Pandit, S.M.

    1995-12-31

    Vibration signature analysis has been commonly used for the machine condition monitoring and the control of errors. However, it has been rarely employed for the analysis of the precision instruments such as an atomic force microscope (AFM). In this work, an AFM was used to collect vibration data from a sample positioning stage under different suspension and support conditions. Certain structural characteristics of the sample positioning stage show up as a result of the vibration signature analysis of the surface height images measured using an AFM. It is important to understand these vibration characteristics in order to reduce vibrational uncertainty, improve the damping and structural design, and to eliminate the imaging imperfections. The choice of method applied for vibration analysis may affect the results. Two methods, the data dependent systems (DDS) analysis and the Welch`s periodogram averaging method were investigated for application to this problem. Both techniques provide smooth spectrum plots from the data. Welch`s periodogram provides a coarse resolution as limited by the number of samples and requires a choice of window to be decided subjectively by the user. The DDS analysis provides sharper spectral peaks at a much higher resolution and a much lower noise floor. A decomposition of the signal variance in terms of the frequencies is provided as well. The technique is based on an objective model adequacy criterion.

  2. Image Analysis and Length Estimation of Biomolecules Using AFM

    PubMed Central

    Sundstrom, Andrew; Cirrone, Silvio; Paxia, Salvatore; Hsueh, Carlin; Kjolby, Rachel; Gimzewski, James K.; Reed, Jason; Mishra, Bud

    2014-01-01

    There are many examples of problems in pattern analysis for which it is often possible to obtain systematic characterizations, if in addition a small number of useful features or parameters of the image are known a priori or can be estimated reasonably well. Often, the relevant features of a particular pattern analysis problem are easy to enumerate, as when statistical structures of the patterns are well understood from the knowledge of the domain. We study a problem from molecular image analysis, where such a domain-dependent understanding may be lacking to some degree and the features must be inferred via machine-learning techniques. In this paper, we propose a rigorous, fully automated technique for this problem. We are motivated by an application of atomic force microscopy (AFM) image processing needed to solve a central problem in molecular biology, aimed at obtaining the complete transcription profile of a single cell, a snapshot that shows which genes are being expressed and to what degree. Reed et al. (“Single molecule transcription profiling with AFM,” Nanotechnology, vol. 18, no. 4, 2007) showed that the transcription profiling problem reduces to making high-precision measurements of biomolecule backbone lengths, correct to within 20–25 bp (6–7.5 nm). Here, we present an image processing and length estimation pipeline using AFM that comes close to achieving these measurement tolerances. In particular, we develop a biased length estimator on trained coefficients of a simple linear regression model, biweighted by a Beaton–Tukey function, whose feature universe is constrained by James–Stein shrinkage to avoid overfitting. In terms of extensibility and addressing the model selection problem, this formulation subsumes the models we studied. PMID:22759526

  3. AFM as an analysis tool for high-capacity sulfur cathodes for Li–S batteries

    PubMed Central

    Sörgel, Seniz; Costa, Rémi; Carlé, Linus; Galm, Ines; Cañas, Natalia; Pascucci, Brigitta; Friedrich, K Andreas

    2013-01-01

    Summary In this work, material-sensitive atomic force microscopy (AFM) techniques were used to analyse the cathodes of lithium–sulfur batteries. A comparison of their nanoscale electrical, electrochemical, and morphological properties was performed with samples prepared by either suspension-spraying or doctor-blade coating with different binders. Morphological studies of the cathodes before and after the electrochemical tests were performed by using AFM and scanning electron microscopy (SEM). The cathodes that contained polyvinylidene fluoride (PVDF) and were prepared by spray-coating exhibited a superior stability of the morphology and the electric network associated with the capacity and cycling stability of these batteries. A reduction of the conductive area determined by conductive AFM was found to correlate to the battery capacity loss for all cathodes. X-ray diffraction (XRD) measurements of Li2S exposed to ambient air showed that insulating Li2S hydrolyses to insulating LiOH. This validates the significance of electrical ex-situ AFM analysis after cycling. Conductive tapping mode AFM indicated the existence of large carbon-coated sulfur particles. Based on the analytical findings, the first results of an optimized cathode showed a much improved discharge capacity of 800 mA·g(sulfur)−1 after 43 cycles. PMID:24205455

  4. AFM analysis of bleaching effects on dental enamel microtopography

    NASA Astrophysics Data System (ADS)

    Pedreira de Freitas, Ana Carolina; Espejo, Luciana Cardoso; Botta, Sergio Brossi; Teixeira, Fernanda de Sa; Luz, Maria Aparecida A. Cerqueira; Garone-Netto, Narciso; Matos, Adriana Bona; Salvadori, Maria Cecilia Barbosa da Silveira

    2010-02-01

    The purpose of this in vitro study was to test a new methodology to evaluate the effects of 35% hydrogen peroxide agent on the microtopography of sound enamel using an atomic force microscope (AFM). The buccal sound surfaces of three extracted human lower incisors were used, without polishing the surfaces to maintain them with natural morphology. These unpolished surfaces were subjected to bleaching procedure with 35% hydrogen peroxide that consisted of 4 applications of the bleaching agent on enamel surfaces for 10 min each application. Surface images were obtained in a 15 μm × 15 μm area using an AFM. The roughness (Ra and RMS) and the power spectral density (PSD) were obtained before and after the bleaching treatment. As results we could inquire that the PSD analyses were very suitable to identifying the morphological changes on the surfaces, while the Ra and RMS parameters were insufficient to represent the morphological alterations promoted by bleaching procedure on enamel. The morphological wavelength in the range of visible light spectrum (380-750 nm) was analyzed, showing a considerable increase of the PSD with the bleaching treatment.

  5. Structural changes of polysulfone membrane use for hemodialysis in the consecutive regime: nanometric analysis by AFM

    NASA Astrophysics Data System (ADS)

    Batina, Nikola; Acosta García, Ma. Cristina; Avalos Pérez, Angélica; Alberto Ramírez, Mario; Franco, Martha; Pérez Gravas, Héctor; Cadena Méndez, Miguel

    2013-08-01

    Nowadays, the hemodialytic treatment of patients with either acute or chronic renal failure has been improved by promoting biocompatibility in the use of new materials and improve membrane surface characteristics. Low and high flux polysulfone membranes (PM) used in dialysis and ultra filtration have been studied in order to understand the geometry and surface chemistry of the pores at inner (nanometric) and outer (micrometric) membrane parts. The surface changes of polysulfone cartridge membrane (PM) during different number of consecutive reuse trials: after 1st, 10th and 23th times of use. The morphology of the hollow fibers surfaces was studied by means of the atomic force microscopy (AFM) imaging and the surface roughness analysis. The roughness of both inner and outer part of PM surface increases with numbers of reuse trails. Thus, small and medium size pores were wiped out when the number of uses changed from zero to 23 on the outer surface. The pore density decreases. The inner part of membrane shows some nanometric size deformation in forms of new openings and raptures. The AFM analysis show differences in the PM morphology at the nanometric level, not previously revealed, which could be important in the evaluation of the PM.

  6. Accelerated design and quality control of impact modifiers for plastics through atomic force microscopy (AFM) analysis

    NASA Astrophysics Data System (ADS)

    Moeller, Gunter

    2011-03-01

    Standard polymer resins are often too brittle or do not meet other mechanical property requirements for typical polymer applications. To achieve desired properties it is common to disperse so called ``impact modifiers'', which are spherical latex particles with diameters of much less than one micrometer, into the pure resin. Understanding and control of the entire process from latex particle formation to subsequent dispersion into polymer resins are necessary to accelerate the development of new materials that meet specific application requirements. In this work AFM imaging and nanoindentation techniques in combination with AFM-based spectroscopic techniques were applied to assess latex formation and dispersion. The size and size distribution of the latex particles can be measured based on AFM amplitude modulation images. AFM phase images provide information about the chemical homogeneity of individual particles. Nanoindentation may be used to estimate their elastic and viscoelastic properties. Proprietary creep and nanoscale Dynamic Mechanical Analysis (DMA) tests that we have developed were used to measure these mechanical properties. The small size of dispersed latex inclusions requires local mechanical and spectroscopic analysis techniques with high lateral and spatial resolution. We applied the CRAVE AFM method, developed at NIST, to perform mechanical analysis of individual latex inclusions and compared results with those obtained using nanoscale DMA. NanoIR, developed by Anasys Inc., and principal component confocal Raman were used for spectroscopic analysis and results from both techniques compared.

  7. Fractal analysis of AFM images of the surface of Bowman's membrane of the human cornea.

    PubMed

    Ţălu, Ştefan; Stach, Sebastian; Sueiras, Vivian; Ziebarth, Noël Marysa

    2015-04-01

    The objective of this study is to further investigate the ultrastructural details of the surface of Bowman's membrane of the human cornea, using atomic force microscopy (AFM) images. One representative image acquired of Bowman's membrane of a human cornea was investigated. The three-dimensional (3-D) surface of the sample was imaged using AFM in contact mode, while the sample was completely submerged in optisol solution. Height and deflection images were acquired at multiple scan lengths using the MFP-3D AFM system software (Asylum Research, Santa Barbara, CA), based in IGOR Pro (WaveMetrics, Lake Oswego, OR). A novel approach, based on computational algorithms for fractal analysis of surfaces applied for AFM data, was utilized to analyze the surface structure. The surfaces revealed a fractal structure at the nanometer scale. The fractal dimension, D, provided quantitative values that characterize the scale properties of surface geometry. Detailed characterization of the surface topography was obtained using statistical parameters, in accordance with ISO 25178-2: 2012. Results obtained by fractal analysis confirm the relationship between the value of the fractal dimension and the statistical surface roughness parameters. The surface structure of Bowman's membrane of the human cornea is complex. The analyzed AFM images confirm a fractal nature of the surface, which is not taken into account by classical surface statistical parameters. Surface fractal dimension could be useful in ophthalmology to quantify corneal architectural changes associated with different disease states to further our understanding of disease evolution.

  8. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.

    PubMed

    Petkovic, Sonja; Badelt, Stefan; Block, Stephan; Flamm, Christoph; Delcea, Mihaela; Hofacker, Ivo; Müller, Sabine

    2015-07-01

    Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions.

  9. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM

    PubMed Central

    Petkovic, Sonja; Badelt, Stefan; Flamm, Christoph; Delcea, Mihaela

    2015-01-01

    Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions. PMID:25999318

  10. AFM and pulsed laser ablation methods for Cultural Heritage: application to archeometric analysis of stone artifacts

    NASA Astrophysics Data System (ADS)

    Barberio, M.; Veltri, S.; Stranges, F.; Bonanno, A.; Xu, F.; Antici, P.

    2015-09-01

    In this paper, we introduce the use of the atomic force microscope (AFM) and of the pulsed laser ablation as methods for morphological diagnostic with nanoscale precision of archeological artifacts and corrosive patina removal from stone artifacts. We test our methodology on stone artifacts extracted from the Church of Sotterra (located in Calabria, South Italy). The AFM microscopy was compared with different petrographic, chemical, optical and morphological analysis methods for identifying the textural characteristics, evaluating the state of preservation and formulating some hypotheses about the provenance and composition of the impurity patina located on the artifact surfaces. We demonstrate that with the nanometric precision obtained with AFM microscopy, it is possible to distinguish the different states of preservation, much better than using conventional petrographic methods. The surface's roughness is evaluated from very small artifact's fragments, reducing the coring at micrometric scale with a minimal damage to the artworks. After the diagnosis, we performed restoration tests using the pulsed laser ablation (PLA) method and compared it with the more common micro-sandblasting under dry conditions. We find that the PLA is highly effective for the removal of the surficial patina, with a control of a few hundreds of nanometers in the cleaning of surface, without introducing chemical or morphological damages to the artifacts. Moreover, PLA can be easily implemented in underwater conditions; this has the great advantage that stone and pottery artifacts for marine archeological sites do not need to be removed from the site.

  11. Crystallinity and compositional changes in carbonated apatites: Evidence from {sup 31}P solid-state NMR, Raman, and AFM analysis

    SciTech Connect

    McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M.Banaszak; Tecklenburg, Mary M.J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

    2013-10-15

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and {sup 31}P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse {sup 31}P NMR linewidth and inverse Raman PO{sub 4}{sup 3−}ν{sub 1} bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3–10.3 wt% CO{sub 3}{sup 2−} range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the {sup 31}P NMR chemical shift frequency and the Raman phosphate ν{sub 1} band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals. - Graphical abstract: Carbonated apatite shows an abrupt change in spectral (NMR, Raman) and morphological (AFM) properties at a composition of about one carbonate substitution per unit cell. Display Omitted - Highlights: • Crystallinity (XRD), particle size (AFM) of carbonated apatites and bone mineral. • Linear relationships among crystallinity, {sup 31}P NMR and Raman inverse bandwidths. • Low and high carbonated apatites use different charge-balancing ion-loss mechanism.

  12. Robust strategies for automated AFM force curve analysis--I. Non-adhesive indentation of soft, inhomogeneous materials.

    PubMed

    Lin, David C; Dimitriadis, Emilios K; Horkay, Ferenc

    2007-06-01

    The atomic force microscope (AFM) has found wide applicability as a nanoindentation tool to measure local elastic properties of soft materials. An automated approach to the processing of AFM indentation data, namely, the extraction of Young's modulus, is essential to realizing the high-throughput potential of the instrument as an elasticity probe for typical soft materials that exhibit inhomogeneity at microscopic scales. This paper focuses on Hertzian analysis techniques, which are applicable to linear elastic indentation. We compiled a series of synergistic strategies into an algorithm that overcomes many of the complications that have previously impeded efforts to automate the fitting of contact mechanics models to indentation data. AFM raster data sets containing up to 1024 individual force-displacement curves and macroscopic compression data were obtained from testing polyvinyl alcohol gels of known composition. Local elastic properties of tissue-engineered cartilage were also measured by the AFM. All AFM data sets were processed using customized software based on the algorithm, and the extracted values of Young's modulus were compared to those obtained by macroscopic testing. Accuracy of the technique was verified by the good agreement between values of Young's modulus obtained by AFM and by direct compression of the synthetic gels. Validation of robustness was achieved by successfully fitting the vastly different types of force curves generated from the indentation of tissue-engineered cartilage. For AFM indentation data that are amenable to Hertzian analysis, the method presented here minimizes subjectivity in preprocessing and allows for improved consistency and minimized user intervention. Automated, large-scale analysis of indentation data holds tremendous potential in bioengineering applications, such as high-resolution elasticity mapping of natural and artificial tissues.

  13. Quantitative multichannel NC-AFM data analysis of graphene growth on SiC(0001)

    PubMed Central

    Held, Christian; Seyller, Thomas

    2012-01-01

    Summary Noncontact atomic force microscopy provides access to several complementary signals, such as topography, damping, and contact potential. The traditional presentation of such data sets in adjacent figures or in colour-coded pseudo-three-dimensional plots gives only a qualitative impression. We introduce two-dimensional histograms for the representation of multichannel NC-AFM data sets in a quantitative fashion. Presentation and analysis are exemplified for topography and contact-potential data for graphene grown epitaxially on 6H-SiC(0001), as recorded by Kelvin probe force microscopy in ultrahigh vacuum. Sample preparations by thermal decomposition in ultrahigh vacuum and in an argon atmosphere are compared and the respective growth mechanisms discussed. PMID:22428109

  14. Comparative quantification and statistical analysis of η′ and η precipitates in aluminum alloy AA7075-T651 by TEM and AFM

    SciTech Connect

    Garcia-Garcia, Adrian Luis Dominguez-Lopez, Ivan Lopez-Jimenez, Luis Barceinas-Sanchez, J.D. Oscar

    2014-01-15

    Quantification of nanometric precipitates in metallic alloys has been traditionally performed using transmission electron microscopy, which is nominally a low throughput technique. This work presents a comparative study of quantification of η′ and η precipitates in aluminum alloy AA7075-T651 using transmission electron microscopy (TEM) and non-contact atomic force microscopy (AFM). AFM quantification was compared with 2-D stereological results reported elsewhere. Also, a method was developed, using specialized software, to characterize nanometric size precipitates observed in dark-field TEM micrographs. Statistical analysis of the quantification results from both measurement techniques supports the use of AFM for precipitate characterization. Once the precipitate stoichiometry has been determined by appropriate analytical techniques like TEM, as it is the case for η′ and η in AA7075-T651, the relative ease with which specimens are prepared for AFM analysis could be advantageous in product and process development, and quality control, where a large number of samples are expected for analysis on a regular basis. - Highlights: • Nanometric MgZn{sub 2} precipitates in AA7075-T651 were characterized using AFM and TEM. • Phase-contrast AFM was used to differentiate metal matrix from MgZn{sub 2} precipitates. • TEM and AFM micrographs were analyzed using commercially available software. • AFM image analysis and TEM 2-D stereology render statistically equivalent results.

  15. Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

    PubMed Central

    McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M.J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

    2013-01-01

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43− ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3–10.3 wt% CO32− range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals. PMID:24273344

  16. Crystallinity and compositional changes in carbonated apatites: Evidence from (31)P solid-state NMR, Raman, and AFM analysis.

    PubMed

    McElderry, John-David P; Zhu, Peizhi; Mroue, Kamal H; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H; Franceschi, Renny T; Holl, Mark M Banaszak; Tecklenburg, Mary M J; Ramamoorthy, Ayyalusamy; Morris, Michael D

    2013-10-01

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and (31)P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse (31)P NMR linewidth and inverse Raman PO4(3-) ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO3(2-) range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the (31)P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

  17. Anomalies in nanostructure size measurements by AFM

    NASA Astrophysics Data System (ADS)

    Mechler, Ádám; Kopniczky, Judit; Kokavecz, János; Hoel, Anders; Granqvist, Claes-Göran; Heszler, Peter

    2005-09-01

    Anomalies in atomic force microscopy (AFM) based size determination of nanoparticles were studied via comparative analysis of experiments and numerical calculations. Single tungsten oxide nanoparticles with a mean diameter of 3nm were deposited on mica and graphite substrates and were characterised by AFM. The size (height) of the nanoparticles, measured by tapping mode AFM, was found to be sensitive to the free amplitude of the oscillating tip, thus indicating that the images were not purely topographical. By comparing the experimental results to model calculations, we demonstrate that the dependence of the nanoparticle size on the oscillation amplitude of the tip is an inherent characteristic of the tapping mode AFM; it is also a function of physical properties such as elasticity and surface energy of the nanoparticle and the sample surface, and it depends on the radius of curvature of the tip. We show that good approximation of the real size can easily be obtained from plots of particle height vs free amplitude of the oscillating tip, although errors might persist for individual experiments. The results are valid for size (height) determination of any nanometer-sized objects imaged by tapping mode AFM.

  18. Raman and AFM study of gamma irradiated plastic bottle sheets

    NASA Astrophysics Data System (ADS)

    Ali, Yasir; Kumar, Vijay; Sonkawade, R. G.; Dhaliwal, A. S.

    2013-02-01

    In this investigation, the effects of gamma irradiation on the structural properties of plastic bottle sheet are studied. The Plastic sheets were exposed with 1.25MeV 60Co gamma rays source at various dose levels within the range from 0-670 kGy. The induced modifications were followed by micro-Raman and atomic force microscopy (AFM). The Raman spectrum shows the decrease in Raman intensity and formation of unsaturated bonds with an increase in the gamma dose. AFM image displays rough surface morphology after irradiation. The detailed Raman analysis of plastic bottle sheets is presented here, and the results are correlated with the AFM observations.

  19. Analysis of Anionic Polymer Dispersant Behavior in Dense Silicon Nitride and Carbide Suspensions Using an AFM

    NASA Astrophysics Data System (ADS)

    Nojiri, M.; Matsui, S.; Hasegawa, H.; Ono, T.; Fukuda, Y.; Tsukada, M.; Kamiya, H.

    2001-06-01

    The paper focuses on the interaction mechanism caused by anionic polymer dispersants in dense silicon nitride and silicon carbide suspensions. An atomic force microscope (AFM) was used to determine the relationship between the macroscopic suspension viscosity and the microscopic structure adsorbing of a polymer dispersant at the solid/liquid interface. The surface interactions within the suspensions were analyzed under various dispersant pH values and additive conditions. The addition of an anionic polymer dispersant decreased the viscosity of silicon nitride and silicon carbide suspension and increased the electrosteric repulsive force on the non-oxide surface in solution at pH > 6, which was the isoelectric point of the materials. Based on the above results, we estimated the adsorption mechanism of anionic polymer dispersants on each solid surface in solution under relatively high pH conditions.

  20. [IR/UV spectroscopic analysis of gangliosides and their microstructures of polymeric aggregates observed by AFM technique].

    PubMed

    Wang, Hai-long; Sun, Run-guang; Zhang, Jing; Hao, Chang-chun

    2009-04-01

    Gangliosides, a kind of acid glycosphingolipid containing sialic acid, plays a very important physiological role in biomembrane as one of the important components of neurocyte membrane. They were extracted from bovine brain by the Folch method and purified by silica gel and DEAE-Sephadex A-25 column chromatograph. Their molecular functional groups and microstructures of polymeric aggregates were studied by infrared spectrum (IR), ultraviolet spectrum (UV) and atomic force microscope (AFM). The experimental results indicate that: 55.2 mg of Gls from 100 g of wet bovine brain had a certain purity, 62.84%. And their UV absorption spectra appeared at 195 nm, near to the results reported by other peoples. Compared with the IR spectra of sialic acid, the experimental results showed that the structures of the products had the units of sialic acid. In order to investigate the aggregate structures of ganglioside. AFM technique was applied in water, and the results showed that gangliosides can form spherical or ellipsoidal structures in water. It was determined that the size of polymeric aggregates of gangliosides varies between 55 and 380 nm, the average size is (148.9+/-66.7) nm; the height is between 1.0 and 5.0 nm, and the average height is (3.25+/-1.01) nm. The experimental results provide a theoretical and experimental basis for investigating biological activity and the exploitation and utilization of neural drugs.

  1. AFM Quantitative Morphological Analysis Of The Step Bunching Instability Formed On GaAs(110) During H-assisted MBE

    NASA Astrophysics Data System (ADS)

    Crespillo, M. L.; Tejedor, P.

    2007-04-01

    Power Spectral Density (PSD) analysis of Atomic Force Microscopy (AFM) images has been applied to study the effect of H-assisted surface oxide cleaning on the step bunching and Bales-Zangwill instabilities that develop during homoepitaxial growth from molecular beams of Ga and As4 on vicinal GaAs(110) substrates at high temperatures and high As:Ga flux ratios, leading to the formation of a characteristic ripple pattern along the [001] tilt direction. As growth proceeds in the presence of chemisorbed H, step bunching gradually vanishes and the ripple pattern breaks up into an array of self-organized nanowires running along the [11¯0] step edge direction.

  2. Nanoscale structural features determined by AFM for single virus particles

    NASA Astrophysics Data System (ADS)

    Chen, Shu-Wen W.; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-10-01

    In this work, we propose ``single-image analysis'', as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  3. Biophysical analysis of bacterial and viral systems. A shock tube study of bio-aerosols and a correlated AFM/nanosims investigation of vaccinia virus

    SciTech Connect

    Gates, Sean Damien

    2013-05-01

    The work presented herein is concerned with the development of biophysical methodology designed to address pertinent questions regarding the behavior and structure of select pathogenic agents. Two distinct studies are documented: a shock tube analysis of endospore-laden bio-aerosols and a correlated AFM/NanoSIMS study of the structure of vaccinia virus.

  4. The importance of correcting for variable probe-sample interactions in AFM-IR spectroscopy: AFM-IR of dried bacteria on a polyurethane film.

    PubMed

    Barlow, Daniel E; Biffinger, Justin C; Cockrell-Zugell, Allison L; Lo, Michael; Kjoller, Kevin; Cook, Debra; Lee, Woo Kyung; Pehrsson, Pehr E; Crookes-Goodson, Wendy J; Hung, Chia-Suei; Nadeau, Lloyd J; Russell, John N

    2016-08-02

    AFM-IR is a combined atomic force microscopy-infrared spectroscopy method that shows promise for nanoscale chemical characterization of biological-materials interactions. In an effort to apply this method to quantitatively probe mechanisms of microbiologically induced polyurethane degradation, we have investigated monolayer clusters of ∼200 nm thick Pseudomonas protegens Pf-5 bacteria (Pf) on a 300 nm thick polyether-polyurethane (PU) film. Here, the impact of the different biological and polymer mechanical properties on the thermomechanical AFM-IR detection mechanism was first assessed without the additional complication of polymer degradation. AFM-IR spectra of Pf and PU were compared with FTIR and showed good agreement. Local AFM-IR spectra of Pf on PU (Pf-PU) exhibited bands from both constituents, showing that AFM-IR is sensitive to chemical composition both at and below the surface. One distinct difference in local AFM-IR spectra on Pf-PU was an anomalous ∼4× increase in IR peak intensities for the probe in contact with Pf versus PU. This was attributed to differences in probe-sample interactions. In particular, significantly higher cantilever damping was observed for probe contact with PU, with a ∼10× smaller Q factor. AFM-IR chemical mapping at single wavelengths was also affected. We demonstrate ratioing of mapping data for chemical analysis as a simple method to cancel the extreme effects of the variable probe-sample interactions.

  5. AFM nanoscale indentation in air of polymeric and hybrid materials with highly different stiffness

    NASA Astrophysics Data System (ADS)

    Suriano, Raffaella; Credi, Caterina; Levi, Marinella; Turri, Stefano

    2014-08-01

    In this study, nanomechanical properties of a variety of polymeric materials was investigated by means of AFM. In particular, selecting different AFM probes, poly(methyl methacrylate) (PMMA), polydimethylsiloxane (PDMS) bulk samples, sol-gel hybrid thin films and hydrated hyaluronic acid hydrogels were indented in air to determine the elastic modulus. The force-distance curves and the indentation data were found to be greatly affected by the cantilever stiffness and by tip geometry. AFM indentation tests show that the choice of the cantilever spring constant and of tip shape is crucially influenced by elastic properties of samples. When adhesion-dominated interactions occur between the tip and the surface of samples, force-displacement curves reveal that a suitable functionalization of AFM probes allows the control of such interactions and the extraction of Young' modulus from AFM curves that would be otherwise unfeasible. By applying different mathematical models depending on AFM probes and materials under investigation, the values of Young's modulus were obtained and compared to those measured by rheological and dynamic mechanical analysis or to literature data. Our results show that a wide range of elastic moduli (10 kPa-10 GPa) can be determined by AFM in good agreement with those measured by conventional macroscopic measurements.

  6. Analysis the effect of different geometries of AFM's cantilever on the dynamic behavior and the critical forces of three-dimensional manipulation.

    PubMed

    Korayem, Moharam Habibnejad; Saraie, Maniya B; Saraee, Mahdieh B

    2017-01-13

    An important challenge when using an atomic force microscope (AFM) is to be able to control the force exerted by the AFM for performing various tasks. Nevertheless, the exerted force is proportional to the deflection of the AFM cantilever, which itself is affected by a cantilever's stiffness coefficient. Many papers have been published so far on the methods of obtaining the stiffness coefficients of AFM cantilevers in 2D; however, a comprehensive model is yet to be presented on 3D cantilever motion. The discrepancies between the equations of the 2D and 3D analysis are due to the number and direction of forces and moments that are applied to a cantilever. Moreover, in the 3D analysis, contrary to the 2D analysis, due to the interaction between the forces and moments applied on a cantilever, its stiffness values cannot be separately expressed for each direction; and instead, a stiffness matrix should be used to correctly derive the relevant equations. In this paper, 3D stiffness coefficient matrices have been obtained for three common cantilever geometries including the rectangular, V-shape and dagger-shape cantilevers. The obtained equations are validated by two methods. In the first approach, the Finite Element Method is combined with the cantilever deflection values computed by using the obtained stiffness matrices. In the second approach, by reducing the problem's parameters, the forces applied on a cantilever along different directions are compared with each other in 2D and 3D cases. Then the 3D manipulation of a stiff nanoparticle is modeled and simulated by using the stiffness matrices obtained for the three cantilever geometries. The obtained results indicate that during the manipulation process, the dagger-shaped and rectangular cantilevers exert the maximum and minimum amounts of forces on the stiff nanoparticle, respectively. Also, by examining the effects of different probe tip geometries, it is realized that a probe tip of cylindrical geometry exerts the

  7. Analysis of local conductance switching by AFM-writing at the LaAlO3/SrTiO3 interface

    NASA Astrophysics Data System (ADS)

    Boselli, Margherita; Li, Danfeng; Liu, Wei; Fête, Alexandre; Gariglio, Stefano; Triscone, Jean-Marc

    2015-03-01

    A two dimensional electron liquid is present at the interface between LaAlO3 and SrTiO3; this system exhibits several interesting physical properties, including tunable superconductivity. In heterostructures with 3 unit cells of LaAlO3, an insulator to metal transition can be induced by the electric field effect. We report here on the use of the atomic force microscopy writing technique developed in the group of J. Levy to locally switch on and off conductivity at the interface. Our results show that a quarz resonator AFM sensor is particularly suitable for this purpose. In this configuration, the measurements can be performed in the dark, strongly reducing photo-doping. Electronic nanostructures are found to be particularly sensitive to the writing procedure and to the ambient humidity. We discuss how these parameters can be optimized to confine electrons in regions down to tens of nanometers. Simulations of the conductance changes upon AFM writing are compared to experiments. The temperature evolution of the conductance shows that nanowires are metallic.

  8. Detail, Face C (rear), showing Interference Analysis System Linear Test ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail, Face C (rear), showing Interference Analysis System Linear Test Array mounted at Level 4A - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  9. Snacking on Television: A Content Analysis of Adolescents’ Favorite Shows

    PubMed Central

    Larson, Nicole I.; Gollust, Sarah E.; Neumark-Sztainer, Dianne

    2016-01-01

    Introduction Snacking is a complex behavior that may be influenced by entertainment media. Research suggests that snacking and unhealthy foods are commonly shown in programming that targets young audiences, but shows selected for study have been limited. We conducted a content analysis on shows that were named as favorites by adolescents to characterize portrayals of snacking on popular television. Methods A diverse sample of 2,130 adolescents (mean age, 14.3 y) listed 3 favorite television shows in a 2010 school-based survey. Three episodes each of the 25 most popular shows were coded for food-related content, including healthfulness, portion size, screen time use, setting, and social context. We also analyzed the characteristics of characters involved in eating incidents, the show type, and the show rating. We used χ2 tests, binomial tests, and multilevel regression models to compare incidence of snacks versus meals, the characteristics of those involved, and snacking across show characteristics. Results Almost half of food incidents on television shows were snacks. Snacks were significantly more likely than meals to be “mostly unhealthy” (69.3% vs 22.6%, P < .001) and were more likely to include screen time use (25.0% of snacking incidents vs 4.0% of meals, P < .001). Young characters and those coded as being of low socioeconomic status or overweight were overrepresented in snacking incidents. Sitcoms and shows rated for a youth audience were significantly more likely to portray snacking than were shows for adult audiences. Conclusion Media awareness and literacy programs should include foods and snacking behaviors among the issues they address. More healthful portrayals of food and dietary intake in entertainment shows’ content would create a healthier media environment for youth. PMID:27197079

  10. AFM-Based Mechanical Nanomanipulation

    NASA Astrophysics Data System (ADS)

    Landolsi, Fakhreddine

    2011-12-01

    Advances in several research areas increase the need for more sophisticated fabrication techniques and better performing materials. Tackling this problem from a bottom-up perspective is currently an active field of research. The bottom-up fabrication procedure offers sub-nanometer accurate manipulation. At this time, candidates to achieve nanomanipulation include chemical (self-assembly), biotechnology methods (DNA-based), or using controllable physical forces (e.g. electrokinetic forces, mechanical forces). In this thesis, new methods and techniques for mechanical nanomanipulation using probe force interaction are developed. The considered probes are commonly used in Atomic Force Microscopes (AFMs) for high resolution imaging. AFM-based mechanical nanomanipulation will enable arranging nanoscale entities such as nanotubes and molecules in a precise and controlled manner to assemble and produce novel devices and systems at the nanoscale. The novelty of this research stems from the development of new modeling of the physics and mechanics of the tip interaction with nanoscale entities, coupled with the development of new smart cantilevers with multiple degrees of freedom. The gained knowledge from the conducted simulations and analysis is expected to enable true precision and repeatability of nanomanipulation tasks which is not feasible with existing methods and technologies.

  11. Characterization of single α-tracks by photoresist detection and AFM analysis-focus on biomedical science and technology.

    PubMed

    Falzone, Nadia; Myhra, Sverre; Chakalova, Radka; Hill, Mark A; Thomson, James; Vallis, Katherine A

    2013-11-07

    The interactions between energetic ions and biological and/or organic target materials have recently attracted theoretical and experimental attention, due to their implications for detector and device technologies, and for therapeutic applications. Most of the attention has focused on detection of the primary ionization tracks, and their effects, while recoil target atom tracks remain largely unexplored. Detection of tracks by a negative tone photoresist (SU-8), followed by standard development, in combination with analysis by atomic force microscopy, shows that both primary and recoil tracks are revealed as conical spikes, and can be characterized at high spatial resolution. The methodology has the potential to provide detailed information about single impact events, which may lead to more effective and informative detector technologies and advanced therapeutic procedures. In comparison with current characterization methods the advantageous features include: greater spatial resolution by an order of magnitude (20 nm); detection of single primary and associated recoil tracks; increased range of fluence (to 2.5 × 10(9) cm(-2)); sensitivity to impacts at grazing angle incidence; and better definition of the lateral interaction volume in target materials.

  12. AFM-IR: Technology and Applications in Nanoscale Infrared Spectroscopy and Chemical Imaging.

    PubMed

    Dazzi, Alexandre; Prater, Craig B

    2016-12-13

    Atomic force microscopy-based infrared spectroscopy (AFM-IR) is a rapidly emerging technique that provides chemical analysis and compositional mapping with spatial resolution far below conventional optical diffraction limits. AFM-IR works by using the tip of an AFM probe to locally detect thermal expansion in a sample resulting from absorption of infrared radiation. AFM-IR thus can provide the spatial resolution of AFM in combination with the chemical analysis and compositional imaging capabilities of infrared spectroscopy. This article briefly reviews the development and underlying technology of AFM-IR, including recent advances, and then surveys a wide range of applications and investigations using AFM-IR. AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage. In the Supporting Information , the authors provide a theoretical section that reviews the physics underlying the AFM-IR measurement and detection mechanisms.

  13. Authenticity and TV Shows: A Multidimensional Analysis Perspective

    ERIC Educational Resources Information Center

    Al-Surmi, Mansoor

    2012-01-01

    Television shows, especially soap operas and sitcoms, are usually considered by English as a second language practitioners as a source of authentic spoken conversational materials presumably because they reflect the linguistic features of natural conversation. However, practitioners are faced with the dilemma of how to assess whether such…

  14. [Application of atomic force microscopy (AFM) in ophthalmology].

    PubMed

    Milka, Michał; Mróz, Iwona; Jastrzebska, Maria; Wrzalik, Roman; Dobrowolski, Dariusz; Roszkowska, Anna M; Moćko, Lucyna; Wylegała, Edward

    2012-01-01

    Atomic force microscopy (AFM) allows to examine surface of different biological objects in the nearly physiological conditions at the nanoscale. The purpose of this work is to present the history of introduction and the potential applications of the AFM in ophthalmology research and clinical practice. In 1986 Binnig built the AFM as a next generation of the scanning tunnelling microscope (STM). The functional principle of AFM is based on the measurement of the forces between atoms on the sample surface and the probe. As a result, the three-dimensional image of the surface with the resolution on the order of nanometres can be obtained. Yamamoto used as the first the AFM on a wide scale in ophthalmology. The first investigations used the AFM method to study structure of collagen fibres of the cornea and of the sclera. Our research involves the analysis of artificial intraocular lenses (IOLs). According to earlier investigations, e.g. Lombardo et al., the AFM was used to study only native IOLs. Contrary to the earlier investigations, we focused our measurements on lenses explanted from human eyes. The surface of such lenses is exposed to the influence of the intraocular aqueous environment, and to the related impacts of biochemical processes. We hereby present the preliminary results of our work in the form of AFM images depicting IOL surface at the nanoscale. The images allowed us to observe early stages of the dye deposit formation as well as local calcinosis. We believe that AFM is a very promising tool for studying the structure of IOL surface and that further observations will make it possible to explain the pathomechanism of artificial intraocular lens opacity formation.

  15. PREFACE: Non-contact AFM Non-contact AFM

    NASA Astrophysics Data System (ADS)

    Giessibl, Franz J.; Morita, Seizo

    2012-02-01

    This special issue is focussed on high resolution non-contact atomic force microscopy (AFM). Non-contact atomic force microscopy was established approximately 15 years ago as a tool to image conducting and insulating surfaces with atomic resolution. Since 1998, an annual international conference has taken place, and although the proceedings of these conferences are a useful source of information, several key developments warrant devoting a special issue to this subject. In the theoretic field, the possibility of supplementing established techniques such as scanning tunneling microscopy (STM) and Kelvin probe microscopy with atomically resolved force micrsoscopy poses many challenges in the calculation of contrast and contrast reversal. The surface science of insulators, self-assembled monolayers and adsorbates on insulators is a fruitful field for the application of non-contact AFM: several articles in this issue are devoted to these subjects. Atomic imaging and manipulation have been pioneered using STM, but because AFM allows the measurement of forces, AFM has had a profound impact in this field as well. Three-dimensional force spectroscopy has allowed many important insights into surface science. In this issue a combined 3D tunneling and force microscopy is introduced. Non-contact AFM typically uses frequency modulation to measure force gradients and was initially used mainly in a vacuum. As can be seen in this issue, frequency modulation is now also used in ambient conditions, allowing better spatial and force resolution. We thank all of the contributors for their time and efforts in making this special issue possible. We are also very grateful to the staff of IOP Publishing for handling the administrative aspects and for steering the refereeing process. Non-contact AFM contents Relation between the chemical force and the tunnelling current in atomic point contacts: a simple model Pavel Jelínek, Martin Ondrácek and Fernando Flores Theoretical simulation of

  16. Characterizing Cell Mechanics with AFM and Microfluidics

    NASA Astrophysics Data System (ADS)

    Walter, N.; Micoulet, A.; Suresh, S.; Spatz, J. P.

    2007-03-01

    Cell mechanical properties and functionality are mainly determined by the cytoskeleton, besides the cell membrane, the nucleus and the cytosol, and depend on various parameters e.g. surface chemistry and rigidity, surface area and time available for cell spreading, nutrients and drugs provided in the culture medium. Human epithelial pancreatic and mammary cancer cells and their keratin intermediate filaments are the main focus of our work. We use Atomic Force Microscopy (AFM) to study cells adhering to substrates and Microfluidic Channels to probe cells in suspension, respectively. Local and global properties are extracted by varying AFM probe tip size and the available adhesion area for cells. Depth-sensing, instrumented indentation tests with AFM show a clear difference in contact stiffness for cells that are spread of controlled substrates and those that are loosely attached. Microfluidic Channels are utilized in parallel to evaluate cell deformation and ``flow resistance'', which are dependent on channel cross section, flow rate, cell nucleus size and the mechanical properties of cytoskeleton and membrane. The results from the study are used to provide some broad and quantitative assessments of the connections between cellular/subcellular mechanics and biochemical origins of disease states.

  17. A review of the application of atomic force microscopy (AFM) in food science and technology.

    PubMed

    Liu, Shaoyang; Wang, Yifen

    2011-01-01

    Atomic force microscopy (AFM) is a powerful nanoscale analysis technique used in food area. This versatile technique can be used to acquire high-resolution sample images and investigate local interactions in air or liquid surroundings. In this chapter, we explain the principles of AFM and review representative applications of AFM in gelatin, casein micelle, carrageenan, gellan gum, starch, and interface. We elucidate new knowledge revealed with AFM as well as ways to use AFM to obtain morphology and rheology information in different food fields.

  18. Fracture Mechanics Testing of Titanium 6AL-4V in AF-M315E

    NASA Technical Reports Server (NTRS)

    Sampson, J. W.; Martinez, J.; McLean, C.

    2016-01-01

    The Green Propellant Infusion Mission (GPIM) will demonstrate the performance of AF-M315E monopropellant on orbit. Flight certification requires a safe-life analysis of the titanium alloy fuel tank to ensure inherent processing flaws will not cause failure during the design life of the tank. Material property inputs for this analysis require testing to determine the stress intensity factor for environment-assisted cracking (KEAC) of Ti 6Al-4V in combination with the AF-M315E monopropellant. Testing of single-edge notched, or SE(B), specimens representing the bulk tank membrane and weld material were performed in accordance with ASTM E1681. Specimens with fatigue pre-cracks were loaded into test fixtures so that the crack tips were exposed to AF-M315E at 50 C for a duration of 1,000 hours. Specimens that did not fail during exposure were opened to inspect the crack surfaces for evidence of crack growth. The threshold stress intensity value, KEAC, is the highest applied stress intensity that produced neither a failure of the specimen during the exposure nor showed evidence of crack growth. The threshold stress intensity factor for environment-assisted cracking of the Ti 6Al-4V forged tank material was found to be at least 22 ksivin and at least 31 ksivin for the weld material when exposed to AF-M315E monopropellant.

  19. Tracer kinetic modeling of [11C]AFM, a new PET imaging agent for the serotonin transporter

    PubMed Central

    Naganawa, Mika; Nabulsi, Nabeel; Planeta, Beata; Gallezot, Jean-Dominique; Lin, Shu-Fei; Najafzadeh, Soheila; Williams, Wendol; Ropchan, Jim; Labaree, David; Neumeister, Alexander; Huang, Yiyun; Carson, Richard E

    2013-01-01

    [11C]AFM, or [11C]2-[2-(dimethylaminomethyl)phenylthio]-5-fluoromethylphenylamine, is a new positron emission tomography (PET) radioligand with high affinity and selectivity for the serotonin transporter (SERT). The purpose of this study was to determine the most appropriate kinetic model to quantify [11C]AFM binding in the healthy human brain. Positron emission tomography data and arterial input functions were acquired from 10 subjects. Compartmental modeling and the multilinear analysis-1(MA1) method were tested using the arterial input functions. The one-tissue model showed a lack of fit in low-binding regions, and the two-tissue model failed to estimate parameters reliably. Regional time–activity curves were well described by MA1. The rank order of [11C]AFM binding potential (BPND) matched well with the known regional SERT densities. For routine use of [11C]AFM, several noninvasive methods for quantification of regional binding were evaluated, including simplified reference tissue models (SRTM and SRTM2), and multilinear reference tissue models (MRTM and MRTM2). The best methods for region of interest (ROI) analysis were MA1, MRTM2, and SRTM2, with fixed population kinetic values ( or b′) for the reference methods. The MA1 and MRTM2 methods were best for parametric imaging. These results showed that [11C]AFM is a suitable PET radioligand to image and quantify SERT in humans. PMID:23921898

  20. High-speed AFM for 1x node metrology and inspection: Does it damage the features?

    NASA Astrophysics Data System (ADS)

    Sadeghian, Hamed; van den Dool, Teun C.; Uziel, Yoram; Bar Or, Ron

    2015-03-01

    This paper aims at unraveling the mystery of damage in high speed AFMs for 1X node and below. With the device dimensions moving towards the 1X node and below, the semiconductor industry is rapidly approaching the point where existing metrology, inspection and review tools face huge challenges in terms of resolution, the ability to resolve 3D, and throughput. In this paper, we critically asses the important issue of damage in high speed AFM for metrology and inspection of semiconductor wafers. The issues of damage in four major scanning modes (contact mode, tapping mode, non-contact mode, and peak force tapping mode) are described to show which modes are suitable for which applications and which conditions are damaging. The effects of all important scanning parameters on resulting damage are taken into account for materials such as silicon, photoresists and low K materials. Finally, we recommend appropriate scanning parameters and conditions for several use cases (FinFET, patterned photoresist, HAR structures) that avoid exceeding a critical contact stress such that sample damage is minimized. In conclusion, we show using our theoretical analysis that selecting parameters that exceed the target contact stress, indeed leads to significant damage. This method provides AFM users for metrology with a better understanding of contact stresses and enables selection of AFM cantilevers and experimental parameters that prevent sample damage.

  1. AFM studies of the crystallization and habit modification of an excipient material, adipic acid.

    PubMed

    Keel, T R; Thompson, C; Davies, M C; Tendler, S J B; Roberts, C J

    2004-08-06

    Atomic force microscopy (AFM) has been used to investigate the (1 0 0) face of crystalline adipic acid, both in air and liquid environments. In air, surface reorganization occurred during scanning of the AFM probe, which has been investigated using single point force-distance analysis under a controlled relative humidity (RH) environment. We suggest such reorganization can be attributed to the influence of a network of water molecules bound to the hydrophilic (1 0 0) surface permitting local AFM tip-enhanced dissolution and reorganization of the solute. In situ imaging was also carried out on the crystals, revealing etch-pit formation during dissolution, and rapid growth at higher levels of supersaturation (sigma), both of which are direct consequences of the hydrophilic nature of the (1 0 0) face. Also presented here are nanoscale observations of the effect of octanoic acid, a structurally-related habit modifier, on crystalline adipic acid. Using AFM, we have been able to show that the presence of octanoic acid at low concentration has little observable affect on the development of the (1 0 0) face; however, as this concentration is increased, there are clear changes in step morphology and growth mode on the (1 0 0) face of the crystal. At a concentration of 1.26 mmol dm(-3) (a concentration corresponding to a molar ratio of approximately 1:175 octanoic acid:adipic acid), growth on the (1 0 0) face is inhibited, with in situ AFM imaging indicating this is a direct consequence of octanoic acid binding to the surface, and pinning the monomolecular growth steps.

  2. Advantages and limitations of OM, SEM, TEM and AFM in the study of ancient decorated pottery

    NASA Astrophysics Data System (ADS)

    Arenas-Alatorre, J.; Silva-Velazquez, Y.; Alva Medina, A.; Rivera, M.

    2010-03-01

    This paper presents results from the study of two fragments of pre-Hispanic pottery, decorated with red pigment, using Optical Microscopy (OM), Scanning Electron Microscopy (SEM), High Resolution Transmission Electron Microscopy (HRTEM), Atomic Force Microscopy (AFM) and Magnetic Force Microscopy (MFM). Capabilities and limitations of these techniques in the analysis of archaeological material are highlighted with special emphasis on TEM, AFM and MFM due to their contribution in the study of the pigment layer at micro and nano scale. The analyzed samples come from the archaeological sites of El Tajin and Xochicalco, both in Mexico. Results of conventional TEM and HRTEM analysis of the red pigment showed nanometric Fe2O3 particles in both samples but different particle shape and size distributions: specimen from El Tajin presented irregular particles between 50-100 nm while that from Xochicalco exhibited semispherical shapes in the 3-25 nm range. AFM images showed the topography of the pigments, which are related to the texture of their surface and thus to the production process. Finally, MFM showed different contrast regions suggesting the presence of ferromagnetic elements forming clusters and domain orientations on the color layer.

  3. Searching events in AFM force-extension curves: A wavelet approach.

    PubMed

    Benítez, R; Bolós, V J

    2017-01-01

    An algorithm, based on the wavelet scalogram energy, for automatically detecting events in force-extension AFM force spectroscopy experiments is introduced. The events to be detected are characterized by a discontinuity in the signal. It is shown how the wavelet scalogram energy has different decay rates at different points depending on the degree of regularity of the signal, showing faster decay rates at regular points and slower rates at singular points (jumps). It is shown that these differences produce peaks in the scalogram energy plot at the event points. Finally, the algorithm is illustrated in a tether analysis experiment by using it for the detection of events in the AFM force-extension curves susceptible to being considered tethers. Microsc. Res. Tech. 80:153-159, 2017. © 2016 Wiley Periodicals, Inc.

  4. New developments at PTB in 3D-AFM with tapping and torsion AFM mode and vector approach probing strategy

    NASA Astrophysics Data System (ADS)

    Dai, G.; Hässler-Grohne, W.; Hüser, D.; Wolff, H.; Fluegge, J.; Bosse, H.

    2011-06-01

    A new 3D-AFM for true 3D measurements of nano structures has been developed at Physikalisch Technische-Bundesanstalt, the national metrology institute of Germany. In its configuration, two piezo actuators are applied to drive the AFM cantilever near its vertical and torsional resonant frequencies. In such a way, the AFM tip can probe the surface with a vertical and/or a lateral oscillation, offering high 3D probing sensitivity. For enhancing measurement flexibility as well as reducing tip wear, a so called "vector approach probing" (VAP) method has been applied. The sample is measured point by point using this method. At each probing point, the tip is approached towards the surface in its normal direction until the desired tip-sample interaction is detected and then immediately withdrawn from the surface. Preliminary experimental results show promising performance of the developed system. The measurement of a line structure of 800 nm height employing a super sharp AFM tip is performed, showing a repeatability of its 3D profiles of better than 1 nm (p-v). A single crystal critical dimension reference material (SCCDRM) having features with almost vertical sidewall is measured using a flared AFM tip. Results show that the feature has averaged left and right sidewall angles of 88.64° and 88.67deg;, respectively. However, the feature width non-uniformity may reach 10 nm within the measurement range of 1 μm. The standard deviation of the averaged middle CD values of 7 repeated measurements reaches 0.35 nm. In addition, an investigation of long term measurement stability is performed on a PTB photomask. The results shows that the 3D-AFM has a drift rate of about 0.00033 nm per line, which confirms the high measurement stability and the very low tip wear.

  5. Formation of sensor array on the AFM chip surface by magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Shumov, I. D.; Kanashenko, S. L.; Ziborov, V. S.; Ivanov, Yu D.; Archakov, A. I.; Pleshakova, T. O.

    2017-01-01

    Development of atomic force microscopy (AFM)-based nanotechnological approaches to highly sensitive detection of proteins is a perspective direction in biomedical research. These approaches use AFM chips to concentrate the target proteins from the test solution volume (buffer solution, diluted biological fluid) onto the chip surface for their subsequent registration on the chip surface by AFM. Atomic force microscope is a molecular detector that enables protein detection at ultra-low (subfemtomolar) concentrations in single-molecule counting mode. Due to extremely high sensitivity of AFM, its application for multiplexed protein detection is of great interest for use in proteomics and diagnostic applications. In this study, AFM chips containing an array of sensor areas have been fabricated. Magnetron sputtering of chromium and tungsten nanolayers has been used to form optically visible metallic marks on the AFM chip surface to provide necessary precision of AFM probe positioning against each sensor area for scanning. It has been demonstrated that the marks formed by magnetron sputtering of Cr and W are stable on the surface of the AFM chips during the following activation and intensive washing of this surface. The results obtained in our present study allow application of the developed chips for multiplexed protein analysis by AFM.

  6. Fracture Growth Testing of Titanium 6AL-4V in AF-M315E

    NASA Technical Reports Server (NTRS)

    Sampson, Jeffrey W.; Martinez, Jonathan; McLean, Christopher

    2015-01-01

    The Green Propellant Infusion Mission (GPIM) will demonstrate the performance of AF-M315E monopropellant in orbit. Flight certification requires a safe-life analysis of the titanium alloy fuel tank to ensure inherent flaws will not cause failure during the design life. Material property inputs for this analysis require testing to determine the stress intensity factor for environmentally-assisted cracking (K (sub EAC)) of Ti 6Al-4V in combination with the AF-M315E monopropellant. Testing of single-edge notched specimens SE(B) representing the bulk tank membrane and weld material were performed in accordance with ASTM E1681. Specimens with fatigue pre-cracks were loaded into test fixtures so that the crack tips were exposed to the monopropellant at 50 degrees Centigrade for a duration of 1,000 hours. Specimens that did not fail during exposure were opened to inspect the crack surfaces for evidence of crack growth. The threshold stress intensity value, KEAC, is the highest applied stress intensity that produced neither a failure of the specimen during the exposure nor showed evidence of crack growth. The threshold stress intensity factor of the Ti 6Al-4V forged tank material when exposed to AF-M315E monopropellant was found to be at least 22.0 kilopounds per square inch. The stress intensity factor of the weld material was at least 31.3 kilopounds per square inch.

  7. Accurate, explicit formulae for higher harmonic force spectroscopy by frequency modulation-AFM.

    PubMed

    Kuchuk, Kfir; Sivan, Uri

    2015-01-01

    The nonlinear interaction between an AFM tip and a sample gives rise to oscillations of the cantilever at integral multiples (harmonics) of the fundamental resonance frequency. The higher order harmonics have long been recognized to hold invaluable information on short range interactions but their utilization has thus far been relatively limited due to theoretical and experimental complexities. In particular, existing approximations of the interaction force in terms of higher harmonic amplitudes generally require simultaneous measurements of multiple harmonics to achieve satisfactory accuracy. In the present letter we address the mathematical challenge and derive accurate, explicit formulae for both conservative and dissipative forces in terms of an arbitrary single harmonic. Additionally, we show that in frequency modulation-AFM (FM-AFM) each harmonic carries complete information on the force, obviating the need for multi-harmonic analysis. Finally, we show that higher harmonics may indeed be used to reconstruct short range forces more accurately than the fundamental harmonic when the oscillation amplitude is small compared with the interaction range.

  8. EEMD based pitch evaluation method for accurate grating measurement by AFM

    NASA Astrophysics Data System (ADS)

    Li, Changsheng; Yang, Shuming; Wang, Chenying; Jiang, Zhuangde

    2016-09-01

    The pitch measurement and AFM calibration precision are significantly influenced by the grating pitch evaluation method. This paper presents the ensemble empirical mode decomposition (EEMD) based pitch evaluation method to relieve the accuracy deterioration caused by high and low frequency components of scanning profile during pitch evaluation. The simulation analysis shows that the application of EEMD can improve the pitch accuracy of the FFT-FT algorithm. The pitch error is small when the iteration number of the FFT-FT algorithms was 8. The AFM measurement of the 500 nm-pitch one-dimensional grating shows that the EEMD based pitch evaluation method could improve the pitch precision, especially the grating line position precision, and greatly expand the applicability of the gravity center algorithm when particles and impression marks were distributed on the sample surface. The measurement indicates that the nonlinearity was stable, and the nonlinearity of x axis and forward scanning was much smaller than their counterpart. Finally, a detailed pitch measurement uncertainty evaluation model suitable for commercial AFMs was demonstrated and a pitch uncertainty in the sub-nanometer range was achieved. The pitch uncertainty was reduced about 10% by EEMD.

  9. An improved measurement of dsDNA elasticity using AFM

    NASA Astrophysics Data System (ADS)

    Nguyen, Thi-Huong; Lee, Sang-Myung; Na, Kyounghwan; Yang, Sungwook; Kim, Jinseok; Yoon, Eui-Sung

    2010-02-01

    The mechanical properties of a small fragment (30 bp) of an individual double-stranded deoxyribonucleic acid (dsDNA) in water have been investigated by atomic force microscopy (AFM). We have stretched three systems including ssDNA, double-fixed dsDNA (one strand of the dsDNA molecules was biotinylated at the 3'-end and thiolated at the 5'-end, this was reversed for the other complementary strand) and single-fixed dsDNA (one strand of the dsDNA molecules was biotinylated at the 3'-end and thiolated at the 5'-end, whereas the other complementary strand was biotinylated at only the 5'-end). The achieved thiolation and biotinylation were to bind ds- or ssDNA to the gold surface and streptavidin-coated AFM tip, respectively. Analysis of the force versus displacement (F-D) curves from tip-DNA-substrate systems shows that the pull-off length (Lo) and stretch length (δ) from the double-fixed system were shorter than those observed in the ssDNA and the single-fixed system. The obtained stretch force (Fst) from the single-fixed dsDNA was much greater than that from the ssDNA even though it was about 10 pN greater than the one obtained in the double-fixed system. As a result, the Young's modulus of the double-fixed dsDNA was greater than that of the single-fixed dsDNA and the ssDNA. A more reliable stiffness of the dsDNA was observed via the double-fixed system, since there is no effect of the unpaired molecules during stretching, which always occurred in the single-fixed system. The unpaired molecules were also observed by comparing the stiffness of ssDNA and single-fixed dsDNA in which the end of one strand was left free.

  10. AFM AND XPS Characterization of Zinc-Aluminum Alloy Coatings with Attention to Surface Dross and Flow Lines

    NASA Astrophysics Data System (ADS)

    Harding, Felipe A.; Alarcon, Nelson A.; Toledo, Pedro G.

    Surfaces of various zinc-aluminum alloy (Zn-Al) coated steel samples are studied with attention to foreign surface dross by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS/ESCA). AFM topographic maps of zinc-aluminum alloy surfaces free of dross reveal the perfect nanoscale details of two kinds of dendrites: branched and globular. In all magnifications the dendrites appear smooth and, in general, very clean. XPS analysis of the extreme surface of a Zn-Al sample reveals Al, Zn, Si and O as the main components. The XPS results show no segregation or separation of phases other than those indicated by the ternary Al-Zn-Si diagram. For surfaces of Zn-Al plagued with impurities, high resolution AFM topographic maps reveal three situations: (1) areas with well-defined dendrites, relatively free of dross; (2) areas with small, millimeter-sized black spots known as dross; and (3) areas with large black stains, known as flow lines. Dendrite deformation and dross accumulation increase notably in the neighborhood, apparently clean to the naked eye, of dross or flow lines. XPS results of areas with dross and flow lines indicate unacceptable high concentration of Si and important Si phase separation. These results, in the light of AFM work, reveal that dross and flow lines are a consequence of a high local concentration of Si from high melting point silica and silicate impurities in the Zn-Al alloy source.

  11. 3D Color Digital Elevation Map of AFM Sample

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This color image is a three dimensional (3D) view of a digital elevation map of a sample collected by NASA's Phoenix Mars Lander's Atomic Force Microscope (AFM).

    The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate, which is the background plane shown in red. This image has been processed to reflect the levelness of the substrate.

    A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

    The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The particle was part of a sample informally called 'Sorceress' delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008). The AFM is part of Phoenix's microscopic station called MECA, or the Microscopy, Electrochemistry, and Conductivity Analyzer.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  12. Structural investigations on native collagen type I fibrils using AFM

    SciTech Connect

    Strasser, Stefan; Zink, Albert; Janko, Marek; Heckl, Wolfgang M.; Thalhammer, Stefan . E-mail: stefan.thalhammer@gsf.de

    2007-03-02

    This study was carried out to determine the elastic properties of single collagen type I fibrils with the use of atomic force microscopy (AFM). Native collagen fibrils were formed by self-assembly in vitro characterized with the AFM. To confirm the inner assembly of the collagen fibrils, the AFM was used as a microdissection tool. Native collagen type I fibrils were dissected and the inner core uncovered. To determine the elastic properties of collagen fibrils the tip of the AFM was used as a nanoindentor by recording force-displacement curves. Measurements were done on the outer shell and in the core of the fibril. The structural investigations revealed the banding of the shell also in the core of native collagen fibrils. Nanoindentation experiments showed the same Young's modulus on the shell as well as in the core of the investigated native collagen fibrils. In addition, the measurements indicate a higher adhesion in the core of the collagen fibrils compared to the shell.

  13. Nano Mechanical Machining Using AFM Probe

    NASA Astrophysics Data System (ADS)

    Mostofa, Md. Golam

    Complex miniaturized components with high form accuracy will play key roles in the future development of many products, as they provide portability, disposability, lower material consumption in production, low power consumption during operation, lower sample requirements for testing, and higher heat transfer due to their very high surface-to-volume ratio. Given the high market demand for such micro and nano featured components, different manufacturing methods have been developed for their fabrication. Some of the common technologies in micro/nano fabrication are photolithography, electron beam lithography, X-ray lithography and other semiconductor processing techniques. Although these methods are capable of fabricating micro/nano structures with a resolution of less than a few nanometers, some of the shortcomings associated with these methods, such as high production costs for customized products, limited material choices, necessitate the development of other fabricating techniques. Micro/nano mechanical machining, such an atomic force microscope (AFM) probe based nano fabrication, has, therefore, been used to overcome some the major restrictions of the traditional processes. This technique removes material from the workpiece by engaging micro/nano size cutting tool (i.e. AFM probe) and is applicable on a wider range of materials compared to the photolithographic process. In spite of the unique benefits of nano mechanical machining, there are also some challenges with this technique, since the scale is reduced, such as size effects, burr formations, chip adhesions, fragility of tools and tool wear. Moreover, AFM based machining does not have any rotational movement, which makes fabrication of 3D features more difficult. Thus, vibration-assisted machining is introduced into AFM probe based nano mechanical machining to overcome the limitations associated with the conventional AFM probe based scratching method. Vibration-assisted machining reduced the cutting forces

  14. Determination of the aflatoxin M1 (AFM1) from milk by direct analysis in real time - mass spectrometry (DART-MS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Certain fungi that grow on crops can produce aflatoxins, which are highly carcinogenic. One of these, aflatoxin B1 can be metabolized by mammals to aflatoxin M1, a form that retains potent carcinogenicity and which can be excreted into milk. Direct analysis in real time (DART) ionization coupled to ...

  15. LET Spectrum Measurements In CR-39 PNTD With AFM

    SciTech Connect

    Johnson, C. E.; DeWitt, J. M.; Benton, E. R.; Yasuda, N.; Benton, E. V.

    2011-06-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range ({approx}<10 {mu}m) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching ({approx}<1 {mu}m) following by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features inherently present in the post-etch detector surface. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/{mu}m. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to 1 GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  16. LET Spectrum Measurements In CR-39 PNTD With AFM

    NASA Astrophysics Data System (ADS)

    Johnson, C. E.; DeWitt, J. M.; Benton, E. R.; Yasuda, N.; Benton, E. V.

    2011-06-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range (˜<10 μm) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching (˜<1 μm) following by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features inherently present in the post-etch detector surface. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/μm. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to 1 GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  17. LET spectrum measurements in Cr-39 PNTD with AFM

    SciTech Connect

    Johnson, Carl Edward; De Witt, Joel M; Benton, Eric R; Yasuda, Nakahiro; Benton, Eugene V

    2010-01-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range ({approx}< 10 {mu}m) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching ({approx}< 1 {mu}m) followed by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/{mu}m. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to I GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  18. Combination STM/AFM and AFM Images of Magnetic Domains

    NASA Astrophysics Data System (ADS)

    Yi, L.; Gallagher, M.; Howells, S.; Chen, T.; Sarid, D.

    1991-12-01

    By employing a cantilevered tip in a scanning tunneling microscope, one obtains images that show an enhancement of features associated with forces whose derivatives vary along the direction of scanning. The theory of this process is described together with experimental results showing magnetic domains on a gold coated floppy disk. Also shown are atomic force microscopy images of a ferrofluid-developed magnetic tape.

  19. An Evaluation of the Impacts of AF-M315E Propulsion Systems for Varied Mission Applications

    NASA Technical Reports Server (NTRS)

    Deans, Matthew C.; Oleson, Steven R.; Fittje, James; Colozza, Anthony; Packard, Tom; Gyekenyesi, John; McLean, Christopher H.; Spores, Ronald A.

    2015-01-01

    The purpose of the AF-M315E COMPASS study is to identify near-term (3-5 years) and long term (5 years +) opportunities for infusion, specifically the thruster and associated component technologies being developed as part of the GPIM project. Develop design reference missions which show the advantages of the AF-M315E green propulsion system. Utilize a combination of past COMPASS designs and selected new designs to demonstrate AF-M315E advantages. Use the COMPASS process to show the puts and takes of using AF-M315E at the integrated system level.

  20. Tip Characterization Method using Multi-feature Characterizer for CD-AFM

    PubMed Central

    Orji, Ndubuisi G.; Itoh, Hiroshi; Wang, Chumei; Dixson, Ronald G.; Walecki, Peter S.; Schmidt, Sebastian W.; Irmer, Bernd

    2016-01-01

    In atomic force microscopy (AFM) metrology, the tip is a key source of uncertainty. Images taken with an AFM show a change in feature width and shape that depends on tip geometry. This geometric dilation is more pronounced when measuring features with high aspect ratios, and makes it difficult to obtain absolute dimensions. In order to accurately measure nanoscale features using an AFM, the tip dimensions should be known with a high degree of precision. We evaluate a new AFM tip characterizer, and apply it to critical dimension AFM (CD-AFM) tips used for high aspect ratio features. The characterizer is made up of comb-shaped lines and spaces, and includes a series of gratings that could be used as an integrated nanoscale length reference. We also demonstrate a simulation method that could be used to specify what range of tip sizes and shapes the characterizer can measure. Our experiments show that for non re-entrant features, the results obtained with this characterizer are consistent to 1 nm with the results obtained by using widely accepted but slower methods that are common practice in CD-AFM metrology. A validation of the integrated length standard using displacement interferometry indicates a uniformity of better than 0.75%, suggesting that the sample could be used as highly accurate and SI traceable lateral scale for the whole evaluation process. PMID:26720439

  1. Hydration states of AFm cement phases

    SciTech Connect

    Baquerizo, Luis G.; Matschei, Thomas; Scrivener, Karen L.; Saeidpour, Mahsa; Wadsö, Lars

    2015-07-15

    The AFm phase, one of the main products formed during the hydration of Portland and calcium aluminate cement based systems, belongs to the layered double hydrate (LDH) family having positively charged layers and water plus charge-balancing anions in the interlayer. It is known that these phases present different hydration states (i.e. varying water content) depending on the relative humidity (RH), temperature and anion type, which might be linked to volume changes (swelling and shrinkage). Unfortunately the stability conditions of these phases are insufficiently reported. This paper presents novel experimental results on the different hydration states of the most important AFm phases: monocarboaluminate, hemicarboaluminate, strätlingite, hydroxy-AFm and monosulfoaluminate, and the thermodynamic properties associated with changes in their water content during absorption/desorption. This data opens the possibility to model the response of cementitious systems during drying and wetting and to engineer systems more resistant to harsh external conditions.

  2. Graphene MEMS: AFM probe performance improvement.

    PubMed

    Martin-Olmos, Cristina; Rasool, Haider Imad; Weiller, Bruce H; Gimzewski, James K

    2013-05-28

    We explore the feasibility of growing a continuous layer of graphene in prepatterned substrates, like an engineered silicon wafer, and we apply this as a mold for the fabrication of AFM probes. This fabrication method proves the fabrication of SU-8 devices coated with graphene in a full-wafer parallel technology and with high yield. It also demonstrates that graphene coating enhances the functionality of SU-8 probes, turning them conductive and more resistant to wear. Furthermore, it opens new experimental possibilities such as studying graphene-graphene interaction at the nanoscale with the precision of an AFM or the exploration of properties in nonplanar graphene layers.

  3. Biophysical properties of cardiomyocyte surface explored by multiparametric AFM.

    PubMed

    Smolyakov, Georges; Cauquil, Marie; Severac, Childerick; Lachaize, Véronique; Guilbeau-Frugier, Céline; Sénard, Jean-Michel; Galés, Céline; Dague, Etienne

    2017-03-02

    PeakForce Quantitative Nanomechanical Mapping (PeakForce QNM) multiparametric AFM mode was adapted to qualitative and quantitative study of the lateral membrane of cardiomyocytes (CMs), extending this powerful mode to the study of soft cells. On living CM, PeakForce QNM depicted the crests and hollows periodic alternation of cell surface architecture previously described using AFM Force Volume (FV) mode. PeakForce QNM analysis provided better resolution in terms of pixel number compared to FV mode and reduced acquisition time, thus limiting the consequences of spontaneous living adult CM dedifferentiation once isolated from the cardiac tissue. PeakForce QNM mode on fixed CMs clearly visualized subsarcolemmal mitochondria (SSM) and their loss following formamide treatment, concomitant with the interfibrillar mitochondria climbing up and forming heaps at the cell surface. Interestingly, formamide-promoted SSM loss allowed visualization of the sarcomeric apparatus ultrastructure below the plasma membrane. High PeakForce QNM resolution led to better contrasted mechanical maps than FV mode and provided correlation between adhesion, dissipation, mechanical and topographical maps. Modified hydrophobic AFM tip enhanced contrast on adhesion and dissipation maps and suggested that CM surface crests and hollows exhibit distinct chemical properties. Finally, two-dimensional Fast Fourier Transform to objectively quantify AFM maps allowed characterization of periodicity of both sarcomeric Z-line and M-band. Overall, this study validated PeakForce QNM as a valuable and innovative mode for the exploration of living and fixed CMs. In the future, it could be applied to depict cell membrane architectural, mechanical and chemical defects as well as sarcomeric abnormalities associated with cardiac diseases.

  4. Conductance of AFM Deformed Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Maiti, Amitesh; Anatram, M. P.; Biegel, Bryan (Technical Monitor)

    2002-01-01

    This viewgraph presentation provides information on the electrical conductivity of carbon nanotubes upon deformation by atomic force microscopy (AFM). The density of states and conductance were computed using four orbital tight-binding method with various parameterizations. Different chiralities develop bandgap that varies with chirality.

  5. Contact nanomechanical measurements with the AFM

    NASA Astrophysics Data System (ADS)

    Geisse, Nicholas

    2013-03-01

    The atomic force microscope (AFM) has found broad use in the biological sciences largely due to its ability to make measurements on unfixed and unstained samples under liquid. In addition to imaging at multiple spatial scales ranging from micro- to nanometer, AFMs are commonly used as nanomechanical probes. This is pertinent for cell biology, as it has been demonstrated that the geometrical and mechanical properties of the extracellular microenvironment are important in such processes as cancer, cardiovascular disease, muscular dystrophy, and even the control of cell life and death. Indeed, the ability to control and quantify these external geometrical and mechanical parameters arises as a key issue in the field. Because AFM can quantitatively measure the mechanical properties of various biological samples, novel insights to cell function and to cell-substrate interactions are now possible. As the application of AFM to these types of problems is widened, it is important to understand the performance envelope of the technique and its associated data analyses. This talk will discuss the important issues that must be considered when mechanical models are applied to real-world data. Examples of the effect of different model assumptions on our understanding of the measured material properties will be shown. Furthermore, specific examples of the importance of mechanical stimuli and the micromechanical environment to the structure and function of biological materials will be presented.

  6. Quantitative nano-mechanics of biological cells with AFM

    NASA Astrophysics Data System (ADS)

    Sokolov, Igor

    2013-03-01

    The importance of study of living cells is hard to overestimate. Cell mechanics is a relatively young, yet not a well-developed area. Besides just a fundamental interest, large practical need has emerged to measure cell mechanics quantitatively. Recent studies revealed a significant correlation between stiffness of biological cells and various human diseases, such as cancer, malaria, arthritis, and even aging. However, really quantitative studies of mechanics of biological cells are virtually absent. It is not even clear if the cell, being a complex and heterogeneous object, can be described by the elastic modulus at all. Atomic force microscopy (AFM) is a natural instrument to study properties of cells in their native environments. Here we will demonstrate that quantitative measurements of elastic modulus of cells with AFM are possible. Specifically, we will show that the ``cell body'' (cell without ``brush'' surface layer, a non-elastic layer surrounding cells) typically demonstrates the response of a homogeneous elastic medium up to the deformation of 10-20%, but if and only if a) the cellular brush layer is taken into account, b) rather dull AFM probes are used. This will be justified with the help of the strong condition of elastic behavior of material: the elastic modulus is shown to be independent on the indentation depth. We will also demonstrate that an attempt either to ignore the brush layer or to use sharp AFM probes will result in the violation of the strong condition, which implies impossibility to use the concept of the elastic modulus to describe cell mechanics in such experiments. Examples of quantitative measurements of the Young's modulus of the cell body and the cell brush parameters will be given for various cells. Address when submitting: Clarkson University, Potsdam, NY 13699

  7. Interlaboratory round robin on cantilever calibration for AFM force spectroscopy.

    PubMed

    te Riet, Joost; Katan, Allard J; Rankl, Christian; Stahl, Stefan W; van Buul, Arend M; Phang, In Yee; Gomez-Casado, Alberto; Schön, Peter; Gerritsen, Jan W; Cambi, Alessandra; Rowan, Alan E; Vancso, G Julius; Jonkheijm, Pascal; Huskens, Jurriaan; Oosterkamp, Tjerk H; Gaub, Hermann; Hinterdorfer, Peter; Figdor, Carl G; Speller, Sylvia

    2011-12-01

    Single-molecule force spectroscopy studies performed by Atomic Force Microscopes (AFMs) strongly rely on accurately determined cantilever spring constants. Hence, to calibrate cantilevers, a reliable calibration protocol is essential. Although the thermal noise method and the direct Sader method are frequently used for cantilever calibration, there is no consensus on the optimal calibration of soft and V-shaped cantilevers, especially those used in force spectroscopy. Therefore, in this study we aimed at establishing a commonly accepted approach to accurately calibrate compliant and V-shaped cantilevers. In a round robin experiment involving eight different laboratories we compared the thermal noise and the Sader method on ten commercial and custom-built AFMs. We found that spring constants of both rectangular and V-shaped cantilevers can accurately be determined with both methods, although the Sader method proved to be superior. Furthermore, we observed that simultaneous application of both methods on an AFM proved an accurate consistency check of the instrument and thus provides optimal and highly reproducible calibration. To illustrate the importance of optimal calibration, we show that for biological force spectroscopy studies, an erroneously calibrated cantilever can significantly affect the derived (bio)physical parameters. Taken together, our findings demonstrated that with the pre-established protocol described reliable spring constants can be obtained for different types of cantilevers.

  8. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic.

    PubMed

    Storfer, Andrew; Alfaro, Michael E; Ridenhour, Benjamin J; Jancovich, James K; Mech, Stephen G; Parris, Matthew J; Collins, James P

    2007-11-01

    Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.

  9. Surface Microstructure of Mo(C)N Coatings Investigated by AFM

    NASA Astrophysics Data System (ADS)

    Kuznetsova, T.; Zubar, T.; Chizhik, S.; Gilewicz, A.; Lupicka, O.; Warcholinski, B.

    2016-12-01

    MoCN coatings have been formed by cathodic arc evaporation using the mixture of acetylene and nitrogen and pure molybdenum target. The surface structure, in conjunction with x-ray data, was analyzed by atomic force microscopy (AFM). The AFM results show differently shaped grain forms on the surface of coatings investigated. The increase in carbon in chemical coatings composition results in the reduction in surface grain size and the increase in roughness of the coatings.

  10. Analysis of competition performance in dressage and show jumping of Dutch Warmblood horses.

    PubMed

    Rovere, G; Ducro, B J; van Arendonk, J A M; Norberg, E; Madsen, P

    2016-12-01

    Most Warmblood horse studbooks aim to improve the performance in dressage and show jumping. The Dutch Royal Warmblood Studbook (KWPN) includes the highest score achieved in competition by a horse to evaluate its genetic ability of performance. However, the records collected during competition are associated with some aspects that might affect the quality of the genetic evaluation based on these records. These aspects include the influence of rider, censoring and preselection of the data. The aim of this study was to quantify the impact of rider effect, censoring and preselection on the genetic analysis of competition data of dressage and show jumping of KWPN. Different models including rider effect were evaluated. To assess the impact of censoring, genetic parameters were estimated in data sets that differed in the degree of censoring. The effect of preselection on variance components was analysed by defining a binary trait (sport-status) depending on whether the horse has a competition record or not. This trait was included in a bivariate model with the competition trait and used all horses registered by KWPN since 1984. Results showed that performance in competition for dressage and show jumping is a heritable trait (h(2) ~ 0.11-0.13) and that it is important to account for the effect of rider in the genetic analysis. Censoring had a small effect on the genetic parameter for highest performance achieved by the horse. A moderate heritability obtained for sport-status indicates that preselection has a genetic basis, but the effect on genetic parameters was relatively small.

  11. Network Analysis Shows Novel Molecular Mechanisms of Action for Copper-Based Chemotherapy

    PubMed Central

    Espinal-Enríquez, Jesús; Hernández-Lemus, Enrique; Mejía, Carmen; Ruiz-Azuara, Lena

    2016-01-01

    The understanding of the mechanisms associated with the action of chemotherapeutic agents is fundamental to assess and account for possible side-effects of such treatments. Casiopeínas have demonstrated a cytotoxic effect by activation of pro-apoptotic processes in malignant cells. Such processes have been proved to activate the apoptotic intrinsic route, as well as cell cycle arrest. Despite this knowledge, the whole mechanism of action of Casiopeínas is yet to be completely understood. In this work we implement a systems biology approach based on two pathway analysis tools (Over-Representation Analysis and Causal Network Analysis) to observe changes in some hallmarks of cancer, induced by this copper-based chemotherapeutic agent in HeLa cell lines. We find that the metabolism of metal ions is exacerbated, as well as cell division processes being globally diminished. We also show that cellular migration and proliferation events are decreased. Moreover, the molecular mechanisms of liver protection are increased in the cell cultures under the actions of Casiopeínas, unlike the case in many other cytotoxic drugs. We argue that this chemotherapeutic agent may be promising, given its protective hepatic function, concomitant with its cytotoxic participation in the onset of apoptotic processes in malignant cells. PMID:26793116

  12. Probing Cytoskeletal Structures by Coupling Optical Superresolution and AFM Techniques for a Correlative Approach

    PubMed Central

    Chacko, Jenu Varghese; Zanacchi, Francesca Cella; Diaspro, Alberto

    2013-01-01

    In this article, we describe and show the application of some of the most advanced fluorescence superresolution techniques, STED AFM and STORM AFM microscopy towards imaging of cytoskeletal structures, such as microtubule filaments. Mechanical and structural properties can play a relevant role in the investigation of cytoskeletal structures of interest, such as microtubules, that provide support to the cell structure. In fact, the mechanical properties, such as the local stiffness and the elasticity, can be investigated by AFM force spectroscopy with tens of nanometers resolution. Force curves can be analyzed in order to obtain the local elasticity (and the Young's modulus calculation by fitting the force curves from every pixel of interest), and the combination with STED/STORM microscopy integrates the measurement with high specificity and yields superresolution structural information. This hybrid modality of superresolution-AFM working is a clear example of correlative multimodal microscopy. PMID:24027190

  13. Nanogap based graphene coated AFM tips with high spatial resolution, conductivity and durability.

    PubMed

    Lanza, Mario; Gao, Teng; Yin, Zixuan; Zhang, Yanfeng; Liu, Zhongfan; Tong, Yuzhen; Shen, Ziyong; Duan, Huiling

    2013-11-21

    After one decade of analyzing the intrinsic properties of graphene, interest into the development of graphene-based devices and micro electromechanical systems is increasing. Here, we fabricate graphene-coated atomic force microscope tips by growing the graphene on copper foil and transferring it onto the apex of a commercially available AFM tip. The resulting tip exhibits surprising enhanced resolution in nanoscale electrical measurements. By means of topographic AFM maps and statistical analyses we determine that this superior performance may be related to the presence of a nanogap between the graphene and the tip apex, which reduces the tip radius and tip-sample contact area. In addition, the graphene-coated tips show a low tip-sample interaction, high conductivity and long life times. The novel fabrication-friendly tip could improve the quality and reliability of AFM experiments, while reducing the cost of AFM-based research.

  14. Nanomechanics of new materials — AFM and computer modelling studies of trichoptera silk

    NASA Astrophysics Data System (ADS)

    Strzelecki, Janusz; Strzelecka, Joanna; Mikulska, Karolina; Tszydel, Mariusz; Balter, Aleksander; Nowak, Wiesław

    2011-04-01

    Caddisfly (Trichopera) can glue diverse material underwater with a silk fiber. This makes it a particularly interesting subject for biomimetcs. Better understanding of silk composition and structure could lead to an adhesive capable to close bleeding wounds or to new biomaterials. However, while spiderweb or silkworm secretion is well researched, caddisfly silk is still poorly understood. Here we report a first nanomechanical analysis of H. Angustipennis caddisfly silk fiber. An Atomic Force Microscope (AFM) imaging shows dense 150 nm bumps on silk surface, which can be identified as one of features responsible for its outstanding adhesive properties. AFM force spectroscopy at the fiber surface showed, among others, characteristic saw like pattern. This pattern is attributed to sacrificial bond stretching and enhances energy dissipation in mechanical deformation. Similarities of some force curves observed on Tegenaria domestica spiderweb and caddisfly silk are also discussed. Steered Molecular Dynamics simulations revealed that the strength of short components of Fib-H HA species molecules, abundant in Trichoptera silk is critically dependent on calcium presence.

  15. Structural studies of sulfur passivated GaAs(001) surfaces with LEED and AFM

    NASA Astrophysics Data System (ADS)

    Wang, Xuewen; Ke, Yenjin; Milano, Steve; Tao, Nongjian; Darici, Yesim

    1997-03-01

    We present the results of auger electron spectroscopy (AES), low-energy electron diffraction (LEED) and atomic force microscopy (AFM) analysis of sulfur passivating layers on the GaAs(001) surface. The GaAs surfaces were passivated with both inorganic ((NH_4)_2S) and organic (ODT) S-based compounds. We prepared the inorganic sulfur-passivated GaAs(001) surfaces with a wet chemical treatment using (NH_4)_2S solution. This was followed by thermal annealing of the treated sample in ultra high vacuum. After ex-situ and in-situ treatments the surface resulted in a (2X1) LEED pattern. The LEED data (I-V curves) was recorded and compared with dynamical LEED calculations for different structural models for the sulfur passivated GaAs(110) surface. The results showed that sulfur passivated (2X1) surface structure is an arsenic-sulfur dimer on gallium terminated substrate. The ex-situ AFM results also showed a (2X1) structure for the inorganic passivation and a very smooth surface for the organic ODT in ethanal treated sample.

  16. tRNA conjugation with chitosan nanoparticles: An AFM imaging study.

    PubMed

    Agudelo, D; Kreplak, L; Tajmir-Riahi, H A

    2016-04-01

    The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.

  17. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis.

    PubMed

    Dunlap, Christopher A

    2015-10-01

    ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

  18. Detection of Pathogens Using AFM and SPR

    NASA Astrophysics Data System (ADS)

    Vaseashta, Ashok

    2005-03-01

    A priori detection of pathogens in food and water has become a subject of paramount importance. Several recent incidents have resulted in the government passing stringent regulations for tolerable amounts of contamination of food products. Identification and/or monitoring of bacterial contamination in food are critical. The conventional methods of pathogen detection require time-consuming steps to arrive disembark at meaningful measurement in a timely manner as the detection time exceeds the time in which perishable food recycles through the food chain distribution. The aim of this presentation is to outline surface plasmon resonance (SPR) and atomic force microscopy (AFM) as two methods for fast detect6ion of pathogens. Theoretical basis of SPR and experimental results of SPR and AFM on E. coli O157:H7 and prion are presented.

  19. HIV-1 Phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

    PubMed Central

    Lamers, Susanna L.; Gray, Rebecca R.; Salemi, Marco; Huysentruyt, Leanne C.; McGrath, Michael

    2010-01-01

    Brain infection by the human immunodeficiency virus type 1 (HIV-1) has been investigated in many reports with a variety of conclusions concerning the time of entry and degree of viral compartmentalization. To address these diverse findings, we sequenced HIV-1 gp120 clones from a wide range of brain, peripheral and meningeal tissues from five patients who died from several HIV-1 associated disease pathologies. High-resolution phylogenetic analysis confirmed previous studies that showed a significant degree of compartmentalization in brain and peripheral tissue subpopulations. Some intermixing between the HIV-1 subpopulations was evident, especially in patients that died from pathologies other than HIV-associated dementia. Interestingly, the major tissue harboring virus from both the brain and peripheral tissues was the meninges. These results show that 1) HIV-1 is clearly capable of migrating out of the brain, 2) the meninges are the most likely primary transport tissues, and 3) infected brain macrophages comprise an important HIV reservoir during highly active antiretroviral therapy. PMID:21055482

  20. Nanomechanics of Yeast Surfaces Revealed by AFM

    NASA Astrophysics Data System (ADS)

    Dague, Etienne; Beaussart, Audrey; Alsteens, David

    Despite the large and well-documented characterization of the microbial cell wall in terms of chemical composition, the determination of the mechanical properties of surface molecules in relation to their function remains a key challenge in cell biology.The emergence of powerful tools allowing molecular manipulations has already revolutionized our understanding of the surface properties of fungal cells. At the frontier between nanophysics and molecular biology, atomic force microscopy (AFM), and more specifically single-molecule force spectroscopy (SMFS), has strongly contributed to our current knowledge of the cell wall organization and nanomechanical properties. However, due to the complexity of the technique, measurements on live cells are still at their infancy.In this chapter, we describe the cell wall composition and recapitulate the principles of AFM as well as the main current methodologies used to perform AFM measurements on live cells, including sample immobilization and tip functionalization.The current status of the progress in probing nanomechanics of the yeast surface is illustrated through three recent breakthrough studies. Determination of the cell wall nanostructure and elasticity is presented through two examples: the mechanical response of mannoproteins from brewing yeasts and elasticity measurements on lacking polysaccharide mutant strains. Additionally, an elegant study on force-induced unfolding and clustering of adhesion proteins located at the cell surface is also presented.

  1. Microhardness, chemical etching, SEM, AFM and SHG studies of novel nonlinear optical crystal -L-threonine formate

    SciTech Connect

    Hanumantha Rao, Redrothu; Kalainathan, S.

    2012-04-15

    Highlights: Black-Right-Pointing-Pointer Microhardness studies of novel LTF crystal reported first time in the literature. Black-Right-Pointing-Pointer Surface studies are done by AFM, chemical etching and SEM. Black-Right-Pointing-Pointer From SHG studies, it is known that LTF is potential NLO crystal. -- Abstract: The crystal L-threonine formate, an organic NLO crystal was synthesized from aqueous solution by slow evaporation technique. The grown crystal surface has been analyzed by scanning electron microscopy (SEM), chemical etching and atomic force microscopy (AFM). SEM analysis reveals pyramidal shaped minute crystallites on the growth surface. The etching study indicates the occurrence of etch pit patterns like striations and step like pattern. The mechanical properties of LTF crystals were evaluated by mechanical testing which reveals certain mechanical characteristics like elastic stiffness constant (C{sub 11}) and young's modulus (E). The Vickers and Knoop microhardness studies have been carried out on LTF crystals over a range of 10-50 g. Hardness anisotropy has been observed in accordance with the orientation of the crystal. AFM image shows major hillock on growth surface. The second harmonic generation (SHG) efficiency has been tested by the Kurtz powder technique using Nd:YAG laser and found to be about 1.21 times in comparison with standard potassium dihydrogen phosphate (KDP) crystals.

  2. Cooperative Genome-Wide Analysis Shows Increased Homozygosity in Early Onset Parkinson's Disease

    PubMed Central

    Nalls, Michael A.; Martinez, Maria; Schulte, Claudia; Holmans, Peter; Gasser, Thomas; Hardy, John; Singleton, Andrew B.; Wood, Nicholas W.; Brice, Alexis; Heutink, Peter; Williams, Nigel; Morris, Huw R.

    2012-01-01

    Parkinson's disease (PD) occurs in both familial and sporadic forms, and both monogenic and complex genetic factors have been identified. Early onset PD (EOPD) is particularly associated with autosomal recessive (AR) mutations, and three genes, PARK2, PARK7 and PINK1, have been found to carry mutations leading to AR disease. Since mutations in these genes account for less than 10% of EOPD patients, we hypothesized that further recessive genetic factors are involved in this disorder, which may appear in extended runs of homozygosity. We carried out genome wide SNP genotyping to look for extended runs of homozygosity (ROHs) in 1,445 EOPD cases and 6,987 controls. Logistic regression analyses showed an increased level of genomic homozygosity in EOPD cases compared to controls. These differences are larger for ROH of 9 Mb and above, where there is a more than three-fold increase in the proportion of cases carrying a ROH. These differences are not explained by occult recessive mutations at existing loci. Controlling for genome wide homozygosity in logistic regression analyses increased the differences between cases and controls, indicating that in EOPD cases ROHs do not simply relate to genome wide measures of inbreeding. Homozygosity at a locus on chromosome19p13.3 was identified as being more common in EOPD cases as compared to controls. Sequencing analysis of genes and predicted transcripts within this locus failed to identify a novel mutation causing EOPD in our cohort. There is an increased rate of genome wide homozygosity in EOPD, as measured by an increase in ROHs. These ROHs are a signature of inbreeding and do not necessarily harbour disease-causing genetic variants. Although there might be other regions of interest apart from chromosome 19p13.3, we lack the power to detect them with this analysis. PMID:22427796

  3. Linkage analysis followed by association show NRG1 associated with cannabis dependence in African-Americans

    PubMed Central

    Han, Shizhong; Yang, Bao-Zhu; Kranzler, Henry R.; Oslin, David; Anton, Raymond; Farrer, Lindsay A.; Gelernter, Joel

    2013-01-01

    Background A genetic contribution to cannabis dependence (CaD) has been established, but susceptibility genes for CaD remain largely unknown. Methods We employed a multi-stage design to identify genetic variants underlying CaD. We first performed a genomewide linkage scan for CaD in 384 African-American (AA) and 354 European-American (EA) families ascertained for genetic studies of cocaine and opioid dependence. We then conducted association analysis under the linkage peak, first using data from a genomewide association study from the Study of Addiction: Genetics and Environment (SAGE), followed by replication studies of prioritized single nucleotide polymorphisms (SNPs) in independent samples. Results We identified the strongest linkage evidence with CaD (lod=2.9) on chromosome 8p21.1 in AAs. In the association analysis of the SAGE sample under the linkage peak, we identified one SNP (rs17664708) associated with CaD in both AAs (minor allele frequency (MAF) = 0.02, OR=2.93, 95% CI=1.47–5.85, P=0.0022) and EAs (MAF=0.096, OR=1.38, 95% CI=1.05–1.81, P=0.02). This SNP, located at NRG1, a susceptibility gene for schizophrenia, was prioritized for further study. We replicated the association of rs17664708 with CaD in an independent sample of AAs (MAF=0.013, OR=2.81, 95% CI=1.23–6.45, P=0.0068). The joint analysis of the two AA samples demonstrated highly significant association between rs17664708 and CaD with adjustment for either global (OR=2.34, 95% CI=1.42–3.85, P=0.00044) or local ancestry (OR=2.33, 95% CI=1.39–3.91, P=0.00075). Conclusions Our study shows that NRG1 is probably a susceptibility gene for CaD, based on convergent evidence of linkage and replicated associations in two independent AA samples. PMID:22520967

  4. Brain regions that show repetition suppression and enhancement: A meta-analysis of 137 neuroimaging experiments.

    PubMed

    Kim, Hongkeun

    2017-04-01

    Repetition suppression and enhancement refer to the reduction and increase in the neural responses for repeated rather than novel stimuli, respectively. This study provides a meta-analysis of the effects of repetition suppression and enhancement, restricting the data used to that involving fMRI/PET, visual stimulus presentation, and healthy participants. The major findings were as follows. First, the global topography of the repetition suppression effects was strikingly similar to that of the "subsequent memory" effects, indicating that the mechanism for repetition suppression is the reduced engagement of an encoding system. The lateral frontal cortex effects involved the frontoparietal control network regions anteriorly and the dorsal attention network regions posteriorly. The left fusiform cortex effects predominantly involved the dorsal attention network regions, whereas the right fusiform cortex effects mainly involved the visual network regions. Second, the category-specific meta-analyses and their comparisons indicated that most parts of the alleged category-specific regions showed repetition suppression for more than one stimulus category. In this regard, these regions may not be "dedicated cortical modules," but are more likely parts of multiple overlapping large-scale maps of simple features. Finally, the global topography of the repetition enhancement effects was similar to that of the "retrieval success" effects, suggesting that the mechanism for repetition enhancement is voluntary or involuntary explicit retrieval during an implicit memory task. Taken together, these results clarify the network affiliations of the regions showing reliable repetition suppression and enhancement effects and contribute to the theoretical interpretations of the local and global topography of these two effects. Hum Brain Mapp 38:1894-1913, 2017. © 2017 Wiley Periodicals, Inc.

  5. Adsorption Studies with AFM of Human Plasma Fibrinogen on Silicon Surfaces

    NASA Astrophysics Data System (ADS)

    Gause, Sheena; Kong, Wendy; Rowe

    2007-11-01

    Fibrinogen (FGN) plays an important role in the clotting of blood. Human plasma fibrinogen (HPF) is a protein that readily adsorbs on biomaterial surfaces. The purpose of this experiment was to use the Atomic Force Microscope to study the adsorption of HPF molecules or FGN onto several silicon surfaces with different orientations and resistivities. The size of the FGN molecules found to be somewhat different of Si(111), (100) and (110) were compared to the size of the FGN molecules in solution (45 nm in length, the end dynodes measures to be 6.5 nm in diameter, and the middle dynode measures to be 5 nm in diameter. For this study, the CPR (Thermo-microscope) Atomic Force Microscope (AFM) was used to observe the amount of fibrinogen molecules adsorbed by Si (111) with a resistance of .0281-.0261 φ cm, Si (111) with a resistance of 1 φ cm, Si (100), and Si (110) surfaces. In finding any single fibrinogen molecules, the appropriate image scans and measurements were taken. After collection and analysis of the data, it was found from AFM that the fibrinogen molecules found on Si (110) mostly resembled fibrinogen molecules found in solution. The other images showed that the fibrinogen molecules adsorbed on Silicon substrates is significantly greater (˜10-20 %) than those in solution.

  6. Adaptive AFM scan speed control for high aspect ratio fast structure tracking

    SciTech Connect

    Ahmad, Ahmad; Schuh, Andreas; Rangelow, Ivo W.

    2014-10-15

    Improved imaging rates in Atomic Force Microscopes (AFM) are of high interest for disciplines such as life sciences and failure analysis of semiconductor wafers, where the sample topology shows high aspect ratios. Also, fast imaging is necessary to cover a large surface under investigation in reasonable times. Since AFMs are composed of mechanical components, they are associated with comparably low resonance frequencies that undermine the effort to increase the acquisition rates. In particular, high and steep structures are difficult to follow, which causes the cantilever to temporarily loose contact to or crash into the sample. Here, we report on a novel approach that does not affect the scanner dynamics, but adapts the lateral scanning speed of the scanner. The controller monitors the control error signal and, only when necessary, decreases the scan speed to allow the z-piezo more time to react to changes in the sample's topography. In this case, the overall imaging rate can be significantly increased, because a general scan speed trade-off decision is not needed and smooth areas are scanned fast. In contrast to methods trying to increase the z-piezo bandwidth, our method is a comparably simple approach that can be easily adapted to standard systems.

  7. Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma

    PubMed Central

    Hansmann, Leo; Blum, Lisa; Ju, Chia-Hsin; Liedtke, Michaela; Robinson, William H.; Davis, Mark M.

    2015-01-01

    It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals and thus high resolution technologies are likely required. We used cytometry by time-of-flight (CyTOF) and next generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related pre-cancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 pre-cancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T, B, and natural killer cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0±0.7% (mean±SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27+) and naïve (CD24loCD38+) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells. PMID:25711758

  8. Proteomic analysis of rice leaves shows the different regulations to osmotic stress and stress signals.

    PubMed

    Shu, Lie-Bo; Ding, Wei; Wu, Jin-Hong; Feng, Fang-Jun; Luo, Li-Jun; Mei, Han-Wei

    2010-11-01

    Following the idea of partial root-zone drying (PRD) in crop cultivation, the morphological and physiological responses to partial root osmotic stress (PROS) and whole root osmotic stress (WROS) were investigated in rice. WROS caused stress symptoms like leaf rolling and membrane leakage. PROS stimulated stress signals, but did not cause severe leaf damage. By proteomic analysis, a total of 58 proteins showed differential expression after one or both treatments, and functional classification of these proteins suggests that stress signals regulate photosynthesis, carbohydrate and energy metabolism. Two other proteins (anthranilate synthase and submergence-induced nickel-binding protein) were upregulated only in the PROS plants, indicating their important roles in stress resistance. Additionally, more enzymes were involved in stress defense, redox homeostasis, lignin and ethylene synthesis in WROS leaves, suggesting a more comprehensive regulatory mechanism induced by osmotic stress. This study provides new insights into the complex molecular networks within plant leaves involved in the adaptation to osmotic stress and stress signals.

  9. Nanoscale thermal AFM of polymers: transient heat flow effects.

    PubMed

    Duvigneau, Joost; Schönherr, Holger; Vancso, G Julius

    2010-11-23

    Thermal transport around the nanoscale contact area between the heated atomic force microscopy (AFM) probe tip and the specimen under investigation is a central issue in scanning thermal microscopy (SThM). Polarized light microscopy and AFM imaging of the temperature-induced crystallization of poly(ethylene terephthalate) (PET) films in the region near the tip were used in this study to unveil the lateral heat transport. The radius of the observed lateral surface isotherm at 133 °C ranged from 2.2 ± 0.5 to 18.7 ± 0.5 μm for tip-polymer interface temperatures between 200 and 300 °C with contact times varying from 20 to 120 s, respectively. In addition, the heat transport into polymer films was assessed by measurements of the thermal expansion of poly(dimethyl siloxane) (PDMS) films with variable thickness on silicon supports. Our data showed that heat transport in the specimen normal (z) direction occurred to depths exceeding 1000 μm using representative non-steady-state SThM conditions (i.e., heating from 40 to 180 °C at a rate of 10 °C s(-1)). On the basis of the experimental results, a 1D steady-state model for heat transport was developed, which shows the temperature profile close to the tip-polymer contact. The model also indicates that ≤1% of the total power generated in the heater area, which is embedded in the cantilever end, is transported into the polymer through the tip-polymer contact interface. Our results complement recent efforts in the evaluation and improvement of existing theoretical models for thermal AFM, as well as advance further developments of SThM for nanoscale thermal materials characterization and/or manipulation via scanning thermal lithography (SThL).

  10. Solvent-mediated repair and patterning of surfaces by AFM

    SciTech Connect

    Elhadj, S; Chernov, A; De Yoreo, J

    2007-10-30

    A tip-based approach to shaping surfaces of soluble materials with nanometer-scale control is reported. The proposed method can be used, for example, to eliminate defects and inhomogeneities in surface shape, repair mechanical or laser-induced damage to surfaces, or perform 3D lithography on the length scale of an AFM tip. The phenomenon that enables smoothing and repair of surfaces is based on the transport of material from regions of high- to low-curvature within the solution meniscus formed in a solvent-containing atmosphere between the surface in question and an AFM tip scanned over the surface. Using in situ AFM measurements of the kinetics of surface remodeling on KDP (KH{sub 2}PO{sub 4}) crystals in humid air, we show that redistribution of solute material during relaxation of grooves and mounds is driven by a reduction in surface free energy as described by the Gibbs-Thomson law. We find that the perturbation from a flat interface evolves according to the diffusion equation where the effective diffusivity is determined by the product of the surface stiffness and the step kinetic coefficient. We also show that, surprisingly, if the tip is instead scanned over or kept stationary above an atomically flat area of the surface, a convex structure is formed with a diameter that is controlled by the dimensions of the meniscus, indicating that the presence of the tip and meniscus reduces the substrate chemical potential beneath that of the free surface. This allows one to create nanometer-scale 3D structures of arbitrary shape without the removal of substrate material or the use of extrinsic masks or chemical compounds. Potential applications of these tip-based phenomena are discussed.

  11. BOREAS AFM-6 Surface Meteorological Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) collected surface meteorological data from 21 May to 20 Sep 1994 near the Southern Study Area-Old Jack Pine (SSA-OJP) tower site. The data are in tabular ASCII files. The surface meteorological data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  12. Development of a 3D-AFM for true 3D measurements of nanostructures

    NASA Astrophysics Data System (ADS)

    Dai, Gaoliang; Häßler-Grohne, Wolfgang; Hüser, Dorothee; Wolff, Helmut; Danzebrink, Hans-Ulrich; Koenders, Ludger; Bosse, Harald

    2011-09-01

    The development of advanced lithography requires highly accurate 3D metrology methods for small line structures of both wafers and photomasks. Development of a new 3D atomic force microscopy (3D-AFM) with vertical and torsional oscillation modes is introduced in this paper. In its configuration, the AFM probe is oscillated using two piezo actuators driven at vertical and torsional resonance frequencies of the cantilever. In such a way, the AFM tip can probe the surface with a vertical and a lateral oscillation, offering high 3D probing sensitivity. In addition, a so-called vector approach probing (VAP) method has been applied. The sample is measured point-by-point using this method. At each probing point, the tip is approached towards the surface until the desired tip-sample interaction is detected and then immediately withdrawn from the surface. Compared to conventional AFMs, where the tip is kept continuously in interaction with the surface, the tip-sample interaction time using the VAP method is greatly reduced and consequently the tip wear is reduced. Preliminary experimental results show promising performance of the developed system. A measurement of a line structure of 800 nm height employing a super sharp AFM tip could be performed with a repeatability of its 3D profiles of better than 1 nm (p-v). A line structure of a Physikalisch-Technische Bundesanstalt photomask with a nominal width of 300 nm has been measured using a flared tip AFM probe. The repeatability of the middle CD values reaches 0.28 nm (1σ). A long-term stability investigation shows that the 3D-AFM has a high stability of better than 1 nm within 197 measurements taken over 30 h, which also confirms the very low tip wear.

  13. Pathogen identification using peptide nanotube biosensors and impedance AFM

    NASA Astrophysics Data System (ADS)

    Maccuspie, Robert I.

    Pathogen identification at highly sensitive levels is crucial to meet urgent needs in fighting the spread of disease or detecting bioterrorism events. Toward that end, a new method for biosensing utilizing fluorescent antibody nanotubes is proposed. Fundamental studies on the self-assembly of these peptide nanotubes are performed, as are applications of aligning these nanotubes on surfaces. As biosensors, these nanotubes incorporate recognition units with antibodies at their ends and fluorescent signaling units at their sidewalls. When viral pathogens were mixed with these antibody nanotubes in solution, the nanotubes rapidly aggregated around the viruses. The size of the aggregates increased as the concentration of viruses increased, as detected by flow cytometry on the order of attomolar concentrations by changes in fluorescence and light scattering intensities. This enabled determination of the concentrations of viruses at trace levels (102 to 106 pfu/mL) within 30 minutes from the receipt of samples to the final quantitative data analysis, as demonstrated on Adenovirus, Herpes Simplex Virus, Influenza, and Vaccinia virus. As another separate approach, impedance AFM is used to study the electrical properties of individual viruses and nanoparticles used as model systems. The design, development, and implementation of the impedance AFM for an Asylum Research platform is described, as well as its application towards studying the impedance of individual nanoparticles as a model system for understanding the fundamental science of how the life cycle of a virus affects its electrical properties. In combination, these approaches fill a pressing need to quantify viruses both rapidly and sensitively.

  14. AFM Structural Characterization of Drinking Water Biofilm ...

    EPA Pesticide Factsheets

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

  15. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Bacillus vanillea’ XY18T (=CGMCC 8629 T =NCCB 100507 T) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this type strain was assembled and yielded a length of 3.72 Mbp and a GC content of 46.3%. Comparative genomic analysis with its ...

  16. EPA Analysis Shows Decreased Toxic Chemical Releases in Massachusetts in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Massachusetts, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  17. EPA Analysis Shows Increased Toxic Chemical Releases in Vermont in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Vermont, the reporting data show that overall releases of pollutants to the environment increased since the previous reporting year (2014).

  18. EPA Analysis Shows Increased Toxic Chemical Releases in Rhode Island in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Rhode Island, the reporting data show that overall releases of pollutants to the environment increased since the previous reporting year (2014).

  19. EPA Analysis Shows Decreased Toxic Chemical Releases in Connecticut in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Connecticut, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  20. EPA Analysis Shows Decreased Toxic Chemical Releases in Maine in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Maine, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  1. SU-8 hollow cantilevers for AFM cell adhesion studies

    NASA Astrophysics Data System (ADS)

    Martinez, Vincent; Behr, Pascal; Drechsler, Ute; Polesel-Maris, Jérôme; Potthoff, Eva; Vörös, Janos; Zambelli, Tomaso

    2016-05-01

    A novel fabrication method was established to produce flexible, transparent, and robust tipless hollow atomic force microscopy (AFM) cantilevers made entirely from SU-8. Channels of 3 μm thickness and several millimeters length were integrated into 12 μm thick and 40 μm wide cantilevers. Connected to a pressure controller, the devices showed high sealing performance with no leakage up to 6 bars. Changing the cantilever lengths from 100 μm to 500 μm among the same wafer allowed the targeting of various spring constants ranging from 0.5 to 80 N m-1 within a single fabrication run. These hollow polymeric AFM cantilevers were operated in the optical beam deflection configuration. To demonstrate the performance of the device, single-cell force spectroscopy experiments were performed with a single probe detaching in a serial protocol more than 100 Saccharomyces cerevisiae yeast cells from plain glass and glass coated with polydopamine while measuring adhesion forces in the sub-nanoNewton range. SU-8 now offers a new alternative to conventional silicon-based hollow cantilevers with more flexibility in terms of complex geometric design and surface chemistry modification.

  2. Enabling accurate gate profile control with inline 3D-AFM

    NASA Astrophysics Data System (ADS)

    Bao, Tianming; Lopez, Andrew; Dawson, Dean

    2009-05-01

    The logic and memory semiconductor device technology strives to follow the aggressive ITRS roadmap. The ITRS calls for increased 3D metrology to meet the demand for tighter process control at 45nm and 32nm nodes. In particular, gate engineering has advanced to a level where conventional metrology by CD-SEM and optical scatterometry (OCD) faces fundamental limitations without involvement of 3D atomic force microscope (3D-AFM or CD-AFM). This paper reports recent progress in 3D-AFM to address the metrology need to control gate dimension in MOSFET transistor formation. 3D-AFM metrology measures the gate electrode at post-etch with the lowest measurement uncertainty for critical gate geometry, including linewidth, sidewall profile, sidewall angle (SWA), line width roughness (LWR), and line edge roughness (LER). 3D-AFM enables accurate gate profile control in three types of metrology applications: reference metrology to validate CD-SEM and OCD, inline depth or 3D monitoring, or replacing TEM for 3D characterization for engineering analysis.

  3. AFM study of forces between silica, silicon nitride and polyurethane pads.

    PubMed

    Sokolov, Igor; Ong, Quy K; Shodiev, Hasan; Chechik, Nina; James, David; Oliver, Mike

    2006-08-15

    Interaction of silica and silicon nitride with polyurethane surfaces is rather poorly studied despite being of great interest for modern semiconductor industry, e.g., for chemical-mechanical planarization (CMP) processes. Here we show the results from the application of the atomic force microscopy (AFM) technique to study the forces between silica or silicon nitride (AFM tips) and polyurethane surfaces in aqueous solutions of different acidity. The polyurethane surface potentials are derived from the measured AFM data. The obtained potentials are in rather good agreement with measurements of zeta-potentials using the streaming-potentials method. Another important parameter, adhesion, is also measured. While the surface potentials of silica are well known, there are ambiguous results on the potentials of silicon nitride that is naturally oxidized. Deriving the surface potential of the naturally oxidized silicon nitride from our measurements, we show that it is not oxidized to silica despite some earlier published expectations.

  4. The Coordination of Verbal and Nonverbal Interaction towards Three Parties: The Analysis of a Talk Show.

    ERIC Educational Resources Information Center

    von Raffler-Engel, Walburga

    A study of randomly selected "Donahue" shows revealed how host Phil Donahue interacts with several parties at one time and how he subordinates various interactions to suit the hierarchy of importance he attributes to each party, with the television viewer being the most important. Donahue organizes his body movement mainly for television…

  5. Molecular analysis of mixed endometrial carcinomas shows clonality in most cases

    PubMed Central

    Hoang, Lien N.; Almadani, Noorah; Li, Xiaodong; Soslow, Robert A; Gilks, C. Blake; Lee, Cheng-Han

    2016-01-01

    Mixed endometrial carcinoma refers to a tumor that is comprised of two or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas - 11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade endometrioid carcinomas (CCC/EC), and 2 mixed clear cell and serous carcinoma (CCC/SC), using targeted next generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin. Eight cases (6 EC/SC, 1 EC/CCC and 1 SC/CCC) showed a serous carcinoma molecular profile that was the same in both components. Five cases (3 CCC/EC and 2 SC/EC) showed a shared endometrioid molecular profile and identical mismatch repair protein (MMR) deficiency in both components. A single SC/EC case harbored the same POLE exonuclease domain mutation in both components. One SC/CCC and one EC/CCC case showed both shared and unique molecular features in the two histotype components, suggesting early molecular divergence from a common clonal origin. In two cases, there were no shared molecular features and these appear to be biologically unrelated synchronous tumors. Overall, these results show that the different histologic components in mixed endometrial carcinomas typically share the same molecular aberrations. Mixed endometrial carcinomas most commonly occur through morphological mimicry, whereby tumors with serous-type molecular profile show morphological features of endometrioid or clear cell carcinoma, or through underlying deficiency in DNA nucleotide repair, with resulting rapid accrual of mutations and intratumoral phenotypic heterogeneity. Less commonly, mixed endometrial carcinomas are the result of early molecular divergence from a common progenitor clone or are synchronous biologically unrelated tumors (collision tumors). PMID:26492180

  6. Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees

    PubMed Central

    Hobaiter, Catherine; Poisot, Timothée; Zuberbühler, Klaus; Hoppitt, William; Gruber, Thibaud

    2014-01-01

    Social network analysis methods have made it possible to test whether novel behaviors in animals spread through individual or social learning. To date, however, social network analysis of wild populations has been limited to static models that cannot precisely reflect the dynamics of learning, for instance, the impact of multiple observations across time. Here, we present a novel dynamic version of network analysis that is capable of capturing temporal aspects of acquisition—that is, how successive observations by an individual influence its acquisition of the novel behavior. We apply this model to studying the spread of two novel tool-use variants, “moss-sponging” and “leaf-sponge re-use,” in the Sonso chimpanzee community of Budongo Forest, Uganda. Chimpanzees are widely considered the most “cultural” of all animal species, with 39 behaviors suspected as socially acquired, most of them in the domain of tool-use. The cultural hypothesis is supported by experimental data from captive chimpanzees and a range of observational data. However, for wild groups, there is still no direct experimental evidence for social learning, nor has there been any direct observation of social diffusion of behavioral innovations. Here, we tested both a static and a dynamic network model and found strong evidence that diffusion patterns of moss-sponging, but not leaf-sponge re-use, were significantly better explained by social than individual learning. The most conservative estimate of social transmission accounted for 85% of observed events, with an estimated 15-fold increase in learning rate for each time a novice observed an informed individual moss-sponging. We conclude that group-specific behavioral variants in wild chimpanzees can be socially learned, adding to the evidence that this prerequisite for culture originated in a common ancestor of great apes and humans, long before the advent of modern humans. PMID:25268798

  7. SR-FTIR Coupled with Principal Component Analysis Shows Evidence for the Cellular Bystander Effect.

    PubMed

    Lipiec, E; Bambery, K R; Lekki, J; Tobin, M J; Vogel, C; Whelan, D R; Wood, B R; Kwiatek, W M

    2015-07-01

    Synchrotron radiation-Fourier transform infrared (SR-FTIR) microscopy coupled with multivariate data analysis was used as an independent modality to monitor the cellular bystander effect. Single, living prostate cancer PC-3 cells were irradiated with various numbers of protons, ranging from 50-2,000, with an energy of either 1 or 2 MeV using a proton microprobe. SR-FTIR spectra of cells, fixed after exposure to protons and nonirradiated neighboring cells (bystander cells), were recorded. Spectral differences were observed in both the directly targeted and bystander cells and included changes in the DNA backbone and nucleic bases, along with changes in the protein secondary structure. Principal component analysis (PCA) was used to investigate the variance in the entire data set. The percentage of bystander cells relative to the applied number of protons with two different energies was calculated. Of all the applied quantities, the dose of 400 protons at 2 MeV was found to be the most effective for causing significant macromolecular perturbation in bystander PC-3 cells.

  8. Complete genome sequence analysis of goatpox virus isolated from China shows high variation.

    PubMed

    Zeng, Xiancheng; Chi, Xuelin; Li, Wei; Hao, Wenbo; Li, Ming; Huang, Xiaohong; Huang, Yifan; Rock, Daniel L; Luo, Shuhong; Wang, Shihua

    2014-09-17

    Goatpox virus (GTPV), a member of the Capripoxvirus genus of the Poxviridae family, is the causative agent of variolo caprina (goatpox). GTPV can cause significant economic losses of domestic ruminants in endemic regions and can threaten breeding stocks. In this study, we report on the compilation of the complete genomic sequence of an isolated GTPV field strain FZ (GTPV_FZ). The 150,194bp GTPV genome consists of a central coding region bounded by two identical 2301bp inverted terminal repeats and contains 151 putative genes. Comparative genomic analysis reveals the apparent genetic relationships among Capripoxviruses are close, but sufficient genomic variants in the field isolate strain FZ have been identified to distinguish it from other GTPV strains and other Capripoxvirus species. Phylogenetic analysis based on the p32 and complete GTPV genome can be used to differentiate SPPVs, GTPVs and LSDVs. These data may contribute to the epidemiological study of the Chinese capripoxvirus and help to develop more specific detection methods to distinguish GTPVs, SPPVs and LSDVs.

  9. Integrated single-cell analysis shows Pichia pastoris secretes protein stochastically.

    PubMed

    Love, Kerry Routenberg; Panagiotou, Vasiliki; Jiang, Bo; Stadheim, Terrance A; Love, J Christopher

    2010-06-01

    The production of heterologous proteins by secretion from cellular hosts is an important determinant for the cost of biotherapeutics. A single-cell analytical method called microengraving was used to examine the heterogeneity in secretion by the methylotrophic yeast Pichia pastoris. We show that constitutive secretion of a human Fc fragment by P. pastoris is not cell-cycle dependent, but rather fluctuates between states of high and low productivity in a stochastic manner.

  10. Ultrastructural analysis of Vitis vinifera leaf tissues showing atypical symptoms of Plasmopara viticola.

    PubMed

    Musetti, R; Stringher, L; Borselli, S; Vecchione, A; Zulini, L; Pertot, I

    2005-01-01

    In an abandoned farm in Tuscany a year by year regression of downy mildew disease on grapevines was observed and a decrease in virulence as well as vigor and fertility of the causal fungus, Plasmopara viticola. Anomalous spots of the fungus (i.e. atypical coloration of leaves or mosaic) on leaf tissues of a sensitive Vitis vinifera grapevine were observed. The anomalous symptoms were often associated with the typical 'oil spots' and were present under environmental conditions favourable for a normal development of the disease. An ultrastructural study was carried out on leaf tissues of grapevine plants aimed at clarifying the cause of this phenomenon and detecting whether there were alterations in P. viticola mycelium and endophytes present. ELISA was also performed to check the presence of grapevine viruses in the plants. TEM results demonstrated that characteristic P. viticola was present in leaf samples showing oil spots, while, both the fungus and the host tissues showed cytological alterations in leaves with mosaic symptoms. Finally, hyphae were absent in leaf tissues without downy mildew spots, but showing severe ultrastructural modifications. Several plant virus infections were found in these grapevines. Literature reports that the development and sporulation of some phytopathogenic fungi inside their hosts can be limited by virus infections. Further experimental approaches are required to determine if resistance to P. viticola can be induced by viral infections in grapevines.

  11. Multiparametric high-resolution imaging of native proteins by force-distance curve-based AFM.

    PubMed

    Pfreundschuh, Moritz; Martinez-Martin, David; Mulvihill, Estefania; Wegmann, Susanne; Muller, Daniel J

    2014-05-01

    A current challenge in the life sciences is to understand how the properties of individual molecular machines adjust in order to meet the functional requirements of the cell. Recent developments in force-distance (FD) curve-based atomic force microscopy (FD-based AFM) enable researchers to combine sub-nanometer imaging with quantitative mapping of physical, chemical and biological properties. Here we present a protocol to apply FD-based AFM to the multiparametric imaging of native proteins under physiological conditions. We describe procedures for experimental FD-based AFM setup, high-resolution imaging of proteins in the native unperturbed state with simultaneous quantitative mapping of multiple parameters, and data interpretation and analysis. The protocol, which can be completed in 1-3 d, enables researchers to image proteins and protein complexes in the native unperturbed state and to simultaneously map their biophysical and biochemical properties at sub-nanometer resolution.

  12. BOREAS AFM-6 Boundary Layer Height Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) site. This data set provides boundary layer height information over the site. The data were collected from 21 May 1994 to 20 Sep 1994 and are stored in tabular ASCII files. The boundary layer height data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  13. BOREAS AFM-06 Mean Wind Profile Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Administration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) tower from 21 May 1994 to 20 Sep 1994. The data set provides wind profiles at 38 heights, containing the variables of wind speed; wind direction; and the u-, v-, and w-components of the total wind. The data are stored in tabular ASCII files. The mean wind profile data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  14. BOREAS AFM-06 Mean Temperature Profile Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) tower from 21 May 1994 to 20 Sep 1994. The data set provides temperature profiles at 15 heights, containing the variables of virtual temperature, vertical velocity, the speed of sound, and w-bar. The data are stored in tabular ASCII files. The mean temperature profile data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  15. Cryogenic AFM-STM for mesoscopic physics

    NASA Astrophysics Data System (ADS)

    Le Sueur, H.

    Electronic spectroscopy based on electron tunneling gives access to the electronic density of states (DOS) in conductive materials, and thus provides detailed information about their electronic properties. During this thesis work, we have developed a microscope in order to perform spatially resolved (10 nm) tunneling spectroscopy, with an unprecedented energy resolution (10 μeV), on individual nanocircuits. This machine combines an Atomic Force Microscope (AFM mode) together with a Scanning Tunneling Spectroscope (STS mode) and functions at very low temperatures (30 mK). In the AFM mode, the sample topography is recorded using a piezoelectric quartz tuning fork, which allows us to locate and image nanocircuits. Tunneling can then be performed on conductive areas of the circuit. With this microscope, we have measured the local DOS in a hybrid Superconductor-Normal metal-Superconductor (S-N-S) structure. In such circuit, the electronic properties of N and S are modified by the superconducting proximity effect. In particular, for short N wires, we have observed a minigap independent of position in the DOS of the N wire, as was previously predicted. Moreover, when varying the superconducting phase difference between the S electrodes, we have measured the modification of the minigap and its disappearance when the phase difference equals π. Our experimental results for the DOS, and its dependences (on phase, position, N length), are quantitatively accounted for by the quasiclassical theory of superconductivity. Some predictions of this theory are observed for the first time. La spectroscopie électronique basée sur l'effet tunnel donne accès à la densité d'états des électrons (DOS) dans les matériaux conducteurs, et renseigne ainsi en détail sur leurs propriétés électroniques. Au cours de cette thèse, nous avons développé un microscope permettant d'effectuer la spectroscopie tunnel résolue spatialement (10 nm) de nanocircuits individuels, avec une r

  16. Mutant AFM 2 of Alcaligenes faecalis for phenol biodegradation using He-Ne laser irradiation.

    PubMed

    Jiang, Yan; Wen, Jianping; Caiyin, Qinggele; Lin, Liangcai; Hu, Zongding

    2006-11-01

    He-Ne laser technology was utilized in this study to investigate the response of Alcaligenes faecalis to laser stimulation. The irradiation experiments were conducted by the adjustment of the output power from 5 to 25 mW and the exposure time from 5 to 25 min. The results showed that the survival rate changed regularly with the variety of irradiation dose, and high positive mutation frequency was determined by both the energy density and the output power. The mutant strain AFM 2 was obtained. Phenol biodegradation assay demonstrated that AFM 2 possessed a more prominent phenol-degrading potential than its parent strain, which presumably attributed to the improvements of phenol hydroxylase and catechol 1,2-dioxygenase activities. The phenol of 2000 mgl(-1) was completely degraded by AFM 2 within 85.5h at 30 degrees C. In addition, the cell growth and phenol degradation kinetics of the mutant strain AFM 2 and its parent strain in batch cultures were also investigated at the wide initial phenol concentration ranging from 0 to 2000 mgl(-1) by Haldane model. The results of these experiments further demonstrated that the mutant strain AFM 2 possessed a higher capacity to resist phenol.

  17. Quantitating membrane bleb stiffness using AFM force spectroscopy and an optical sideview setup.

    PubMed

    Gonnermann, Carina; Huang, Chaolie; Becker, Sarah F; Stamov, Dimitar R; Wedlich, Doris; Kashef, Jubin; Franz, Clemens M

    2015-03-01

    AFM-based force spectroscopy in combination with optical microscopy is a powerful tool for investigating cell mechanics and adhesion on the single cell level. However, standard setups featuring an AFM mounted on an inverted light microscope only provide a bottom view of cell and AFM cantilever but cannot visualize vertical cell shape changes, for instance occurring during motile membrane blebbing. Here, we have integrated a mirror-based sideview system to monitor cell shape changes resulting from motile bleb behavior of Xenopus cranial neural crest (CNC) cells during AFM elasticity and adhesion measurements. Using the sideview setup, we quantitatively investigate mechanical changes associated with bleb formation and compared cell elasticity values recorded during membrane bleb and non-bleb events. Bleb protrusions displayed significantly lower stiffness compared to the non-blebbing membrane in the same cell. Bleb stiffness values were comparable to values obtained from blebbistatin-treated cells, consistent with the absence of a functional actomyosin network in bleb protrusions. Furthermore, we show that membrane blebs forming within the cell-cell contact zone have a detrimental effect on cell-cell adhesion forces, suggesting that mechanical changes associated with bleb protrusions promote cell-cell detachment or prevent adhesion reinforcement. Incorporating a sideview setup into an AFM platform therefore provides a new tool to correlate changes in cell morphology with results from force spectroscopy experiments.

  18. Morphology of Vapor-Deposited Ice at Low Temperatures by Atomic Force Microscopy (AFM)

    NASA Astrophysics Data System (ADS)

    Fain, , Jr.; Donev, J. M. K.; Tait, B. R. Long, Jr.; Yu, Q.

    2002-03-01

    The morphology of multilayer films of ice on various substrates is measured by AFM as a function of vapor-deposition and annealing temperatures below 150K. The films are deposited in-situ in UHV from an effusive doser at 67 degrees from the surface normal. For depositions near 100K on clean Au(111), previous measurements by Donev et al. using needle-sensor AFM indicate that 3-D clustering starts near 120K for initially flat thin films of amorphous solid water (ASW). For depositions below 85K on clean Au(111), preliminary measurements using non-contact AFM (nc-AFM) indicate that clustering does not occur during annealing until bulk diffusion becomes operative at T>140K. Deposition at glancing angle at the lower temperatures is known to increase porosity and is also expected to decrease the number of crystalline nuclei in the ASW. For depositions near 100K on mica that had been annealed in UHV, preliminary measurements using ncAFM show clustering near 120K. Supported by U. W. Nanotechnology Fellowship (J.M.K.D.), Mary Gates Fellowship (B. R. L.), and M. J. Murdock Charitable Trust.

  19. Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

    PubMed Central

    2012-01-01

    Background Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far. Results A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism. Conclusions The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency. PMID:22433273

  20. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

    PubMed Central

    2011-01-01

    Background In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach. Results The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL. Conclusions Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in

  1. Visualization of internal structure of banana starch granule through AFM.

    PubMed

    Peroni-Okita, Fernanda H G; Gunning, A Patrick; Kirby, Andrew; Simão, Renata A; Soares, Claudinéia A; Cordenunsi, Beatriz R

    2015-09-05

    Atomic force microscopy (AFM) is a high resolution technique for studying the external and internal structures of starch granules. For this purpose granules were isolated from bananas and embedded in a non-penetrating resin. To achieve image contrast of the ultrastructure, the face of the cut blocks were wetted in steam and force modulation mode imaging was used. Images of starch from green bananas showed large variation of height across the granule due to a locational specific absorption of water and swelling of amorphous regions; the data reveal that the center of the granules are structurally different and have different viscoelastic properties. Images of starches from ripe bananas showed an even greater different level of organization: absence of growth rings around the hilum; the central region of the granule is richer in amylose; very porous surface with round shaped dark structures; the size of blocklets are larger than the green fruits.

  2. AMS 14C analysis of teeth from archaeological sites showing anomalous esr dating results

    NASA Astrophysics Data System (ADS)

    Grün, Rainer; Abeyratne, Mohan; Head, John; Tuniz, Claudio; Hedges, Robert E. M.

    We have carried out AMS radiocarbon analysis on two groups of samples: the first one gave reasonable ESR age estimates and the second one yielded serious age underestinations. All samples were supposedly older than 35 ka, the oldest being around 160 ka. Two pretreatment techniques were used for radiocarbon dating: acid evolution and thermal release. Heating to 600, 750 and 900°C combined with total de-gassing at these temperatures was chosen to obtain age estimates on the organic fraction, secondary carbonates and original carbonate present in the hydroxyapatite mineral phase, respectively. All radiocarbon results present serious age underestimations. The secondary carbonate fraction gives almost modern results indicating an extremely rapid exchange of this component. Owing to this very rapid carbonate exchange it is not likely that the ESR signals used for dating are associated with the secondary carbonates. One tooth from Tabun with independent age estimates of >150 ka was further investigated by the Oxford AMS laboratory, yielding an age estimate of 1930±100 BP on the residual collagen from dentine and 18,000±160 BP on the carbonate component of the enamel bioapatite. We did not, however, find an explanation of why some samples give serious ESR underestimatioils whilst many others provide reasonable results.

  3. PCR-DGGE analysis of the bacterial composition of a kaolin slurry showing altered rheology.

    PubMed

    Papp, Ildikó; Balázs, Margit; Tombácz, Etelka; Babcsán, Norbert; Kesserű, Péter; Kiss, István; Szvetnik, Attila

    2012-04-01

    Kaolin is an important industrial raw material and a basis of a range of different products. Microbial spoilage is a detrimental process observed especially in kaolin slurries, leading to low quality products and economic loss. Although the alteration of kaolin slurries in ceramic industry was observed, the process and the microbial background have not been analyzed in details. This study provides the first data using a cultivation independent molecular biological approach (PCR-DGGE) regarding the bacterial composition of an altered kaolin slurry. The results show that potential exopolymer (EPS) producer bacteria (e.g. Acinetobacter, Pseudomonas) appear in the altered kaolin slurry, which may have an important role in the modification of kaolin slurries.

  4. Retrospective Analysis of Patient Presentations at the Sydney (Australia) Royal Easter Show from 2012 to 2014.

    PubMed

    Crabtree, Nathan; Mo, Shirley; Ong, Leon; Jegathees, Thuvarahan; Wei, Daniel; Fahey, David; Liu, Jia Jenny

    2017-04-01

    Introduction Comprehensive studies on the relationship between patient demographics and subsequent treatment and disposition at a single mass-gathering event are lacking. The Sydney Royal Easter Show (SRES; Sydney Olympic Park, New South Wales, Australia) is an annual, 14-day, agricultural mass-gathering event occurring around the Easter weekend, attracting more than 800,000 patrons per year. In this study, patient records from the SRES were analyzed to examine relationships between weather, crowd size, day of week, and demographics on treatment and disposition. This information would help to predict factors affecting patient treatment and disposition to guide ongoing training of first responders and to evaluate the appropriateness of staffing skills mix at future events. Hypothesis Patient demographics, environmental factors, and attendance would influence the nature and severity of presentations at the SRES, which would influence staffing requirements.

  5. Analysis of Cylinder-pressure-indicator Diagrams Showing Effects of Mixture Strength and Spark Timing

    NASA Technical Reports Server (NTRS)

    Gerrish, Harold C; Voss, Fred

    1940-01-01

    An investigation was made to determine the effect of mixture strength and of normal as well as optimum spark timing on the combustion, on the cylinder temperature, and on the performance characteristics of an engine. A single-cylinder test unit utilizing an air-cooled cylinder and a carburetor and operating with gasoline having an octane rating of 92 was used. The investigation covered a range of fuel-air ratios from 0.053 to 0.118. Indicator diagrams and engine-performance data were taken for each change in engine conditions. Examination of the indicator shows that for fuel-air ratios less than and greater than 0.082 the rate and the amount of effective fuel burned decreased. For a fuel-air ratio of 0.118 the combustion efficiency was only 58 percent. Advancing the spark timing increased the rate of pressure rise. This effect was more pronounced with leaner mixtures.

  6. Aflatoxin M1 Concentration in Various Dairy Products: Evidence for Biologically Reduced Amount of AFM1 in Yoghurt

    PubMed Central

    RAHIMIRAD, Amir; MAALEKINEJAD, Hassan; OSTADI, Araz; YEGANEH, Samal; FAHIMI, Samira

    2014-01-01

    Abstract Background Aflatoxin M1 (AFM1), a carcinogenic substance is found in milk and dairy products. The effect of season and type of dairy products on AFMi level in northern Iran was investigated in this study. Methods Three hundred samples (each season 75 samples) including raw and pasteurized milk, yoghurt, cheese, and cream samples were collected from three distinct milk producing farms. The samples were subjected to chemical and solid phase extractions and were analyzed by using HPLC technique. Recovery percentages, limit of detection and limit of quantification values were determined. Results Seventy percent and 98% were the minimum and maximum recoveries for cheese and raw milk, respectively and 0.021 and 0.063 ppb were the limit of detection and limit of quantification values for AFM1. We found that in autumn and winter the highest level (0.121 ppb) of AFM1 in cheese and cream samples and failed to detect any AFM1 in spring samples. Interestingly, our data showed that the yoghurt samples had the lowest level of AFM1 in all seasons. Conclusion There are significant differences between the AFM1 levels in dairy products in various seasons and also various types of products, suggesting spring and summer yoghurt samples as the safest products from AFM1 level point of view. PMID:25927044

  7. Retrospective analysis showing the water method increased adenoma detection rate — a hypothesis generating observation

    PubMed Central

    Leung, Joseph W; Do, Lynne D; Siao-Salera, Rodelei M; Ngo, Catherine; Parikh, Dhavan A; Mann, Surinder K

    2011-01-01

    Background A water method developed to attenuate discomfort during colonoscopy enhanced cecal intubation in unsedated patients. Serendipitously a numerically increased adenoma detection rate (ADR) was noted. Objective To explore databases of sedated patients examined by the air and water methods to identify hypothesis-generating findings. Design: Retrospective analysis. Setting: VA endoscopy center. Patients: creening colonoscopy. Interventions: From 1/2000–6/2006 the air method was used - judicious air insufflation to permit visualization of the lumen to aid colonoscope insertion and water spray for washing mucosal surfaces. From 6/2006–11/2009 the water method was adopted - warm water infusion in lieu of air insufflation and suction removal of residual air to aid colonoscope insertion. During colonoscope withdrawal adequate air was insufflated to distend the colonic lumen for inspection, biopsy and polypectomy in a similar fashion in both periods. Main outcome measurements: ADR. Results The air (n=683) vs. water (n=495) method comparisons revealed significant differences in overall ADR 26.8% (183 of 683) vs. 34.9% (173 of 495) and ADR of adenomas >9 mm, 7.2% vs. 13.7%, respectively (both P<0.05, Fisher's exact test). Limitations: Non-randomized data susceptible to bias by unmeasured parameters unrelated to the methods. Conclusion Confirmation of the serendipitous observation of an impact of the water method on ADR provides impetus to call for randomized controlled trials to test hypotheses related to the water method as an approach to improving adenoma detection. Because of recent concerns over missed lesions during colonoscopy, the provocative hypothesis-generating observations warrant presentation. PMID:21686105

  8. Lead-iodide nanowire perovskite with methylviologen showing interfacial charge-transfer absorption: a DFT analysis.

    PubMed

    Fujisawa, Jun-ichi; Giorgi, Giacomo

    2014-09-07

    Methylviologen lead-iodide perovskite (MVPb2I6) is a self-assembled one-dimensional (1-D) material consisting of lead-iodide nanowires and intervening organic electron-accepting molecules, methylviologen (MV(2+)). MVPb2I6 characteristically shows optical interfacial charge-transfer (ICT) transitions from the lead-iodide nanowire to MV(2+) in the visible region and unique ambipolar photoconductivity, in which electrons are transported through the three-dimensional (3-D) organic network and holes along the 1-D lead-iodide nanowire. In this work, we theoretically study the electronic band-structure and photocarrier properties of MVPb2I6 by density functional theory (DFT) calculations. Our results clearly confirm the experimentally reported type-II band alignment, whose valence band mainly consists of 5p (I) orbitals of the lead-iodide nanowires and the conduction band of the lowest unoccupied molecular orbital of MV(2+). The DFT calculation also reveals weak charge-transfer interactions between the lead-iodide nanowires and MV(2+). In addition, the electronic distributions of the valence and conduction bands indicate the 3-D transport of electrons and 1-D transport of holes, supporting the reported experimental result.

  9. Transcriptome analysis of Bifidobacterium longum strains that show a differential response to hydrogen peroxide stress.

    PubMed

    Oberg, Taylor S; Ward, Robert E; Steele, James L; Broadbent, Jeff R

    2015-10-20

    Consumer and commercial interest in foods containing probiotic bifidobacteria is increasing. However, because bifidobacteria are anaerobic, oxidative stress can diminish cell viability during production and storage of bioactive foods. We previously found Bifidobacterium longum strain NCC2705 had significantly greater intrinsic and inducible resistance to hydrogen peroxide (H2O2) than strain D2957. Here, we explored the basis for these differences by examining the transcriptional responses of both strains to sub-lethal H2O2 exposure for 5- or 60-min. Strain NCC2705 had 288 genes that were differentially expressed after the 5-min treatment and 114 differentially expressed genes after the 60-min treatment. In contrast, strain D2957 had only 21 and 90 differentially expressed genes after the 5- and 60-min treatments, respectively. Both strains showed up-regulation of genes coding enzymes implicated in oxidative stress resistance, such as thioredoxin, thioredoxin reductase, peroxiredoxin, ferredoxin, glutaredoxin, and anaerobic ribonucleotide reductase, but induction levels were typically highest in NCC2705. Compared to D2957, NCC2705 also had more up-regulated genes involved in transcriptional regulation and more down-regulated genes involved in sugar transport and metabolism. These results provide a greater understanding of the molecular basis for oxidative stress resistance in B. longum and the factors that contribute to strain-to-strain variability in survival in bioactive food products.

  10. AFM, SEM and TEM Studies on Porous Anodic Alumina

    PubMed Central

    2010-01-01

    Porous anodic alumina (PAA) has been intensively studied in past decade due to its applications for fabricating nanostructured materials. Since PAA’s pore diameter, thickness and shape vary too much, a systematical study on the methods of morphology characterization is meaningful and essential for its proper development and utilization. In this paper, we present detailed AFM, SEM and TEM studies on PAA and its evolvements with abundant microstructures, and discuss the advantages and disadvantages of each method. The sample preparation, testing skills and morphology analysis are discussed, especially on the differentiation during characterizing complex cross-sections and ultrasmall nanopores. The versatility of PAAs is also demonstrated by the diversity of PAAs’ microstructure. PMID:20672104

  11. AFM, SEM and TEM Studies on Porous Anodic Alumina

    NASA Astrophysics Data System (ADS)

    Zhu, Yuan Yuan; Ding, Gu Qiao; Ding, Jian Ning; Yuan, Ning Yi

    2010-04-01

    Porous anodic alumina (PAA) has been intensively studied in past decade due to its applications for fabricating nanostructured materials. Since PAA’s pore diameter, thickness and shape vary too much, a systematical study on the methods of morphology characterization is meaningful and essential for its proper development and utilization. In this paper, we present detailed AFM, SEM and TEM studies on PAA and its evolvements with abundant microstructures, and discuss the advantages and disadvantages of each method. The sample preparation, testing skills and morphology analysis are discussed, especially on the differentiation during characterizing complex cross-sections and ultrasmall nanopores. The versatility of PAAs is also demonstrated by the diversity of PAAs’ microstructure.

  12. Transcriptome Analysis Showed a Differential Signature between Invasive and Non-invasive Corticotrophinomas

    PubMed Central

    de Araújo, Leonardo Jose Tadeu; Lerario, Antonio Marcondes; de Castro, Margaret; Martins, Clarissa Silva; Bronstein, Marcello Delano; Machado, Marcio Carlos; Trarbach, Ericka Barbosa; Villares Fragoso, Maria Candida Barisson

    2017-01-01

    ACTH-dependent hypercortisolism caused by a pituitary adenoma [Cushing’s disease (CD)] is the most common cause of endogenous Cushing’s syndrome. CD is often associated with several morbidities, including hypertension, diabetes, osteoporosis/bone fractures, secondary infections, and increased cardiovascular mortality. While the majority (≈80%) of the corticotrophinomas visible on pituitary magnetic resonance imaging are microadenomas (MICs, <10 mm of diameter), some tumors are macroadenomas (MACs, ≥10 mm) with increased growth potential and invasiveness, exceptionally exhibiting malignant demeanor. In addition, larger and invasive MACs are associated with a significant increased risk of local complications, such as hypopituitarism and visual defects. Given the clinical and molecular heterogeneity of corticotrophinomas, the aim of this study was to investigate the pattern of genetic differential expression between MIC and MAC, including the invasiveness grade as a criterion for categorizing these tumors. In this study, were included tumor samples from patients with clinical, laboratorial, radiological, and histopathological diagnosis of hypercortisolism due to an ACTH-producing pituitary adenoma. Differential gene expression was studied using an Affymetrix microarray platform in 12 corticotrophinomas, classified as non-invasive MIC (n = 4) and MAC (n = 5), and invasive MAC (n = 3), according to modified Hardy criteria. Somatic mutations in USP8 were also investigated, but none of the patients exhibited USP8 variants. Differential expression analysis demonstrated that non-invasive MIC and MAC have a similar genetic signature, while invasive MACs exhibited a differential expression profile. Among the genes differentially expressed, we highlighted CCND2, ZNF676, DAPK1, and TIMP2, and their differential expression was validated through quantitative real-time PCR in another cohort of 15 non-invasive and 3 invasive cortocotrophinomas. We also

  13. An AFM study of calcite dissolution in concentrated electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Ruiz Agudo, E.; Putnis, C. V.; Putnis, A.; Rodriguez-Navarro, C.

    2009-04-01

    Calcite-solution interactions are of a paramount importance in a range of processes such as the removal of heavy metals, carbon dioxide sequestration, landscape modeling, weathering of building stone and biomineralization. Water in contact with minerals often carries significant amounts of solutes; additionally, their concentration may vary due to evaporation and condensation. It is well known that calcite dissolution is affected dramatically by the presence of such solutes. Here we present investigations on the dissolution of calcite in the presence of different electrolytes. Both bulk (batch reactors) experiments and nanoscale (in situ AFM) techniques are used to study the dissolution of calcite in a range of solutions containing alkaly cations balanced by halide anions. Previous works have indicated that the ionic strength has little influence in calcite dissolution rates measured from bulk experiments (Pokrovsky et al. 2005; Glendhill and Morse, 2004). Contrary to these results, our quantitative analyses of AFM observations show an enhancement of the calcite dissolution rate with increasing electrolyte concentration. Such an effect is concentration-dependent and it is most evident in concentrated solutions. AFM experiments have been carried out in a fluid cell using calcite cleavage surfaces in contact with solutions of simple salts of the alkaly metals and halides at different undersaturations with respect to calcite to try to specify the effect of the ionic strength on etch pit spreading rate and calcite dissolution rate. These results show that the presence of soluble salts may critically affect the weathering of carbonate rocks in nature as well as the decay of carbonate stone in built cultural heritage. References: Pokrosky, O.S.; Golubev, S.V.; Schott, J. Dissolution kinetics of calcite, dolomite and magnesite at 25°C and 0 to 50 atm pCO2. Chemical Geology, 2005, 217 (3-4) 239-255. Glendhill, D.K.; Morse, J.W. Dissolution kinetics of calcite in Na

  14. SPR and AFM study of engineered biomolecule immobilisation techniques.

    PubMed

    Craig, Ian; McLaughlin, James A

    2006-01-01

    A comparative study into two novel and diverse schemes designed to improve immobilization of biomolecules for biosensing purposes is presented. In the first method a silicon rich matrix is created using PECVD. The second method involves creating nano-patterns on the sensor surface to create a large number of surface discontinuities to which the proteins will bind preferentially. The basic theory of SPR is provided to show the importance of the surface sensitive nature of this optical transduction technique. The present work suggests that both may prove both for SPR and other biosensing applications. Of the two schemes proposed, the results for nano-patterning seem to suggest that it is promoting better surface attachment of biomolecules. The results of SPR and AFM studies are presented that have shown that each of these schemes promotes improved binding of various proteins.

  15. Study of the sensitivity and resonant frequency of the torsional modes of an AFM cantilever with a sidewall probe based on a nonlocal elasticity theory.

    PubMed

    Abbasi, Mohammad; Karami Mohammadi, Ardeshir

    2015-05-01

    A relationship based on a nonlocal elasticity theory is developed to investigate the torsional sensitivity and resonant frequency of an atomic force microscope (AFM) with assembled cantilever probe (ACP). This ACP comprises a horizontal cantilever and a vertical extension, and a tip located at the free end of the extension, which makes the AFM capable of topography at sidewalls of microstructures. First, the governing differential equations of motion and boundary conditions for dynamic analysis are obtained by a combination of the basic equations of nonlocal elasticity theory and Hamilton's principle. Afterward, a closed-form expression for the sensitivity of vibration modes has been obtained using the relationship between the resonant frequency and contact stiffness of cantilever and sample. These analysis accounts for a better representation of the torsional behavior of an AFM with sidewall probe where the small-scale effect are significant. The results of the proposed model are compared with those of classical beam theory. The results show that the sensitivities and resonant frequencies of ACP predicted by the nonlocal elasticity theory are smaller than those obtained by the classical beam theory.

  16. Preparation of DNA and nucleoprotein samples for AFM imaging

    PubMed Central

    Lyubchenko, Yuri L.

    2010-01-01

    Sample preparation techniques allowing reliable and reproducible imaging of DNA with various structures, topologies and complexes with proteins are reviewed. The major emphasis is given to methods utilizing chemical functionalization of mica, enabling preparation of the surfaces with required characteristics. The methods are illustrated by examples of imaging of different DNA structures. Special attention is given to the possibility of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time-lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein-DNA complexes is illustrated by a few examples of imaging site-specific complexes, as well as such systems as chromatin. The time-lapse AFM studies of protein-DNA complexes including very recent advances with the use of high-speed AFM are reviewed. PMID:20864349

  17. Structure and Dynamics of Four-way DNA Junctions Dynamics Revealed by Single-Molecule AFM

    NASA Astrophysics Data System (ADS)

    Lyubchenko, Yuri

    2004-03-01

    For-way DNA junctions (Holliday junctions) are critical intermediates for homologous, site-specific recombination, DNA repair and replication. A wealth of structural information is available for immobile four-way junctions. However, these data cannot give the answer on the mechanism of branch migration, the major property of the Holliday junction. Two models for the mechanism of branch migration were suggested. According to the early model of Alberts-Meselson-Sigal, exchanging DNA strands around the junction remain parallel during branch migration. Kinetic studies of branch migration suggest an alternative model in which the junction adopts an extended conformation. We tested these models using a Holliday junction undergoing branch migration. Note that it was the first time when the dynamics of the four-way DNA junction capable of branch migration had been analyzed. We applied time-lapse atomic force microscopy (single molecule dynamics AFM) to image directly loosely bound DNA at liquid-surface interface. These experiments show that mobile Holliday junctions adopt an unfolded conformation during branch migration. This conformation of the junction remains unchanged until strand separation. The data obtained support the model for branch migration having the extended conformation of the Holliday junction. The analysis of the Holliday junctions dynamics at conditions limiting branch migration revealed a broad movement of the arms suggesting that the range of mobility of these junctions is much wider than detected before. Further applications of the time-lapse AFM approach in attempt to resolve the subpopulations of the junctions conformers and the prospects for analyses of dynamics of complex biological systems will be discussed.

  18. Manufacturing process of nanofluidics using afm probe

    NASA Astrophysics Data System (ADS)

    Karingula, Varun Kumar

    A new process for fabricating a nano fluidic device that can be used in medical application is developed and demonstrated. Nano channels are fabricated using a nano tip in indentation mode on AFM (Atomic Force Microscopy). The nano channels are integrated between the micro channels and act as a filter to separate biomolecules. Nano channels of 4 to7 m in length, 80nm in width, and at varying depths from 100nm to 850 nm allow the resulting device to separate selected groups of lysosomes and other viruses. Sharply developed vertical micro channels are produced from a deep reaction ion etching followed by deposition of different materials, such as gold and polymers, on the top surface, allowing the study of alternative ways of manufacturing a nanofluidic device. PDMS (Polydimethylsiloxane) bonding is performed to close the top surface of the device. An experimental setup is used to test and validate the device by pouring fluid through the channels. A detailed cost evaluation is conducted to compare the economical merits of the proposed process. It is shown that there is a 47:7% manufacturing time savings and a 60:6% manufacturing cost savings.

  19. Microrheology using a custom-made AFM

    NASA Astrophysics Data System (ADS)

    Kosgodagan Acharige, Sebastien; Benzaquen, Michael; Steinberger, Audrey

    In the past few years, a new method was developed to measure local properties of liquids (X. Xiong et al., Phys. Rev. E 80, 2009). This method consists of gluing a micron-sized glass fiber at the tip of an AFM cantilever and probing the liquid with it. In ENS Lyon, this method was perfected (C. Devailly et al., EPL, 106 5, 2014) with the help of an interferometer developped in the same laboratory (L. Bellon et al., Opt. Commun. 207 49, 2002 and P. Paolino et al., Rev. Sci. Instrum. 84, 2013), which background noise can reach 10-14 m /√{ Hz } . This method allows us to measure a wide range of viscosities (1 mPa . s to 500 mPa . s) of transparent and opaque fluids using a small sample volume ( 5 mL). In this presentation, I will briefly describe the interferometer developped in ENS Lyon, then explain precisely the microrheology measurements and then compare the experimental results to a model developped by M. Benzaquen. This work is supported financially by the ANR project NANOFLUIDYN (Grant Number ANR-13-BS10-0009).

  20. BOREAS AFM-07 SRC Surface Meteorological Data

    NASA Technical Reports Server (NTRS)

    Osborne, Heather; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Young, Kim; Wittrock, Virginia; Shewchuck, Stan; Smith, David E. (Technical Monitor)

    2000-01-01

    The Saskatchewan Research Council (SRC) collected surface meteorological and radiation data from December 1993 until December 1996. The data set comprises Suite A (meteorological and energy balance measurements) and Suite B (diffuse solar and longwave measurements) components. Suite A measurements were taken at each of ten sites, and Suite B measurements were made at five of the Suite A sites. The data cover an approximate area of 500 km (North-South) by 1000 km (East-West) (a large portion of northern Manitoba and northern Saskatchewan). The measurement network was designed to provide researchers with a sufficient record of near-surface meteorological and radiation measurements. The data are provided in tabular ASCII files, and were collected by Aircraft Flux and Meteorology (AFM)-7. The surface meteorological and radiation data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  1. AFM tip effect on a thin liquid film.

    PubMed

    Ledesma-Alonso, R; Legendre, D; Tordjeman, Ph

    2013-06-25

    We study the interaction between an AFM probe and a liquid film deposited over a flat substrate. We investigate the effects of the physical and geometrical parameters, with a special focus on the film thickness E, the probe radius R, and the distance D between the probe and the free surface. Deformation profiles have been calculated from the numerical simulations of the Young-Laplace equation by taking into account the probe/liquid and the liquid/substrate interactions, characterized by the Hamaker constants, Hpl and Hls. We demonstrate that the deformation of a shallow film is determined by a particular characteristic length λF = (2πγE(4)/Hls)(1/2), resulting from the balance between the capillary force (γ is the surface tension) and the van der Waals liquid/substrate attraction. For the case of a bulk liquid, the extent of the interface deformation is simply controlled by the capillary length λC = (γ/Δρg)(1/2). These trends point out two asymptotic regimes, which in turn are bounded by two characteristic film thicknesses Eg = (Hls/2πΔρg)(1/4) and Eγ = (R(2)Hls/2πγ)(1/4). For E > Eg, the bulk behavior is recovered, and for E < Eγ, we show the existence of a particular shallow film regime in which a localized tip effect is observed. This tip effect is characterized by the small magnitude of the deformation and an important restriction of its radial extent λF localized below the probe. In addition, we have found that the film thickness has a significant effect on the threshold separation distance Dmin below which the irreversible jump-to-contact process occurs: Dmin is probe radius-dependent for the bulk whereas it is film-thickness-dependent for shallow films. These results have an important impact on the optimal AFM scanning conditions.

  2. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the…

  3. Combined AFM nano-machining and reactive ion etching to fabricate high aspect ratio structures.

    PubMed

    Peng, Ping; Shi, Tielin; Liao, Guanglan; Tang, Zirong

    2010-11-01

    In this paper, a new combined method of sub-micron high aspect ratio structure fabrication is developed which can be used for production of nano imprint template. The process includes atomic force microscope (AFM) scratch nano-machining and reactive ion etching (RIE) fabrication. First, 40 nm aluminum film was deposited on the silicon substrate by magnetron sputtering, and then sub-micron grooves were fabricated on the aluminum film by nano scratch using AFM diamond tip. As aluminum film is a good mask for etching silicon, high aspect ratio structures were finally fabricated by RIE process. The fabricated structures were studied by SEM, which shows that the grooves are about 400 nm in width and 5 microm in depth. To obtain sub-micron scale groove structures on the aluminum film, experiments of nanomachining on aluminum films under various machining conditions were conducted. The depths of the grooves fabricated using different scratch loads were also studied by the AFM. The result shows that the material properties of the film/substrate are elastic-plastic following nearly a bilinear law with isotropic strain hardening. Combined AFM nanomachining and RIE process provides a relative lower cost nano fabrication technique than traditional e-beam lithography, and it has a good prospect in nano imprint template fabrication.

  4. AFM imaging of fenestrated liver sinusoidal endothelial cells.

    PubMed

    Braet, F; Wisse, E

    2012-12-01

    Each microscope with its dedicated sample preparation technique provides the investigator with a specific set of data giving an instrument-determined (or restricted) insight into the structure and function of a tissue, a cell or parts thereof. Stepwise improvements in existing techniques, both instrumental and preparative, can sometimes cross barriers in resolution and image quality. Of course, investigators get really excited when completely new principles of microscopy and imaging are offered in promising new instruments, such as the AFM. The present paper summarizes a first phase of studies on the thin endothelial cells of the liver. It describes the preparation-dependent differences in AFM imaging of these cells after isolation. Special point of interest concerned the dynamics of the fenestrae, thought to filter lipid-carrying particles during their transport from the blood to the liver cells. It also describes the attempts to image the details of these cells when alive in cell cultures. It explains what physical conditions, mainly contributed to the scanning stylus, are thought to play a part in the limitations in imaging these cells. The AFM also offers promising specifications to those interested in cell surface details, such as membrane-associated structures, receptors, coated pits, cellular junctions and molecular aggregations or domains. The AFM also offers nano-manipulation possibilities, strengths and elasticity measurements, force interactions, affinity measurements, stiffness and other physical aspects of membranes and cytoskeleton. The potential for molecular approaches is there. New developments in cantilever construction and computer software promise to bring real time video imaging to the AFM. Home made accessories for the first generation of AFM are now commodities in commercial instruments and make the life of the AFM microscopist easier. Also, the combination of different microscopies, such as AFM and TEM, or AFM and SEM find their way to the

  5. High-speed AFM of human chromosomes in liquid

    NASA Astrophysics Data System (ADS)

    Picco, L. M.; Dunton, P. G.; Ulcinas, A.; Engledew, D. J.; Hoshi, O.; Ushiki, T.; Miles, M. J.

    2008-09-01

    Further developments of the previously reported high-speed contact-mode AFM are described. The technique is applied to the imaging of human chromosomes at video rate both in air and in water. These are the largest structures to have been imaged with high-speed AFM and the first imaging in liquid to be reported. A possible mechanism that allows such high-speed contact-mode imaging without significant damage to the sample is discussed in the context of the velocity dependence of the measured lateral force on the AFM tip.

  6. Versatile method for AFM-tip functionalization with biomolecules: fishing a ligand by means of an in situ click reaction

    NASA Astrophysics Data System (ADS)

    Kumar, Rakesh; Ramakrishna, Shivaprakash N.; Naik, Vikrant V.; Chu, Zonglin; Drew, Michael E.; Spencer, Nicholas D.; Yamakoshi, Yoko

    2015-04-01

    A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions.A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions. Electronic supplementary information (ESI) available: Experimental details with synthesis and characterization of compounds. Procedures for modifications of Au surfaces and AFM tips. AFM images and full PM-IRRAS spectra of modified surfaces. Detailed procedure for QCM measurement. A table showing ligand-receptor interaction probability. NMR, IR and MS charts. See DOI: 10.1039/c5nr01495f

  7. Introduction to atomic force microscopy (AFM) in biology.

    PubMed

    Goldsbury, Claire S; Scheuring, Simon; Kreplak, Laurent

    2009-11-01

    The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nanoscale to the microscale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described.

  8. BOREAS AFM-12 1-km AVHRR Seasonal Land Cover Classification

    NASA Technical Reports Server (NTRS)

    Steyaert, Lou; Hall, Forrest G.; Newcomer, Jeffrey A. (Editor); Knapp, David E. (Editor); Loveland, Thomas R.; Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-12 team's efforts focused on regional scale Surface Vegetation and Atmosphere (SVAT) modeling to improve parameterization of the heterogeneous BOREAS landscape for use in larger scale Global Circulation Models (GCMs). This regional land cover data set was developed as part of a multitemporal one-kilometer Advanced Very High Resolution Radiometer (AVHRR) land cover analysis approach that was used as the basis for regional land cover mapping, fire disturbance-regeneration, and multiresolution land cover scaling studies in the boreal forest ecosystem of central Canada. This land cover classification was derived by using regional field observations from ground and low-level aircraft transits to analyze spectral-temporal clusters that were derived from an unsupervised cluster analysis of monthly Normalized Difference Vegetation Index (NDVI) image composites (April-September 1992). This regional data set was developed for use by BOREAS investigators, especially those involved in simulation modeling, remote sensing algorithm development, and aircraft flux studies. Based on regional field data verification, this multitemporal one-kilometer AVHRR land cover mapping approach was effective in characterizing the biome-level land cover structure, embedded spatially heterogeneous landscape patterns, and other types of key land cover information of interest to BOREAS modelers.The land cover mosaics in this classification include: (1) wet conifer mosaic (low, medium, and high tree stand density), (2) mixed coniferous-deciduous forest (80% coniferous, codominant, and 80% deciduous), (3) recent visible bum, vegetation regeneration, or rock outcrops-bare ground-sparsely vegetated slow regeneration bum (four classes), (4) open water and grassland marshes, and (5) general agricultural land use/ grasslands (three classes). This land cover mapping approach did not detect small subpixel-scale landscape

  9. Non-collinear magnetism and exchange bias at the FM NiFe/AFM NiMn interface: local spin density FLAPW study

    NASA Astrophysics Data System (ADS)

    Nakamura, K.; Freeman, A. J.; Wang, D.-S.; Zhong, L.; Fernandez-de-Castro, J.

    2001-03-01

    Magnetism at interfaces, such as the exchange bias between ferromagnetic (FM) and antiferromagnetic (AFM) materials, has attracted great attention because of technological applications. In order to investigate magnetic structures at the FM/AFM interface, we have implemented the FLAPW (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, PRB 24, 864(1981)) methodologies including non-collinear magnetism, in which the magnetic moment direction as well as the magnitude can vary continuously all over space. We first demonstrate this approach to determine the structure of a magnetic structure at an interface between FM NiFe and AFM NiMn. Although both bulk systems each show collinear FM and AFM structures, we found that a perpendicular magnetic orientation at their interface is energetically favorable, where the magnetic moments of the FM NiFe tend to lie perpendicular to those of AFM NiMn.

  10. Implications of the contact radius to line step (CRLS) ratio in AFM for nanotribology measurements.

    PubMed

    Helt, James M; Batteas, James D

    2006-07-04

    Investigating the mechanisms of defect generation and growth at surfaces on the nanometer scale typically requires high-resolution tools such as the atomic force microscope (AFM). To accurately assess the kinetics and activation parameters of defect production over a wide range of loads (F(z)), the AFM data should be properly conditioned. Generally, AFM wear trials are performed over an area defined by the length of the slow (L(sscan)) and fast scan axes. The ratio of L(sscan) to image resolution (res, lines per image) becomes an important experimental parameter in AFM wear trials because it defines the magnitude of the line step (LS = L(sscan)/res), the distance the AFM tip steps along the slow scan axis. Comparing the contact radius (a) to the line step (LS) indicates that the overlap of successive scans will result unless the contact radius-line step ratio (CRLS) is < or =(1)/(2). If this relationship is not considered, then the scan history (e.g., contact frequency) associated with a single scan is not equivalent at different loads owing to the scaling of contact radius with load (a proportional variant F(z)(1/3)). Here, we present a model in conjunction with empirical wear tests on muscovite mica to evaluate the effects of scan overlap on surface wear. Using the Hertz contact mechanics definition of a, the CRLS model shows that scan overlap pervades AFM wear trials even under low loads. Such findings indicate that simply counting the number of scans (N(scans)) in an experiment underestimates the full history conveyed to the surface by the tip and translates into an error in the actual extent to which a region on the surface is contacted. Utilizing the CRLS method described here provides an approach to account for image scan history accurately and to predict the extent of surface wear. This general model also has implications for any AFM measurement where one wishes to correlate scan-dependent history to image properties as well as feature resolution in scanned

  11. Combination of ToF-SIMS imaging and AFM to study the early stages of corrosion in Al-Cu thin films

    SciTech Connect

    Seyeux, A.; Missert, Nancy; Frankel, Gerald; Unocic, Kinga A; Klein, L. H.; Galtayries, A.; Marcus, P

    2011-01-01

    The pitting corrosion of Al-Cu thin film alloys was investigated using samples that were heat treated in air to form through-thickness Al2Cu particles within an Al-0.5%Cu matrix. Time-of-Flight SIMS (ToF-SIMS) analysis revealed Cu-rich regions 250 - 800 nm in lateral extent near the metal/oxide interface. Following exposure that generated pitting corrosion, secondary electron, secondary ion, and AFM images showed pits with size and density similar to those of the Cu-rich regions. The role of the Cu-rich regions is addressed.

  12. Brain tumor classification using AFM in combination with data mining techniques.

    PubMed

    Huml, Marlene; Silye, René; Zauner, Gerald; Hutterer, Stephan; Schilcher, Kurt

    2013-01-01

    Although classification of astrocytic tumors is standardized by the WHO grading system, which is mainly based on microscopy-derived, histomorphological features, there is great interobserver variability. The main causes are thought to be the complexity of morphological details varying from tumor to tumor and from patient to patient, variations in the technical histopathological procedures like staining protocols, and finally the individual experience of the diagnosing pathologist. Thus, to raise astrocytoma grading to a more objective standard, this paper proposes a methodology based on atomic force microscopy (AFM) derived images made from histopathological samples in combination with data mining techniques. By comparing AFM images with corresponding light microscopy images of the same area, the progressive formation of cavities due to cell necrosis was identified as a typical morphological marker for a computer-assisted analysis. Using genetic programming as a tool for feature analysis, a best model was created that achieved 94.74% classification accuracy in distinguishing grade II tumors from grade IV ones. While utilizing modern image analysis techniques, AFM may become an important tool in astrocytic tumor diagnosis. By this way patients suffering from grade II tumors are identified unambiguously, having a less risk for malignant transformation. They would benefit from early adjuvant therapies.

  13. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    . Measuring these units was not attempted before and most studies have assumed that the growth unit consisted of individual protein molecules. The linescan mode of AFM instruments allows the crystal surface to be scanned along a single line. By scanning across a growth step an image showing the motion of the step is obtained. Normally such an image shows a straight line for continuous and constant step velocity. In this study by increasing the scan rate and by decreasing the step velocity (by decreasing the supersaturation), we were able to capture images of individual growth events, shown by jump discontinuities in the step line. By suitable integration of the image the growth unit dimension in the scanned direction can be obtained. Since multiple units can be involved in the growth process it is necessary to collect a statistically relevant sample before drawing conclusions about the growth mechanism. This technique was successfully employed to obtain the dimensions of growth units for the (110) face, showing that they consisted of various aggregates corresponding to the 43 helices in the crystal structure.

  14. Proteomic Analysis of Aortae from Human Lipoprotein(a) Transgenic Mice Shows an Early Metabolic Response Independent of Atherosclerosis

    PubMed Central

    Rodger, Euan J.; Suetani, Rachel J.; Jones, Gregory T.; Kleffmann, Torsten; Carne, Alan; Legge, Michael; McCormick, Sally P. A.

    2012-01-01

    Background Elevated low density lipoprotein (LDL) and lipoprotein(a) are independent risk factors for the development of atherosclerosis. Using a proteomic approach we aimed to determine early changes in arterial protein expression in transgenic mice containing both human LDL and lipoprotein(a) in circulation. Methods and Results Plasma lipid analyses showed the lipoprotein(a) transgenic mice had significantly higher lipid levels than wildtype, including a much increased LDL and high density lipoprotein (HDL) cholesterol. Analysis of aortae from lipoprotein(a) mice showed lipoprotein(a) accumulation but no lipid accumulation or foam cells, leaving the arteries essentially atherosclerosis free. Using two-dimensional gel electrophoresis and mass spectrometry, we identified 34 arterial proteins with significantly altered abundance (P<0.05) in lipoprotein(a) transgenic mice compared to wildtype including 17 that showed a ≥2 fold difference. Some proteins of interest showed a similarly altered abundance at the transcript level. These changes collectively indicated an initial metabolic response that included a down regulation in energy, redox and lipid metabolism proteins and changes in structural proteins at a stage when atherosclerosis had not yet developed. Conclusions Our study shows that human LDL and lipoprotein(a) promote changes in the expression of a unique set of arterial proteins which may be early indicators of the metabolic disturbances preceding atherosclerosis. PMID:22276189

  15. Low tip damage AFM technique development for nano structures characterization

    NASA Astrophysics Data System (ADS)

    Liu, Biao; Wang, Charles C.; Huang, Po-Fu; Uritsky, Yuri

    2010-06-01

    Ambient dynamic mode (tapping mode or intermittent-contact mode) AFM imaging has been used extensively for the characterization of the topography of nano structures. However, the results are beset with artifacts, because hard tapping of the AFM tip on sample surface usually causes premature tip damage. Through careful study of the cantilever amplitude and phase signals as functions of tip-to-sample distance, principle of non-contact AFM operation was discovered to enable high resolution and low tip damage AFM image acquisition [1, 2]. However, current study discovers that the conventional way of acquiring amplitude and phase versus distance curves gives erroneous non-contact operating range, because the tip gets damaged during the data acquisition process. A new technique is developed to reliably map the operating parameters of an intact tip that ensures the AFM be operated with the correct non-contact settings. Two examples are given to illustrate the successful applications of this new technique. The first example involves the size characterization of polystyrene latex (PSL) nano particles used for light scattering tool calibration. The second example is the development of robust recipes for the measurement of the depth of phase-shift mask trenches.

  16. New insights into the mucoadhesion of pectins by AFM roughness parameters in combination with SPR.

    PubMed

    Joergensen, Lars; Klösgen, Beate; Simonsen, Adam Cohen; Borch, Jonas; Hagesaether, Ellen

    2011-06-15

    The object of this study was to assess the mucoadhesion of the three main commercially available types of pectin by atomic force microscopy (AFM) and surface Plasmon resonance (SPR). Polyacrylic acid and polyvinyl pyrrolidone were used as positive and negative control, respectively. Image analysis of the AFM scans revealed a significant change of roughness parameters when low-ester pectin was introduced to mica supported bovine submaxillarymucin, indicating a high mucoadhesion for this type of pectin. Only minor changes were observed with high-ester and amidated pectin. The same ranking order of adhesion affinity was confirmed by SPR. In conclusion, a high specific mucin interaction of pectin with a high charge density was demonstrated directly on a molecular scale without interference from the viscoelastic properties or the intra-molecular interactions between the polymer chains themselves, using two independent methods.

  17. Fractal properties of macrophage membrane studied by AFM.

    PubMed

    Bitler, A; Dover, R; Shai, Y

    2012-12-01

    Complexity of cell membrane poses difficulties to quantify corresponding morphology changes during cell proliferation and damage. We suggest using fractal dimension of the cell membrane to quantify its complexity and track changes produced by various treatments. Glutaraldehyde fixed mouse RAW 264.7 macrophage membranes were chosen as model system and imaged in PeakForce QNM (quantitative nanomechanics) mode of AFM (atomic force microscope). The morphology of the membranes was characterized by fractal dimension. The parameter was calculated for set of AFM images by three different methods. The same calculations were done for the AFM images of macrophages treated with colchicine, an inhibitor of the microtubule polymerization, and microtubule stabilizing agent taxol. We conclude that fractal dimension can be additional and useful parameter to characterize the cell membrane complexity and track the morphology changes produced by different treatments.

  18. AFM of biological complexes: what can we learn?

    PubMed Central

    Gaczynska, Maria; Osmulski, Pawel A.

    2009-01-01

    The term “biological complexes” broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected nonmembrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications. PMID:19802337

  19. Sub-diffraction nano manipulation using STED AFM.

    PubMed

    Chacko, Jenu Varghese; Canale, Claudio; Harke, Benjamin; Diaspro, Alberto

    2013-01-01

    In the last two decades, nano manipulation has been recognized as a potential tool of scientific interest especially in nanotechnology and nano-robotics. Contemporary optical microscopy (super resolution) techniques have also reached the nanometer scale resolution to visualize this and hence a combination of super resolution aided nano manipulation ineluctably gives a new perspective to the scenario. Here we demonstrate how specificity and rapid determination of structures provided by stimulated emission depletion (STED) microscope can aid another microscopic tool with capability of mechanical manoeuvring, like an atomic force microscope (AFM) to get topological information or to target nano scaled materials. We also give proof of principle on how high-resolution real time visualization can improve nano manipulation capability within a dense sample, and how STED-AFM is an optimal combination for this job. With these evidences, this article points to future precise nano dissections and maybe even to a nano-snooker game with an AFM tip and fluorospheres.

  20. Optimization of phase contrast in bimodal amplitude modulation AFM

    PubMed Central

    Damircheli, Mehrnoosh; Payam, Amir F

    2015-01-01

    Summary Bimodal force microscopy has expanded the capabilities of atomic force microscopy (AFM) by providing high spatial resolution images, compositional contrast and quantitative mapping of material properties without compromising the data acquisition speed. In the first bimodal AFM configuration, an amplitude feedback loop keeps constant the amplitude of the first mode while the observables of the second mode have not feedback restrictions (bimodal AM). Here we study the conditions to enhance the compositional contrast in bimodal AM while imaging heterogeneous materials. The contrast has a maximum by decreasing the amplitude of the second mode. We demonstrate that the roles of the excited modes are asymmetric. The operational range of bimodal AM is maximized when the second mode is free to follow changes in the force. We also study the contrast in trimodal AFM by analyzing the kinetic energy ratios. The phase contrast improves by decreasing the energy of second mode relative to those of the first and third modes. PMID:26114079

  1. Mounting of Escherichia coli spheroplasts for AFM imaging.

    SciTech Connect

    Sullivan, Claretta J; Morrell-Falvey, Jennifer L; Allison, David P; Doktycz, Mitchel John

    2005-11-01

    The cytoplasmic membrane of Escherichia coli (E. coli) is the location of numerous, chemically specific transporters and recognition elements. Investigation of this membrane in vivo by atomic force microscopy (AFM) requires removal of the cell wall and stable immobilization of the spheroplast. AFM images demonstrate that spheroplasts can be secured with warm gelatin applied to the mica substrate just before the addition of a spheroplast suspension. The resulting preparation can be repeatedly imaged by AFM over the course of several hours. Confocal fluorescence imaging confirms the association of the spheroplasts with the gelatin layer. Gelatin molecules are known to reorder into a network after heating. Entrapment within this gelatin network is believed to be responsible for the immobilization of spheroplasts on mica.

  2. The influence of aminophylline on the nanostructure and nanomechanics of T lymphocytes: an AFM study

    NASA Astrophysics Data System (ADS)

    Huang, Xun; He, Jiexiang; Liu, Mingxian; Zhou, Changren

    2014-09-01

    Although much progress has been made in the illustration of the mechanism of aminophylline (AM) treating asthma, there is no data about its effect on the nanostructure and nanomechanics of T lymphocytes. Here, we presented atomic force spectroscopy (AFM)-based investigations at the nanoscale level to address the above fundamental biophysical questions. As increasing AM treatment time, T lymphocytes' volume nearly double increased and then decreased. The changes of nanostructural features of the cell membrane, i.e., mean height of particles, root-mean-square roughness (Rq), crack and fragment appearance, increased with AM treatment time. T lymphocytes were completely destroyed with 96-h treatment, and they existed in the form of small fragments. Analysis of force-distance curves showed that the adhesion force of cell surface decreased significantly with the increase of AM treatment time, while the cell stiffness increased firstly and then decreased. These changes were closely correlated to the characteristics and process of cell oncosis. In total, these quantitative and qualitative changes of T lymphocytes' structure and nanomechanical properties suggested that AM could induce T lymphocyte oncosis to exert anti-inflammatory effects for treating asthma. These findings provide new insights into the T lymphocyte oncosis and the anti-inflammatory mechanism and immune regulation actions of AM.

  3. Surface morphology changes of lignin filled natural rubber latex films investigated using AFM in relation to tensile strengths

    NASA Astrophysics Data System (ADS)

    Asrul, M.; Othman, M.; Zakaria, M.

    2015-07-01

    The paper describes the preparation of lignin filled natural rubber latex composite and the consequential changes in tensile strength observed with varying lignin loading. The changes in tensile strength were shown to be associated with the changes in surface morphology as investigated via AFM. From the AFM analysis it can be inferred that lignin filled rubber latex film which exhibited an increase in tensile strength also demonstrated better phase homogeneity with lowest surface roughness value in comparison to the rest of the lignin filled rubber latex films analysed.

  4. Mapping individual cosmid DNAs by direct AFM imaging.

    PubMed

    Allison, D P; Kerper, P S; Doktycz, M J; Thundat, T; Modrich, P; Larimer, F W; Johnson, D K; Hoyt, P R; Mucenski, M L; Warmack, R J

    1997-05-01

    Individual cosmid clones have been restriction mapped by directly imaging, with the atomic force microscope (AFM), a mutant EcoRI endonuclease site-specifically bound to DNA. Images and data are presented that locate six restriction sites, predicted from gel electrophoresis, on a 35-kb cosmid isolated from mouse chromosome 7. Measured distances between endonuclease molecules bound to lambda DNA, when compared to known values, demonstrate the accuracy of AFM mapping to better than 1%. These results may be extended to identify other important site-specific protein-DNA interactions, such as transcription factor and mismatch repair enzyme binding, difficult to resolve by current techniques.

  5. BOREAS AFM-04 Twin Otter Aircraft Flux Data

    NASA Technical Reports Server (NTRS)

    MacPherson, J. Ian; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Desjardins, Raymond L.; Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS AFM-5 team collected and processed data from the numerous radiosonde flights during the project. The goals of the AFM-05 team were to provide large-scale definition of the atmosphere by supplementing the existing AES aerological network, both temporally and spatially. This data set includes basic upper-air parameters collected from the network of upper-air stations during the 1993, 1994, and 1996 field campaigns over the entire study region. The data are contained in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  6. Determining surface properties with bimodal and multimodal AFM.

    PubMed

    Forchheimer, D; Borysov, Stanislav S; Platz, D; Haviland, David B

    2014-12-05

    Conventional dynamic atomic force microscopy (AFM) can be extended to bimodal and multimodal AFM in which the cantilever is simultaneously excited at two or more resonance frequencies. Such excitation schemes result in one additional amplitude and phase images for each driven resonance, and potentially convey more information about the surface under investigation. Here we present a theoretical basis for using this information to approximate the parameters of a tip-surface interaction model. The theory is verified by simulations with added noise corresponding to room-temperature measurements.

  7. GPIM AF-M315E Propulsion System

    NASA Technical Reports Server (NTRS)

    Spores, Ronald A.; Masse, Robert; Kimbrel, Scott; McLean, Chris

    2014-01-01

    The NASA Space Technology mission Directorate's (STMD) Green Propellant Infusion Mission (GPIM) Technology Demonstration Mission (TDM) will demonstrate an operational AF-M315E green propellant propulsion system. Aerojet-Rocketdyne is responsible for the development of the propulsion system payload. This paper statuses the propulsion system module development, including thruster design and system design; Initial test results for the 1N engineering model thruster are presented. The culmination of this program will be high-performance, green AF-M315E propulsion system technology at TRL 7+, with components demonstrated to TRL 9, ready for direct infusion to a wide range of applications for the space user community.

  8. Atom probe, AFM, and STM studies on vacuum-fired stainless steels.

    PubMed

    Stupnik, A; Frank, P; Leisch, M

    2009-04-01

    The surface morphology of grades 304L and 316LN stainless steels, after low-temperature bake-out process and vacuum annealing, has been studied by atomic force microscopy (AFM) and scanning tunnelling microscopy (STM). The local elemental composition on the surface before and after thermal treatment has been investigated by atom probe (AP) depth profiling measurements. After vacuum annealing, AFM and STM show significant changes in the surface structure and topology. Recrystallization and surface reconstruction is less pronounced on the 316LN stainless steel. AP depth profiling analyses result in noticeable nickel enrichment on the surface of grade 304L samples. Since hydrogen recombination is almost controlled by surface structure and composition, a strong influence on the outgassing behaviour by the particular surface microstructure can be deduced.

  9. Development of a novel nanoindentation technique by utilizing a dual-probe AFM system

    PubMed Central

    Sahin, Ferat; Yablon, Dalia

    2015-01-01

    Summary A novel instrumentation approach to nanoindentation is described that exhibits improved resolution and depth sensing. The approach is based on a multi-probe scanning probe microscopy (SPM) tool that utilizes tuning-fork based probes for both indentation and depth sensing. Unlike nanoindentation experiments performed with conventional AFM systems using beam-bounce technology, this technique incorporates a second probe system with an ultra-high resolution for depth sensing. The additional second probe measures only the vertical movement of the straight indenter attached to a tuning-fork probe with a high spring constant and it can also be used for AFM scanning to obtain an accurate profiling. Nanoindentation results are demonstrated on silicon, fused silica, and Corning Eagle Glass. The results show that this new approach is viable in terms of accurately characterizing mechanical properties of materials through nanoindentation with high accuracy, and it opens doors to many other exciting applications in the field of nanomechanical characterization. PMID:26665072

  10. Linkage Analysis in a Dutch Population Isolate Shows No Major Gene for Left-Handedness or Atypical Language Lateralization

    PubMed Central

    Ophoff, Roel A.; Aukes, Maartje F.; Cantor, Rita M.; Boks, Marco P.; Dauwan, Meenakshi; de Visser, Kees L.; Kahn, René S.; Sommer, Iris E.

    2015-01-01

    Cerebral dominance of language function and hand preference are suggested to be heritable traits with possible shared genetic background. However, joined genetic studies of these traits have never been conducted. We performed a genetic linkage study in 37 multigenerational human pedigrees of both sexes (consisting of 355 subjects) enriched with left-handedness in which we also measured language lateralization. Hand preference was measured with the Edinburgh Handedness Inventory, and language lateralization was measured with functional transcranial Doppler during language production. The estimated heritability of left-handedness and language lateralization in these pedigrees is 0.24 and 0.31, respectively. A parametric major gene model was tested for left-handedness. Nonparametric analyses were performed for left-handedness, atypical lateralization, and degree of language lateralization. We did not observe genome-wide evidence for linkage in the parametric or nonparametric analyses for any of the phenotypes tested. However, multiple regions showed suggestive evidence of linkage. The parametric model showed suggestive linkage for left-handedness in the 22q13 region [heterogeneity logarithm of odds (HLOD) = 2.18]. Nonparametric multipoint analysis of left-handedness showed suggestive linkage in the same region [logarithm of odds (LOD) = 2.80]. Atypical language lateralization showed suggestive linkage in the 7q34 region (LODMax = 2.35). For strength of language lateralization, we observed suggestive linkage in the 6p22 (LODMax = 2.54), 7q32 (LODMax = 1.93), and 9q33 (LODMax = 2.10) regions. We did not observe any overlap of suggestive genetic signal between handedness and the extent of language lateralization. The absence of significant linkage argues against the presence of a major gene coding for both traits; rather, our results are suggestive of these traits being two independent polygenic complex traits. PMID:26063907

  11. Measuring protein isoelectric points by AFM-based force spectroscopy using trace amounts of sample

    NASA Astrophysics Data System (ADS)

    Guo, Shifeng; Zhu, Xiaoying; Jańczewski, Dominik; Lee, Serina Siew Chen; He, Tao; Teo, Serena Lay Ming; Vancso, G. Julius

    2016-09-01

    Protein charge at various pH and isoelectric point (pI) values is important in understanding protein function. However, often only trace amounts of unknown proteins are available and pI measurements cannot be obtained using conventional methods. Here, we show a method based on the atomic force microscope (AFM) to determine pI using minute quantities of proteins. The protein of interest is immobilized on AFM colloidal probes and the adhesion force of the protein is measured against a positively and a negatively charged substrate made by layer-by-layer deposition of polyelectrolytes. From the AFM force-distance curves, pI values with an estimated accuracy of ±0.25 were obtained for bovine serum albumin, myoglobin, fibrinogen and ribonuclease A over a range of 4.7-9.8. Using this method, we show that the pI of the ‘footprint’ of the temporary adhesive proteins secreted by the barnacle cyprid larvae of Amphibalanus amphitrite is in the range 9.6-9.7.

  12. Measuring protein isoelectric points by AFM-based force spectroscopy using trace amounts of sample.

    PubMed

    Guo, Shifeng; Zhu, Xiaoying; Jańczewski, Dominik; Lee, Serina Siew Chen; He, Tao; Teo, Serena Lay Ming; Vancso, G Julius

    2016-09-01

    Protein charge at various pH and isoelectric point (pI) values is important in understanding protein function. However, often only trace amounts of unknown proteins are available and pI measurements cannot be obtained using conventional methods. Here, we show a method based on the atomic force microscope (AFM) to determine pI using minute quantities of proteins. The protein of interest is immobilized on AFM colloidal probes and the adhesion force of the protein is measured against a positively and a negatively charged substrate made by layer-by-layer deposition of polyelectrolytes. From the AFM force-distance curves, pI values with an estimated accuracy of ±0.25 were obtained for bovine serum albumin, myoglobin, fibrinogen and ribonuclease A over a range of 4.7-9.8. Using this method, we show that the pI of the 'footprint' of the temporary adhesive proteins secreted by the barnacle cyprid larvae of Amphibalanus amphitrite is in the range 9.6-9.7.

  13. Do invasive species show higher phenotypic plasticity than native species and, if so, is it adaptive? A meta-analysis.

    PubMed

    Davidson, Amy Michelle; Jennions, Michael; Nicotra, Adrienne B

    2011-04-01

    Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.

  14. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

    PubMed

    Hijri, Mohamed

    2016-04-01

    An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

  15. AFM-based quantification of conformational changes in DNA caused by reactive oxygen species.

    PubMed

    Berg, Florian; Wilken, Janine; Helm, Christiane A; Block, Stephan

    2015-01-08

    Radical induced modification of DNA plays an important role in many pathological pathways like cancer development, aging, etc. In this work, we quantify radical-induced DNA damage that causes transitions from double to single stranded DNA using atomic force microscopy (AFM). The plasmid pBR322 is attacked by free hydroxyl radicals that are produced by Fenton's reaction; the strength of the radical attack is controlled via the ratio of hydroxyl radical molecules to DNA base pairs. The extent of DNA modification is assessed by AFM tapping mode (TM) imaging of the plasmids (after adsorption onto PAH-functionalized mica) in air. As single stranded DNA chains (height ∼2 Å) are much smaller than intact DNA strands (∼5 Å), their fraction can be quantified based on the height distribution, which allows a simplified data analysis in comparison to similar AFM-based approaches. It is found that the amount of damaged DNA strands increases with increasing strength of radical attack, and decreases if ROS scavengers like sodium acetate are added. Competition curves are calculated for the interaction of hydroxyl radicals with DNA and sodium acetate, which finally allows calculation of relative rate constants for the respective reactions.

  16. On the determination of elastic moduli of cells by AFM based indentation

    PubMed Central

    Ding, Yue; Xu, Guang-Kui; Wang, Gang-Feng

    2017-01-01

    The atomic force microscopy (AFM) has been widely used to measure the mechanical properties of biological cells through indentations. In most of existing studies, the cell is supposed to be linear elastic within the small strain regime when analyzing the AFM indentation data. However, in experimental situations, the roles of large deformation and surface tension of cells should be taken into consideration. Here, we use the neo-Hookean model to describe the hyperelastic behavior of cells and investigate the influence of surface tension through finite element simulations. At large deformation, a correction factor, depending on the geometric ratio of indenter radius to cell radius, is introduced to modify the force-indent depth relation of classical Hertzian model. Moreover, when the indent depth is comparable with an intrinsic length defined as the ratio of surface tension to elastic modulus, the surface tension evidently affects the indentation response, indicating an overestimation of elastic modulus by the Hertzian model. The dimensionless-analysis-based theoretical predictions, which include both large deformation and surface tension, are in good agreement with our finite element simulation data. This study provides a novel method to more accurately measure the mechanical properties of biological cells and soft materials in AFM indentation experiments. PMID:28368053

  17. A study of water droplet between an AFM tip and a substrate using dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Pal, Souvik; Lan, Chuanjin; Li, Zhen; Hirleman, E. Daniel; Ma, Yanbao

    2014-11-01

    Formation of a water droplet between a sharp AFM tip and a substrate due to capillary condensation affects the tip-substrate interaction. As a consequence, AFM measurements lose precision and often produce incorrect sample topology. Understanding the physics of liquid bridges is also important in the field of Dip-pen nanolithography (DPN). Significant research is being carried out to understand the mechanics of the formation of the liquid bridge and its dependence of surface properties, ambient conditions etc. The in-between length scale, i.e., mesoscale (~100 nm) associated with this phenomenon presents a steep challenge for experimental measurements. In addition, molecular dynamics (MD) can be computationally prohibitive to model the entire system, especially over microseconds to seconds. Theoretical analysis using Young Laplace equation has so far provided some qualitative insights only. We study this system using Dissipative Particle Dynamics (DPD) which is a simulation technique suitable for describing mesoscopic hydrodynamic behavior of fluids. In this work, we carry out simulations to improve understanding of the process of formation of the meniscus, the mechanics of manipulation and control of its shape, and better estimation of capillary forces. The knowledge gained through our study will help in correcting the AFM measurements affected by capillary condensation. Moreover, it will improve understanding of more accurate droplet manipulation in DPN.

  18. Multilayer silicon rich oxy-nitride films characterization by SIMS, VASE and AFM

    NASA Astrophysics Data System (ADS)

    Barozzi, M.; Vanzetti, L.; Iacob, E.; Bersani, M.; Anderle, M.; Pucker, G.; Kompocholis, C.; Ghulinyan, M.; Bellutti, P.

    2008-03-01

    In this work secondary ion mass spectrometry (SIMS), variable angle spectroscopy ellipsometry (VASE) and atomic force microscopy (AFM) are used to investigate the structure, composition and morphology of multilayer SRON films. Three/four SRON sequential layers were deposited on silicon wafers by PECVD and silicon, nitrogen and oxygen content was varied by changing the N2O/SiH4 ratio. The total thickness of the resulting SRON stack is about 50nm. SIMS analyses of NCs+, OCs+, SiCs+, in MCs+ methodology are performed by a Cameca SC-ultra instrument. Depth profiles are obtained at 500eV of primary beam impact energy with sample rotation. An approximate method to obtain silicon concentration is used. Total layer thickness are obtained from both SIMS and VASE measurements. In addition, we compare the thickness of the single layers obtained from VASE with the SIMS depth profiles. A detailed analysis of films morphology is obtained by AFM. The SRON stack is sputtered by SIMS until a certain layer is exposed, which is then analyzed by AFM. The sputtered layers are then etched in HF solution to better resolve the exposed nano-crystals.

  19. On the determination of elastic moduli of cells by AFM based indentation.

    PubMed

    Ding, Yue; Xu, Guang-Kui; Wang, Gang-Feng

    2017-04-03

    The atomic force microscopy (AFM) has been widely used to measure the mechanical properties of biological cells through indentations. In most of existing studies, the cell is supposed to be linear elastic within the small strain regime when analyzing the AFM indentation data. However, in experimental situations, the roles of large deformation and surface tension of cells should be taken into consideration. Here, we use the neo-Hookean model to describe the hyperelastic behavior of cells and investigate the influence of surface tension through finite element simulations. At large deformation, a correction factor, depending on the geometric ratio of indenter radius to cell radius, is introduced to modify the force-indent depth relation of classical Hertzian model. Moreover, when the indent depth is comparable with an intrinsic length defined as the ratio of surface tension to elastic modulus, the surface tension evidently affects the indentation response, indicating an overestimation of elastic modulus by the Hertzian model. The dimensionless-analysis-based theoretical predictions, which include both large deformation and surface tension, are in good agreement with our finite element simulation data. This study provides a novel method to more accurately measure the mechanical properties of biological cells and soft materials in AFM indentation experiments.

  20. Study of mechanical behavior of AFM silicon tips under mechanical load

    NASA Astrophysics Data System (ADS)

    Kopycinska-Mueller, M.; Gluch, J.; Köhler, B.

    2016-11-01

    In this paper we address critical issues concerning calibration of AFM based methods used for nanoscale mechanical characterization of materials. It has been shown that calibration approaches based on macroscopic models for contact mechanics may yield excellent results in terms of the indentation modulus of the sample, but fail to provide a comprehensive and actual information concerning the tip-sample contact radius or the mechanical properties of the tip. Explanations for the severely reduced indentation modulus of the tip included the inadequacies of the models used for calculations of the tip-sample contact stiffness, discrepancies in the actual and ideal shape of the tip, presence of the amorphous silicon phase within the silicon tip, as well as negligence of the actual size of the stress field created in the tip during elastic interactions. To clarify these issues, we investigated the influence of the mechanical load applied to four AFM silicon tips on their crystalline state by exposing them to systematically increasing loads, evaluating the character of the tip-sample interactions via the load-unload stiffness curves, and assessing the state of the tips from HR-TEM images. The results presented in this paper were obtained in a series of relatively simple and basic atomic force acoustic microscopy (AFAM) experiments. The novel combination of TEM imaging of the AFM tips with the analysis of the load-unload stiffness curves gave us a detailed insight into their mechanical behavior under load conditions. We were able to identify the limits for the elastic interactions, as well as the hallmarks for phase transformation and dislocation formation and movement. The comparison of the physical dimensions of the AFM tips, geometry parameters determined from the values of the contact stiffness, and the information on the crystalline state of the tips allowed us a better understanding of the nanoscale contact.

  1. Geochemical analysis of potash mine seep oils, collapsed breccia pipe oil shows and selected crude oils, Eddy County, New Mexico

    USGS Publications Warehouse

    Palacas, J.G.; Snyder, R.P.; Baysinger, J.P.; Threlkeld, C.N.

    1982-01-01

    Oil shows, in the form of oil stains and bleeding oil, in core samples from two breccia pipes, Hills A and C, Eddy County, New Mexico, and seepage oils in a potash mine near Hill C breccia pipe are geochemically similar. The geochemical similarities strongly suggest that they belong to the same family of oils and were derived from similar sources. The oils are relatively high in sulfur (0.89 to 1.23 percent), rich in hydrocarbons (average 82 percent), relatively high in saturated hydrocarbon/aromatic hydrocarbon ratios (average 2.9), and based on analysis of seep oils alone, have a low API gravity (average 19.4?). The oils are for the most part severely biodegraded as attested by the loss of n-paraffin molecules. Geochemical comparison of seven crude oils collected in the vicinity of the breccia pipes indicates that the Yates oils are the likely source of the above family of oils. Six barrels of crude oil that were dumped into a potash exploration borehole near Hill C breccia pipe, to release stuck casing, are considered an unlikely source of the breccia pipe and mine seep oils. Volumetric and hydrodynamic constraints make it highly improbable that such a small volume of 'dumped' oil could migrate over distances ranging from about 600 feet to 2.5 miles to the sites of the oil shows.

  2. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses.

    PubMed

    Brum, Jennifer R; Schenck, Ryan O; Sullivan, Matthew B

    2013-09-01

    Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.

  3. AFM Structural Characterization of Drinking Water Biofilm under Physiological Conditions

    EPA Science Inventory

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air...

  4. Probing the Double Layer: Effect of Image Forces on AFM

    PubMed Central

    Sachs, Frederick

    2006-01-01

    Force probes such as AFM tips or laser trap latex beads have a dielectric constant much less than that of the water that they displace. Thus when a probe approaches a charged surface under water it will be repelled simply based upon the image forces, and these can be of nN magnitude. PMID:16714346

  5. Cantilever's behavior in the AC mode of an AFM

    SciTech Connect

    Nunes, V.B.; Zanette, S.I.; Caride, A.O.; Prioli, R.; Rivas, A.M.F

    2003-03-15

    In this paper, a model with a small number of parameters is used to simulate the motion of a cantilever in the AC mode of an atomic force microscope (AFM). The results elucidate the transition dependence-from noncontact to tapping operating mode-on the height of the contamination layer and on the stiffness of the sample.

  6. Enzymatic nanolithography of FRET peptide layer using V8 protease-immobilized AFM probe.

    PubMed

    Nakamura, Chikashi; Miyamoto, Chie; Obataya, Ikuo; Takeda, Seiji; Yabuta, Masayuki; Miyake, Jun

    2007-04-15

    In our study, a method based on Enzymatic nanolithography was successfully performed in a buffered solution using Staphylococcal serine V8 protease and AFM. To estimate the lithographing activity of the protease immobilized on the AFM tip to peptides immobilized on a substrate, we designed fluorescence resonance energy transfer (FRET) peptides as reporter peptides that showed enzymatic action specific to the V8 protease. When the protease digested the reporter peptide a quencher residue was released from the peptide and resulted in the appearance of fluorescence. In the designed 9-mer peptides, TAMRA functioned as a good quencher for FAM. When the fluorescence resonance energy transfer peptides immobilized on a glass substrate were hydrolyzed by V8 protease at the C-terminal of glutamic acid, fluorescence of a reporter dye was observed because of the release of a quencher from the substrate. After contacting and lateral scanning of the protease-immobilized AFM tip to the reporter peptide layer, a fluorescent area was observed by imaging using total internal refection fluorescence microscopy (TIRFM). The increment of fluorescence intensity of the digested peptide indicates the performance of lithography. Lithographing rates increased in inverse relation to scanning rates of the probe. The maximum limit of the scanning rate, i.e., that was too fast to permit cutting of the peptide on the substrate, and the lithographing performance are discussed in this study.

  7. A low-cost AFM setup with an interferometer for undergraduates and secondary-school students

    NASA Astrophysics Data System (ADS)

    Bergmann, Antje; Feigl, Daniela; Kuhn, David; Schaupp, Manuel; Quast, Günter; Busch, Kurt; Eichner, Ludwig; Schumacher, Jens

    2013-07-01

    Atomic force microscopy (AFM) is an important tool in nanotechnology. This method makes it possible to observe nanoscopic surfaces beyond the resolution of light microscopy. In order to provide undergraduate and secondary-school students with insights into this world, we have developed a very robust low-cost AFM setup with a Fabry-Perot interferometer as a detecting device. This setup is designed to be operated almost completely manually and its simplicity gives access to a profound understanding of the working principle. Our AFM is operated in a constant height mode, i.e. the topography of the sample surface is represented directly by the deflection of the cantilever. Thus, the measuring procedure can be understood even by secondary-school students; furthermore, it is the method with the lowest cost, totalling not more than 10-15 k Euros. Nevertheless, we are able to examine a large variety of sample topographies such as CD and DVD surfaces, IC structures, blood cells, butterfly wings or moth eyes. Furthermore, force-distance curves can be recorded and the tensile moduli of some materials can be evaluated. We present our setup in detail and describe its working principles. In addition, we show various experiments which have already been performed by students.

  8. Bacterial adhesion to protein-coated surfaces: An AFM and QCM-D study

    NASA Astrophysics Data System (ADS)

    Strauss, Joshua; Liu, Yatao; Camesano, Terri A.

    2009-09-01

    Bacterial adhesion to biomaterials, mineral surfaces, or other industrial surfaces is strongly controlled by the way bacteria interact with protein layers or organic matter and other biomolecules that coat the materials. Despite this knowledge, many studies of bacterial adhesion are performed under clean conditions, instead of in the presence of proteins or organic molecules. We chose fetal bovine serum (FBS) as a model protein, and prepared FBS films on quartz crystals. The thickness of the FBS layer was characterized using atomic force microscopy (AFM) imaging under liquid and quartz crystal microbalance with dissipation (QCM-D). Next, we characterized how the model biomaterial surface would interact with the nocosomial pathogen Staphylococcus epidermidis. An AFM probe was coated with S. epidermidis cells and used to probe a gold slide that had been coated with FBS or another protein, fibronectin (FN). These experiments show that AFM and QCM-D can be used in complementary ways to study the complex interactions between bacteria, proteins, and surfaces.

  9. Fabrication of nanochannels with ladder nanostructure at the bottom using AFM nanoscratching method

    PubMed Central

    2014-01-01

    This letter presents a novel atomic force microscopy (AFM)-based nanomanufacturing method combining the tip scanning with the high-precision stage movement to fabricate nanochannels with ladder nanostructure at the bottom by continuous scanning with a fixed scan size. Different structures can be obtained according to the matching relation of the tip feeding velocity and the precision stage moving velocity. This relationship was first studied in detail to achieve nanochannels with different ladder nanostructures at the bottom. Machining experiments were then performed to fabricate nanochannels on an aluminum alloy surface to demonstrate the capability of this AFM-based fabrication method presented in this study. Results show that the feed value and the tip orientation in the removing action play important roles in this method which has a significant effect on the machined surfaces. Finally, the capacity of this method to fabricate a large-scale nanochannel was also demonstrated. This method has the potential to advance the existing AFM tip-based nanomanufacturing technique of the formation these complex structures by increasing the removal speed, simplifying the processing procedure and achieving the large-scale nanofabrication. PMID:24940171

  10. Investigation of surface changes of nanoparticles using TM-AFM phase imaging.

    PubMed

    Dong, Rong; Yu, Liya E

    2003-06-15

    Tapping-mode AFM (TM-AFM) phase imaging was utilized to characterize the surface changes of nanosize particles, in regard to the effects of different amounts of condensed water and organic coatings on particle surfaces. Model nanoparticles were continuously examined under various relative humidity (RH) levels by concurrently obtaining both topographic and phase images. The condensed water appeared to soften particle surfaces and to increase tip-sample attractive interaction over relatively stiff surfaces, which were shown with dark phase contrasts and negative phase shift values in phase images. Under high RH, a massive amount of water gave the particles a droplet-like surface, which reversed the original negative phase shifts to positive values with bright contrasts. Glutaric-acid coatings provided a compliant surface with high viscosity resulting in a dark phase contrast, whereas water droplets containing relatively low viscosity gave a bright phase contrast and positive phase shift. Overall, our results show that it is essential to describe the physical properties of a sample surface as solid, soft, or droplet-like material in order to derive a meaningful understanding of the surface changes of nanosize particles based on TM-AFM phase images. In contrast to other phase imaging studies, this work clearly correlates continuous surface changes with phase images, demonstrating a promising approach to characterize environmental nanoparticles.

  11. Robust deposition of lambda DNA on mica for imaging by AFM in air.

    PubMed

    Cervantes, Nancy Anabel Gerling; Gutiérrez-Medina, Braulio

    2014-01-01

    Long DNA molecules remain difficult to image by atomic force microscopy (AFM) because of their tendency to entanglement and spontaneous formation of networks. We present a comparison of two different DNA deposition methods operating at room temperature and humidity conditions, aimed at reproducible imaging of isolated and relaxed λ DNA conformations by AFM in air. We first demonstrate that a standard deposition procedure, consisting in adsorption of DNA in the presence of divalent cations followed by washing and air-drying steps, yields a coexistence of different types of λ DNA networks with a only a few isolated DNA chains. In contrast, deposition using a spin-coating-based technique results in reproducible coverage of a significant fraction of the substrate area by isolated and relaxed λ DNA molecules, with the added benefit of a reduction in the effect of a residual layer that normally embeds DNA strands and leads to an apparent DNA height closer to the expected value. Furthermore, we show that deposition by spin-coating is also well-suited to visualize DNA-protein complexes. These results indicate that spin-coating is a simple, powerful alternative for reproducible sample preparation for AFM imaging.

  12. Brain Correlates of Cognitive Remediation in Schizophrenia: Activation Likelihood Analysis Shows Preliminary Evidence of Neural Target Engagement

    PubMed Central

    Ramsay, Ian S.; MacDonald, Angus W.

    2015-01-01

    Cognitive remediation training (CRT) for schizophrenia has been found to improve cognitive functioning and influence neural plasticity. However, with various training approaches and mixed findings, the mechanisms driving generalization of cognitive skills from CRT are unclear. In this meta-analysis of extant imaging studies examining CRT’s effects, we sought to clarify whether varying approaches to CRT suggest common neural changes and whether such mechanisms are restorative or compensatory. We conducted a literature search to identify studies appropriate for inclusion in an activation likelihood estimation (ALE) meta-analysis. Our criteria required studies to consist of training-based interventions designed to improve patients’ cognitive or social functioning, including generalization to untrained circumstances. Studies were also required to examine changes in pre- vs posttraining functional activation using functional magnetic resonance imaging or positron emission tomography. The literature search identified 162 articles, 9 of which were appropriate for inclusion. ALE analyses comparing pre- and posttraining brain activation showed increased activity in the lateral and medial prefrontal cortex (PFC), parietal cortex, insula, and the caudate and thalamus. Notably, activation associated with CRT in the left PFC and thalamus partially overlapped with previous meta-analytically identified areas associated with deficits in working memory, executive control, and facial emotion processing in schizophrenia. We conclude that CRT interventions from varying theoretic modalities elicit plasticity in areas that support cognitive and socioemotional processes in this early set of studies. While preliminary, these changes appear to be both restorative and compensatory, though thalamocortical areas previously associated with dysfunction may be common sources of plasticity for cognitive remediation in schizophrenia. PMID:25800249

  13. XPS and AFM Study of GaAs Surface Treatment

    SciTech Connect

    Contreras-Guerrero, R.; Wallace, R. M.; Aguirre-Francisco, S.; Herrera-Gomez, A.; Lopez-Lopez, M.

    2008-11-13

    Obtaining smooth and atomically clean surfaces is an important step in the preparation of a surface for device manufacturing. In this work different processes are evaluated for cleaning a GaAs surface. A good surface cleaning treatment is that which provides a high level of uniformity and controllability of the surface. Different techniques are useful as cleaning treatments depending on the growth process to be used. The goal is to remove the oxygen and carbon contaminants and then form a thin oxide film to protect the surface, which is easy to remove later with thermal desorption mechanism like molecular beam epitaxy (MBE) with minimal impact to the surface. In this study, atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) were used to characterize the structure of the surface, the composition, as well as detect oxygen and carbon contaminant on the GaAs surface. This study consists in two parts. The first part the surface was subjected to different chemical treatments. The chemical solutions were: (a)H{sub 2}SO{sub 4}:H{sub 2}O{sub 2}:H{sub 2}O(4:1:100), (b) HCl: H{sub 2}O(1:3), (c)NH{sub 4}OH 29%. The treatments (a) and (b) reduced the oxygen on the surface. Treatment (c) reduces carbon contamination. In the second part we made MOS devices on the surfaces treated. They were characterized by CV and IV electrical measurements. They show frequency dispersion.

  14. Expression analysis of human pterygium shows a predominance of conjunctival and limbal markers and genes associated with cell migration

    PubMed Central

    Aryankalayil-John, M.; Campos, M.M.; Fariss, R.N.; Rowsey, J.; Agarwalla, N.; Reid, T.W.; Dushku, N.; Cox, C.A.; Carper, D.; Wistow, G.

    2009-01-01

    Purpose Pterygium is a vision-impairing fibrovascular lesion that grows across the corneal surface and is associated with sunlight exposure. To increase our understanding of the cells types involved in pterygium, we have used expressed sequence tag analysis to examine the transcriptional repertoire of isolated pterygium and to identify marker genes for tissue origin and cell migration. Methods An unnormalized unamplified cDNA library was prepared from 15 pooled specimens of surgically removed pterygia as part of the NEIBank project. Gene expression patterns were compared with existing data for human cornea, limbus, and conjunctiva, and expression of selected genes was verified by immunofluorescence localization in normal eye ocular surface and in pterygium. Results Sequence analysis of 2,976 randomly selected clones produced over 1,800 unique clusters, potentially representing single genes. The most abundant complementary DNAs from pterygium include clusterin, keratins 13 (Krt13) and 4 (Krt4), S100A9/calgranulin B, and spermidine/spermine N1-acetyltransferase (SAT1). Markers for both conjunctiva (such as keratin 13/4 and AQP3) and corneal epithelium (such as keratin 12/3 and AQP5) were present. Immunofluorescence of Krt12 and 13 in the normal ocular surface showed specificity of Krt12 in cornea and Krt13 in conjunctival and limbal epithelia, with a fairly sharp boundary at the limbal–corneal border. In the pterygium there was a patchy distribution of both Krt12 and 13 up to a normal corneal epithelial region specific for Krt12. Immunoglobulins were also among the prominently expressed transcripts. Several of the genes expressed most abundantly in excised pterygium, particularly S100A9 and SAT1, have roles in cell migration. SAT1 exerts its effects through control of polyamine levels. IPENSpm, a polyamine analogue, showed a significant ability to reduce migration in primary cultures of pterygium. A number of genes highly expressed in cornea were not found in

  15. Scanning hall probe microscopy (SHPM) using quartz crystal AFM feedback.

    PubMed

    Dede, M; Urkmen, K; Girişen, O; Atabak, M; Oral, A; Farrer, I; Ritchie, D

    2008-02-01

    Scanning Hall Probe Microscopy (SHPM) is a quantitative and non-invasive technique for imaging localized surface magnetic field fluctuations such as ferromagnetic domains with high spatial and magnetic field resolution of approximately 50 nm and 7 mG/Hz(1/2) at room temperature. In the SHPM technique, scanning tunneling microscope (STM) or atomic force microscope (AFM) feedback is used to keep the Hall sensor in close proximity of the sample surface. However, STM tracking SHPM requires conductive samples; therefore the insulating substrates have to be coated with a thin layer of gold. This constraint can be eliminated with the AFM feedback using sophisticated Hall probes that are integrated with AFM cantilevers. However it is very difficult to micro fabricate these sensors. In this work, we have eliminated the difficulty in the cantilever-Hall probe integration process, just by gluing a Hall Probe chip to a quartz crystal tuning fork force sensor. The Hall sensor chip is simply glued at the end of a 32.768 kHz or 100 kHz Quartz crystal, which is used as force sensor. An LT-SHPM system is used to scan the samples. The sensor assembly is dithered at the resonance frequency using a digital Phase Locked Loop circuit and frequency shifts are used for AFM tracking. SHPM electronics is modified to detect AFM topography and the frequency shift, along with the magnetic field image. Magnetic domains and topography of an Iron Garnet thin film crystal, NdFeB demagnetised magnet and hard disk samples are presented at room temperature. The performance is found to be comparable with the SHPM using STM feedback.

  16. Absorption Spectroscopy and Imaging from the Visible through Mid-IR with 20 nm Resolution Using AFM probes

    NASA Astrophysics Data System (ADS)

    Centrone, Andrea

    2015-03-01

    Correlated nanoscale composition and optical property maps are important to engineer nanomaterials in applications ranging from photovoltaics to sensing and therapeutics. Wavelengths (λs) from the visible to near-IR probe electronic transitions in materials, providing information regarding band gap and defects while light in mid-IR probes vibrational transitions and provide chemical composition. However, light diffraction limits the lateral resolution of conventional micro-spectroscopic techniques to approximately λ/2, which is insufficient to image nanomaterials. Additionally, the λ-dependent resolution impedes direct comparison of spectral maps from different spectral ranges. Photo Thermal Induced Resonance (PTIR) is a novel technique that circumvents light diffraction by employing an AFM tip as a local detector for measuring light absorption with λ-independent nanoscale resolution. Our PTIR setup combines an AFM microscope with three lasers providing λ-tunability from 500 nm to 16000 nm continuously. The AFM tip transduces locally the sample thermal expansion induced by light absorption into large cantilever oscillations. Local absorption spectra (electronic or vibrational) and maps are obtained recording the amplitude of the tip deflection as a function of λ and position, respectively. The working principles of the PTIR technique will be described first, and nano-patterned polymer samples will be used to evaluate its lateral resolution, sensitivity and linearity. Results show that the PTIR signal intensity is proportional to the local absorbed energy suggesting applicability of this technique for quantitative chemical analysis at nanoscale, at least for thin (less than 1000 nm thick) samples. Additionally, a λ-independent resolution as high as 20 nm is demonstrated across the whole spectral range. In the second part of the talk, PTIR will be applied to image the dark plasmonic resonance of gold Asymmetric Split Ring Resonators (A-SRRs) in the mid

  17. Sharp high-aspect-ratio AFM tips fabricated by a combination of deep reactive ion etching and focused ion beam techniques.

    PubMed

    Caballero, David; Villanueva, Guillermo; Plaza, Jose Antonio; Mills, Christopher A; Samitier, Josep; Errachid, Abdelhamid

    2010-01-01

    The shape and dimensions of an atomic force microscope tip are crucial factors to obtain high resolution images at the nanoscale. When measuring samples with narrow trenches, inclined sidewalls near 90 degrees or nanoscaled structures, standard silicon atomic force microscopy (AFM) tips do not provide satisfactory results. We have combined deep reactive ion etching (DRIE) and focused ion beam (FIB) lithography techniques in order to produce probes with sharp rocket-shaped silicon AFM tips for high resolution imaging. The cantilevers were shaped and the bulk micromachining was performed using the same DRIE equipment. To improve the tip aspect ratio we used FIB nanolithography technique. The tips were tested on narrow silicon trenches and over biological samples showing a better resolution when compared with standard AFM tips, which enables nanocharacterization and nanometrology of high-aspect-ratio structures and nanoscaled biological elements to be completed, and provides an alternative to commercial high aspect ratio AFM tips.

  18. Nanotechnology for forensic sciences: analysis of PDMS replica of the case head of spent cartridges by optical microscopy, SEM and AFM for the ballistic identification of individual characteristic features of firearms.

    PubMed

    Valle, Francesco; Bianchi, Michele; Tortorella, Silvia; Pierini, Giovanni; Biscarini, Fabio; D'Elia, Marcello

    2012-10-10

    A novel application of replica molding to a forensic problem, viz. the accurate reproduction of the case head of gun and rifle cartridges, prior and after been shot, is presented. The fabrication of an arbitrary number of identical copies of the region hit by the firing pin and by the breech face is described. The replicas can be (i) handled without damaging the original evidence, (ii) distributed to different law enforcement agencies for comparison against other evidences found on crime scenes or ballistic tests of seized firearms, (iii) maintained on a file by the laboratories. A detailed analysis of the morphological features of the replicas has been carried out by standard microscopy techniques as well as by advanced microscopy such as scanning probe and scanning electron leading to a quantitative morphological characterization of the case heads down to the nanometer scale. The assignment of the cartridge replicas to the shooting weapon is demonstrated to hold below the micron scale, while it is hindered at the nanometer level both by the manufacturing differences and by eventual modifications occurring on the firing pin.

  19. AFM Manipulation of Viruses: Substrate Interactions and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Falvo, M. R.; Superfine, R.; Washburn, S.; Finch, M.; Taylor, R. M.; Chi, V.; Brooks, F. P.; Ferrari, F.; Samulski, R.

    1996-03-01

    Using an AFM tip as a manipulation tool, we have translated, rotated, and dissected individual Tobacco Mosaic Virus (TMV) and Adenovirus particles. We have implemented a teleoperation system which allows manual control of the relative tip-sample position while also allowing conventional AFM operation for imaging resulting structure. Using simple tip trajectories to bend the rod-shaped TMV, we observed a variety of resulting structures and mechanical failures. The distributed adhesive interaction between the virus and the sample surface, as well as the local tip-virus interaction affect the distortion in the shape of the virus. Experiments were performed in air as well as in liquid on graphite and Si substrates. The in-liquid experiments allow tuning of the environmental conditions, including osmolarity and pH, which are known to profoundly affect the virus structure. A continuum mechanical model relating mechanical properties to observations provides insight into the constraints for successful nondestructive manipulation.

  20. Nano-Bio-Mechanics of Neuroblastoma Cells Using AFM

    NASA Astrophysics Data System (ADS)

    Bastatas, Lyndon; Matthews, James; Kang, Min; Park, Soyeun

    2011-10-01

    We have conducted an in vitro study to determine the elastic moduli of neurobalstoma cell lines using atomic force microscopy. Using a panel of cell lines established from neuroblastoma patients at different stages of disease progress and treatment, we have investigated the differences in elastic moduli during a course of cancer progression and chemotherapy. The cells were grown on the hard substrates that are chemically functionalized to enhance adhesion. We have performed the AFM indentation experiments with different applied forces from the AFM probe. For the purpose of the comparison between cell lines, the indentations were performed only on cell centers. The obtained force-distance curves were analyzed using the Hertz model in order to extract the elastic moduli. We have found that the elastic moduli of human neuroblastoma cells significantly varied during the disease progression. We postulate that the observed difference might be affected by the treatment and chemotherapy.

  1. BOREAS AFM-5 Level-1 Upper Air Network Data

    NASA Technical Reports Server (NTRS)

    Barr, Alan; Hrynkiw, Charmaine; Newcomer, Jeffrey A. (Editor); Hall, Forrest G. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-5 team collected and processed data from the numerous radiosonde flights during the project. The goals of the AFM-05 team were to provide large-scale definition of the atmosphere by supplementing the existing Atmospheric Environment Service (AES) aerological network, both temporally and spatially. This data set includes basic upper-air parameters collected from the network of upper-air stations during the 1993, 1994, and 1996 field campaigns over the entire study region. The data are contained in tabular ASCII files. The level-1 upper-air network data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files also are available on a CD-ROM (see document number 20010000884).

  2. Automated assembly of holder chips to AFM probes

    NASA Astrophysics Data System (ADS)

    Reinhart, Gunther; Jacob, Dirk; Fouchier, Marc

    2001-10-01

    At the Belgian institute IMEC techniques for the production of electrically conductive atomic force microscope (AFM) probes are developed. To facilitate handling of the fragile probes, holder chips are required. The assembly of such holder chips, which can be split up into the application of solder paste, the positioning of the holder chip and the soldering of the chip, is a crucial manufacturing step, that, until now, was performed manually for economic reasons. With the help of a modular micro assembly tool, developed by the Institute for Machine Tools and Industrial Management (iwb) of the Technische Universitaet Muenchen, an economical automated assembly of the holder chips was developed. Thanks to our integrated sensor technology, even the automated assembly onto the extremely fragile membranes of moulded AFM probes was possible. In particular, the dispensing process of the solder paste onto the membranes was improved by the integration of a non-contact sensor for the needle clearance.

  3. Tip convolution on HOPG surfaces measured in AM-AFM and interpreted using a combined experimental and simulation approach

    NASA Astrophysics Data System (ADS)

    Hu, Xiaoli; Chan, Nicholas; Martini, Ashlie; Egberts, Philip

    2017-01-01

    Amplitude modulated atomic force microscopy (AM-AFM) was used to examine the influence of the size of the AFM tip apex on the measured surface topography of single highly oriented pyrolytic graphite (HOPG) atomic steps. Experimental measurements were complemented by molecular dynamics simulations of AM-AFM and the results from both were evaluated by comparison of the measured or simulated width of the topography at the step to that predicted using simple rigid-body geometry. The results showed that the step width, which is a reflection of the resolution of the measurement, increased with tip size, as expected, but also that the difference between the measured/simulated step width and the geometric calculation was tip size dependent. The simulations suggested that this may be due to the deformation of the bodies and the effect of that deformation on the interaction force and oscillation amplitude. Overall, this study showed that the resolution of AM-AFM measurements of atomic steps can be correlated to tip size and that this relationship is affected by the deformation of the system.

  4. Leading Change: Transitioning the AFMS into a High Reliability Organization

    DTIC Science & Technology

    2016-02-16

    AIR WAR COLLEGE AIR UNIVERSITY LEADING CHANGE: TRANSITIONING THE AFMS INTO A HIGH RELIABILTY ORGANIZATION by Robert K. Bogart...academic research paper are those of the author and do not reflect the official policy or position of the US government, the Department of Defense, or Air ...University. In accordance with Air Force Instruction 51-303, it is not copyrighted, but is the property of the United States government. iii

  5. Investigation of biopolymer networks by means of AFM

    NASA Astrophysics Data System (ADS)

    Keresztes, Z.; Rigó, T.; Telegdi, J.; Kálmán, E.

    Natural hydrogel alginate was investigated by means of atomic force microscopy (AFM) to gain microscale information on the morphological and rheological properties of the biopolymer network cross-linked by various cations. Local rheological properties of the gels measured by force spectroscopy gave correlation between increasing ion selectivity and increasing polymer elasticity. Adhesive forces acting between the surface of the gel and the probe, and also the intrinsic rheological properties of bulk polymers affect the microscopical image formation.

  6. Adiabatic Compression Sensitivity of AF-M315E

    DTIC Science & Technology

    2015-07-01

    the development of green rocket propellants . The Air Force Research Laboratory’s (AFRL) monopropellant, AF-M315E, has been selected for...art rocket fuels and propellants . A known quantity of liquid propellant is placed in a metal U-tube and held isothermally in a preheated mixture of... Propellant Infusion Mission (GPIM) program. As the propulsion system developed by Aerojet- Rocketdyne for this propellant advances in maturity, studies

  7. Nanoscale rippling on polymer surfaces induced by AFM manipulation

    PubMed Central

    2015-01-01

    Summary Nanoscale rippling induced by an atomic force microscope (AFM) tip can be observed after performing one or many scans over the same area on a range of materials, namely ionic salts, metals, and semiconductors. However, it is for the case of polymer films that this phenomenon has been widely explored and studied. Due to the possibility of varying and controlling various parameters, this phenomenon has recently gained a great interest for some technological applications. The advent of AFM cantilevers with integrated heaters has promoted further advances in the field. An alternative method to heating up the tip is based on solvent-assisted viscoplastic deformations, where the ripples develop upon the application of a relatively low force to a solvent-rich film. An ensemble of AFM-based procedures can thus produce nanoripples on polymeric surfaces quickly, efficiently, and with an unprecedented order and control. However, even if nanorippling has been observed in various distinct modes and many theoretical models have been since proposed, a full understanding of this phenomenon is still far from being achieved. This review aims at summarizing the current state of the art in the perspective of achieving control over the rippling process on polymers at a nanoscale level. PMID:26733086

  8. Near-Field Spectroscopy with Nanoparticles Deposited by AFM

    NASA Technical Reports Server (NTRS)

    Anderson, Mark S.

    2008-01-01

    An alternative approach to apertureless near-field optical spectroscopy involving an atomic-force microscope (AFM) entails less complexity of equipment than does a prior approach. The alternative approach has been demonstrated to be applicable to apertureless near-field optical spectroscopy of the type using an AFM and surface enhanced Raman scattering (SERS), and is expected to be equally applicable in cases in which infrared or fluorescence spectroscopy is used. Apertureless near-field optical spectroscopy is a means of performing spatially resolved analyses of chemical compositions of surface regions of nanostructured materials. In apertureless near-field spectroscopy, it is common practice to utilize nanostructured probe tips or nanoparticles (usually of gold) having shapes and dimensions chosen to exploit plasmon resonances so as to increase spectroscopic-signal strengths. To implement the particular prior approach to which the present approach is an alternative, it is necessary to integrate a Raman spectrometer with an AFM and to utilize a special SERS-active probe tip. The resulting instrumentation system is complex, and the tasks of designing and constructing the system and using the system to acquire spectro-chemical information from nanometer-scale regions on a surface are correspondingly demanding.

  9. Tissue section AFM: In situ ultrastructural imaging of native biomolecules

    PubMed Central

    Graham, Helen K.; Hodson, Nigel W.; Hoyland, Judith A.; Millward-Sadler, Sarah J.; Garrod, David; Scothern, Anthea; Griffiths, Christopher E.M.; Watson, Rachel E.B.; Cox, Thomas R.; Erler, Janine T.; Trafford, Andrew W.; Sherratt, Michael J.

    2010-01-01

    Conventional approaches for ultrastructural high-resolution imaging of biological specimens induce profound changes in bio-molecular structures. By combining tissue cryo-sectioning with non-destructive atomic force microscopy (AFM) imaging we have developed a methodology that may be applied by the non-specialist to both preserve and visualize bio-molecular structures (in particular extracellular matrix assemblies) in situ. This tissue section AFM technique is capable of: i) resolving nm–µm scale features of intra- and extracellular structures in tissue cryo-sections; ii) imaging the same tissue region before and after experimental interventions; iii) combining ultrastructural imaging with complimentary microscopical and micromechanical methods. Here, we employ this technique to: i) visualize the macro-molecular structures of unstained and unfixed fibrillar collagens (in skin, cartilage and intervertebral disc), elastic fibres (in aorta and lung), desmosomes (in nasal epithelium) and mitochondria (in heart); ii) quantify the ultrastructural effects of sequential collagenase digestion on a single elastic fibre; iii) correlate optical (auto fluorescent) with ultrastructural (AFM) images of aortic elastic lamellae. PMID:20144712

  10. Nanoscale Nucleosome Dynamics Assessed with Time-lapse AFM

    PubMed Central

    Lyubchenko, Yuri L.

    2013-01-01

    A fundamental challenge associated with chromosomal gene regulation is accessibility of DNA within nucleosomes. Recent studies performed by various techniques, including single-molecule approaches, led to the realization that nucleosomes are dynamic structures rather than static systems, as it was once believed. Direct data is required in order to understand the dynamics of nucleosomes more clearly and answer fundamental questions, including: What is the range of nucleosome dynamics? Does a non-ATP dependent unwrapping process of nucleosomes exist? What are the factors facilitating the large scale opening and unwrapping of nucleosomes? This review summarizes the results of nucleosome dynamics obtained with time-lapse AFM, including a high-speed version (HS-AFM) capable of visualizing molecular dynamics on the millisecond time scale. With HS-AFM, the dynamics of nucleosomes at a sub-second time scale was observed allowing one to visualize various pathways of nucleosome dynamics, such as sliding and unwrapping, including complete dissociation. Overall, these findings reveal new insights into the dynamics of nucleosomes and the novel mechanisms controlling spontaneous chromatin dynamics. PMID:24839467

  11. Nanotribological properties and mechanisms of alkylthiol and biphenyl thiol self-assembled monolayers studied by AFM

    NASA Astrophysics Data System (ADS)

    Bhushan, Bharat; Liu, Huiwen

    2001-06-01

    Five kinds of alkylthiol and biphenyl thiol monolayers with different surface terminals, spacer chains, and head groups were prepared using a self-assembly method. The adhesion, friction, and wear properties were measured using atomic force microscopy (AFM). It is found that hexadecane thiol (HDT) with a-CH3 terminal exhibits the smallest adhesive force and friction force because of the terminal group with its low work of adhesion and high-compliance long carbon chain. Experimental results and a meniscus analysis indicate that the adhesive force varies linearly with work of adhesion of self-assembled monolayers (SAMs). A molecular spring model is presented to clarify the lubrication mechanisms of SAMs. The molecular spring constant, as well as the inter molecular forces, dictates the magnitude of the coefficients of friction of SAMs. 4,4'-dihydroxybiphenyl (DHBp) on Si(111), due to its rigid biphenyl spacer chains, stronger interface bonds, and a hard substrate, has the best wear resistance. For all of the SAMs, the wear depth with normal load curves show critical normal loads. Below the critical normal load, SAMs undergo orientation, while at the critical normal load SAMs undergo severe wear at the interface due to the weak interfacial bond strengths. The influence of relative humidity on adhesive and frictional forces of SAMs can be mainly understood by comparing their terminal polarization properties and work of adhesion. At higher humidity, water capillary condensation can either increase friction through increased adhesion in the contact zone or reduce friction through an enhanced water-lubricating effect.

  12. High-fidelity AFM scanning stage based on multilayer ceramic capacitors.

    PubMed

    Chen, Jian; Zhang, Lian Sheng; Feng, Zhi Hua

    2016-05-01

    A kind of multilayer ceramic capacitors (MLCCs) has been verified to have good micro-actuating properties, thus making them good candidates for nano-positioning. In this paper, we successfully employed the MLCCs as lateral scanners for a tripod scanning stage. The MLCC-based lateral scanners display hysteresis under 1.5% and a nonlinearity less than 2% even with the simplest open-loop voltage drive. The developed scanning stage was integrated into a commercial AFM to evaluate its imaging performance. Experimental results showed that sample images with high fidelities were obtained. SCANNING 38:184-190, 2016. © 2015 Wiley Periodicals, Inc.

  13. Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments.

    PubMed

    Dague, E; Jauvert, E; Laplatine, L; Viallet, B; Thibault, C; Ressier, L

    2011-09-30

    Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.

  14. Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments

    NASA Astrophysics Data System (ADS)

    Dague, E.; Jauvert, E.; Laplatine, L.; Viallet, B.; Thibault, C.; Ressier, L.

    2011-09-01

    Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.

  15. Virulent strain of Lichtheimia corymbifera shows increased phagocytosis by macrophages as revealed by automated microscopy image analysis.

    PubMed

    Kraibooj, Kaswara; Park, Hea-Reung; Dahse, Hans-Martin; Skerka, Christine; Voigt, Kerstin; Figge, Marc Thilo

    2014-12-01

    Lichtheimia corymbifera is a ubiquitous soilborne zygomycete fungus, which is an opportunistic human pathogen in immunocompromised patients. The fungus can cause life-threatening diseases by attacking the lung during early stages of invasion and by disseminating during later phases causing systemic infection. Since infections have drastically increased during the last decades, it is a major goal to investigate the mechanisms underlying pathogenicity of L. corymbifera. One of the first barriers, which the fungus needs to cope with in the lung tissue, is phagocytosis by alveolar macrophages. Here, we report on phagocytosis assays for murine alveolar macrophages co-incubated with resting, swollen and opsonised spores of a virulent and an attenuated L. corymbifera strain. A major finding of this study is the significantly increased phagocytosis ratio of the virulent strain if compared to the attenuated strain. We quantify the phagocytosis by performing automated analysis of fluorescence microscopy images and by computing ratios for (i) fungal phagocytosis, (ii) fungal adhesion to phagocytes and (iii) fungal aggregation and spore cluster distribution in space. Automation of the image analysis yields objective results that overcome the disadvantages of manual analyses being time consuming, error-prone and subjective. Therefore, it can be expected that automated image analysis of confrontation assays will play a crucial role in future investigations of host-pathogen interactions.

  16. Optimization of functionalization conditions for protein analysis by AFM

    NASA Astrophysics Data System (ADS)

    Arroyo-Hernández, María; Daza, Rafael; Pérez-Rigueiro, Jose; Elices, Manuel; Nieto-Márquez, Jorge; Guinea, Gustavo V.

    2014-10-01

    Activated vapor silanization (AVS) is used to functionalize silicon surfaces through deposition of amine-containing thin films. AVS combines vapor silanization and chemical vapor deposition techniques and allows the properties of the functionalized layers (thickness, amine concentration and topography) to be controlled by tuning the deposition conditions. An accurate characterization is performed to correlate the deposition conditions and functional-film properties. In particular, it is shown that smooth surfaces with a sufficient surface density of amine groups may be obtained with this technique. These surfaces are suitable for the study of proteins with atomic force microscopy.

  17. Global gene analysis of oocytes from early stages in human folliculogenesis shows high expression of novel genes in reproduction.

    PubMed

    Markholt, S; Grøndahl, M L; Ernst, E H; Andersen, C Yding; Ernst, E; Lykke-Hartmann, K

    2012-02-01

    The pool of primordial follicles in humans is laid down during embryonic development and follicles can remain dormant for prolonged intervals, often decades, until individual follicles resume growth. The mechanisms that induce growth and maturation of primordial follicles are poorly understood but follicles once activated either continue growth or undergo atresia. We have isolated pure populations of oocytes from human primordial, intermediate and primary follicles using laser capture micro-dissection microscopy and evaluated the global gene expression profiles by whole-genome microarray analysis. The array data were confirmed by qPCR for selected genes. A total of 6301 unique genes were identified as significantly expressed representing enriched specific functional categories such as 'RNA binding', 'translation initiation' and 'structural molecule activity'. Several genes, some not previously known to be associated with early oocyte development, were identified with exceptionally high expression levels, such as the anti-proliferative transmembrane protein with an epidermal growth factor-like and two follistatin-like domains (TMEFF2), the Rho-GTPase-activating protein oligophrenin 1 (OPHN1) and the mitochondrial-encoded ATPase6 (ATP6). Thus, the present study provides not only a technique to capture and perform transcriptome analysis of the sparse material of human oocytes from the earliest follicle stages but further includes a comprehensive basis for our understanding of the regulatory factors and pathways present during early human folliculogenesis.

  18. Comparative Analysis of Clinical Samples Showing Weak Serum Reaction on AutoVue System Causing ABO Blood Typing Discrepancies

    PubMed Central

    Jo, Su Yeon; Lee, Ju Mi; Kim, Hye Lim; Sin, Kyeong Hwa; Lee, Hyeon Ji; Chang, Chulhun Ludgerus

    2017-01-01

    Background ABO blood typing in pre-transfusion testing is a major component of the high workload in blood banks that therefore requires automation. We often experienced discrepant results from an automated system, especially weak serum reactions. We evaluated the discrepant results by the reference manual method to confirm ABO blood typing. Methods In total, 13,113 blood samples were tested with the AutoVue system; all samples were run in parallel with the reference manual method according to the laboratory protocol. Results The AutoVue system confirmed ABO blood typing of 12,816 samples (97.7%), and these results were concordant with those of the manual method. The remaining 297 samples (2.3%) showed discrepant results in the AutoVue system and were confirmed by the manual method. The discrepant results involved weak serum reactions (<2+ reaction grade), extra serum reactions, samples from patients who had received stem cell transplants, ABO subgroups, and specific system error messages. Among the 98 samples showing ≤1+ reaction grade in the AutoVue system, 70 samples (71.4%) showed a normal serum reaction (≥2+ reaction grade) with the manual method, and 28 samples (28.6%) showed weak serum reaction in both methods. Conclusions ABO blood tying of 97.7% samples could be confirmed by the AutoVue system and a small proportion (2.3%) needed to be re-evaluated by the manual method. Samples with a 2+ reaction grade in serum typing do not need to be evaluated manually, while those with ≤1+ reaction grade do. PMID:28028997

  19. Analysis of the Relationship Between Predictors of No-Show Appointment Behavior and the Benefit of Automated Patient Reminders

    DTIC Science & Technology

    2006-05-31

    number of patients who miss their appointment, clinics have been able to achieve greater efficiency through demand forecasting (Dove and Schneider, 1981 ... 1981 ). Lending further creditability to the predictive value of patient specific characteristics, Goldman, Freidin, Cook, Eigner and Grich ( 1981 ) found...independently correlated with no-show behavior (Goldman et al., 1981 ). As administrators and clinicians grapple with the best method for curbing the

  20. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway.

    PubMed

    Muñoz-Ramírez, Zilia Y; Mendez-Tenorio, Alfonso; Kato, Ikuko; Bravo, Maria M; Rizzato, Cosmeri; Thorell, Kaisa; Torres, Roberto; Aviles-Jimenez, Francisco; Camorlinga, Margarita; Canzian, Federico; Torres, Javier

    2017-01-01

    Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.

  1. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

    PubMed Central

    Muñoz-Ramírez, Zilia Y.; Mendez-Tenorio, Alfonso; Kato, Ikuko; Bravo, Maria M.; Rizzato, Cosmeri; Thorell, Kaisa; Torres, Roberto; Aviles-Jimenez, Francisco; Camorlinga, Margarita; Canzian, Federico; Torres, Javier

    2017-01-01

    Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk. PMID:28293542

  2. Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

    PubMed Central

    Lees, John A.; Kremer, Philip H. C.; Manso, Ana S.; Croucher, Nicholas J.; Ferwerda, Bart; Serón, Mercedes Valls; Oggioni, Marco R.; Parkhill, Julian; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2017-01-01

    Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness. PMID:28348877

  3. Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

    NASA Astrophysics Data System (ADS)

    Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

    2016-11-01

    K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach –conditional time-delayed correlations (CTC) – using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.

  4. Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

    PubMed Central

    Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

    2016-01-01

    K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach –conditional time-delayed correlations (CTC) – using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras. PMID:27845397

  5. Unspecific membrane protein-lipid recognition: combination of AFM imaging, force spectroscopy, DSC and FRET measurements.

    PubMed

    Borrell, Jordi H; Montero, M Teresa; Morros, Antoni; Domènech, Òscar

    2015-11-01

    In this work, we will describe in quantitative terms the unspecific recognition between lactose permease (LacY) of Escherichia coli, a polytopic model membrane protein, and one of the main components of the inner membrane of this bacterium. Supported lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) (3:1, mol/mol) in the presence of Ca(2+) display lateral phase segregation that can be distinguished by atomic force microscopy (AFM) as well as force spectroscopy. LacY shows preference for fluid (Lα) phases when it is reconstituted in POPE : POPG (3:1, mol/mol) proteoliposomes at a lipid-to-protein ratio of 40. When the lipid-to-protein ratio is decreased down to 0.5, two domains can be distinguished by AFM. While the upper domain is formed by self-segregated units of LacY, the lower domain is constituted only by phospholipids in gel (Lβ) phase. On the one hand, classical differential scanning calorimetry (DSC) measurements evidenced the segregation of a population of phospholipids and point to the existence of a boundary region at the lipid-protein interface. On the other hand, Förster Resonance Energy Transfer (FRET) measurements in solution evidenced that POPE is selectively recognized by LacY. A binary pseudophase diagram of POPE : POPG built from AFM observations enables to calculate the composition of the fluid phase where LacY is inserted. These results are consistent with a model where POPE constitutes the main component of the lipid-LacY interface segregated from the fluid bulk phase where POPG predominates.

  6. Analysis of HCV genotypes from blood donors shows three new HCV type 6 subgroups exist in Myanmar.

    PubMed

    Shinji, Toshiyuki; Kyaw, Yi Yi; Gokan, Katsunori; Tanaka, Yasuhito; Ochi, Koji; Kusano, Nobuchika; Mizushima, Takaaki; Fujioka, Shin-ichi; Shiraha, Hidenori; Lwin, Aye Aye; Shiratori, Yasushi; Mizokami, Masashi; Khin, Myo; Miyahara, Masayuki; Okada, Shigeru; Koide, Norio

    2004-06-01

    The prevalence of hepatitis C virus (HCV) genotypes in Myanmar in comparison with the rest of Southeast Asia is not well known. Serum samples were obtained from 201 HCV antibody-positive volunteer blood donors in and around the Myanmar city of Yangon. Of these, the antibody titers of 101 samples were checked by serial dilution using HCV antibody PA test II and Terasaki microplate as a low-cost method. To compare antibody titers by this method and RNA identification, we also checked HCV-RNA using the Amplicor 2.0 test. Most high-titer groups were positive for HCV-RNA. Of the 201 samples, 110 were successfully polymerase chain reaction (PCR) amplified. Among them, 35 (31.8%) were of genotype 1, 52 (47.3%) were of genotype 3, and 23 (20.9%) were of type 6 variants, and phylogenetic analysis of these type 6 variants revealed that 3 new type 6 subgroups exist in Myanmar. We named the subgroups M6-1, M6-2, and M6-3. M6-1 and M6-2 were relatively close to types 8 and 9, respectively. M6-3, though only found in one sample, was a brand-new subgroup. These subtypes were not seen in Vietnam, where type 6 group variants are widely spread. These findings may be useful for analyzing how and when these subgroups were formed.

  7. Phylogenetic analysis shows that Neolithic slate plaques from the southwestern Iberian Peninsula are not genealogical recording systems.

    PubMed

    García Rivero, Daniel; O'Brien, Michael J

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500-2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it.

  8. Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

    PubMed Central

    Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

  9. Anatomical network analysis shows decoupling of modular lability and complexity in the evolution of the primate skull.

    PubMed

    Esteve-Altava, Borja; Boughner, Julia C; Diogo, Rui; Villmoare, Brian A; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon's general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates.

  10. Phylogenetic Analysis Shows That Neolithic Slate Plaques from the Southwestern Iberian Peninsula Are Not Genealogical Recording Systems

    PubMed Central

    García Rivero, Daniel; O'Brien, Michael J.

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500–2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it. PMID:24558384

  11. Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.

    PubMed

    Lloyd, Karen G; May, Megan K; Kevorkian, Richard T; Steen, Andrew D

    2013-12-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

  12. Optical fiber fluorescence spectroscopy for detecting AFM1 in milk

    NASA Astrophysics Data System (ADS)

    Mignani, A. G.; Cucci, C.; Ciaccheri, L.; Dall'Asta, C.; Galaverna, G.; Dossena, A.; Marchelli, R.

    2008-04-01

    Fluorescence spectroscopy carried out by means of optical fibers was used for the rapid screening of M1 aflatoxin in milk, enabling the detection of concentrations up to the legal limit, which is 50 ppt. A compact fluorometric device equipped with a LED source, a miniaturized spectrometer, and optical fibers for illumination/detection of the measuring micro-cell was tested for measuring threshold values of AFM1 in pre-treated milk samples. Multivariate processing of the spectral data made it possible to obtain a preliminary screening at the earlier stages of the industrial process, as well as to discard contaminated milk stocks before their inclusion in the production chain.

  13. High-speed AFM probe with micromachined membrane tip

    NASA Astrophysics Data System (ADS)

    Kim, Byungki; Kwak, Byung Hyung; Jamil, Faize

    2008-08-01

    This paper presents a micromachined silicon membrane type AFM tip designed to move nearly 1µm by electrostatic force. Since the tip can be vibrated in small amplitude with AC voltage input and can be displaced up to 1μm by DC voltage input, an additional piezo actuator is not required for scanning of submicron features. The micromachined membrane tips are designed to have 100 kHz ~ 1 MHz resonant frequency. Displacement of the membrane tip is measured by an optical interferometer using a micromachined diffraction grating on a quartz wafer which is positioned behind the membrane tip.

  14. Theoretical modelling of AFM for bimetallic tip-substrate interactions

    NASA Technical Reports Server (NTRS)

    Bozzolo, Guillermo; Ferrante, John

    1991-01-01

    Recently, a new technique for calculating the defect energetics of alloys based on Equivalent Crystal Theory was developed. This new technique successfully predicts the bulk properties for binary alloys as well as segregation energies in the dilute limit. The authors apply this limit for the calculation of energy and force as a function of separation of an atomic force microscope (AFM) tip and substrate. The study was done for different combinations of tip and sample materials. The validity of the universality discovered for the same metal interfaces is examined for the case of different metal interactions.

  15. The Advancing State of AF-M315E Technology

    NASA Technical Reports Server (NTRS)

    Masse, Robert; Spores, Ronald A.; McLean, Chris

    2014-01-01

    The culmination of twenty years of applied research in hydroxyl ammonium nitrate (HAN)-based monopropellants, the NASA Space Technology mission Directorate's (STMD) Green Propellant Infusion Mission (GPIM) will achieve the first on-orbit demonstration of an operational AF-M315E green propellant propulsion system by the end of 2015. Following an contextual overview of the completed flight design of the GPIM propellant storage and feed system, results of first operation of a flight-representative heavyweight 20-N engineering model thruster (to be conducted in mid-2014) are presented with performance comparisons to prior lab model (heavyweight) test articles.

  16. Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species

    USGS Publications Warehouse

    Larson, James H.; McCalla, Sunnie; Chapman, Duane C.; Rees, Christopher B.; Knights, Brent C.; Vallazza, Jon; George, Amy E.; Richardson, William B.; Amberg, Jon

    2016-01-01

    Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-c oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually Notropis sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to over- lap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.

  17. Efficacy of extended thrombo-prophylaxis in major abdominal surgery: what does the evidence show? A meta-analysis.

    PubMed

    Bottaro, Federico Jorge; Elizondo, Maria Cristina; Doti, Carlos; Bruetman, Julio Enrique; Perez Moreno, Pablo Diego; Bullorsky, Eduardo Oscar; Ceresetto, Jose Manuel

    2008-06-01

    Venous thromboembolism (VTE) is a frequent complication following major abdominal surgery. The use of low-molecular-weight heparins (LMWH) to prevent thrombotic events in these patients is a common and well documented practice. However, there is some controversy surrounding the duration of the prophylaxis, as it has been suggested that the risk persists for several weeks after surgery. The objective of this meta-analysis is to systematically review the clinical studies that compared safety and efficacy of extended use of LMWH (for three to four weeks after surgery) versus conventional in-hospital prophylaxis. An electronic data base search was performed. Only randomized, controlled studies were eligible. Data on the incidence of deep vein thrombosis (DVT), VTE and bleeding were extracted. Only three studies fulfilled the inclusion criteria. The indication for surgery was neoplastic disease in 70.6% (780/1104) of patients. The administration of extended LMWH prophylaxis significantly reduced the incidence of VTE, 5.93% (23/388) versus 13.6% (55/405), RR 0.44 (CI 95% 0.28 - 0.7); DVT 5.93% (23/388) versus 12.9% (52/402), RR 0.46 (CI 95% 0.29 - 0.74); proximal DVT 1% (4/388) versus 4.72% (19/402), RR 0.24 (CI 95% 0.09 - 0.67). We found no significant difference in major or minor bleeding between the two groups: 3.85% (21/545) in the extended thrombo-prophylaxis (ETP) group versus 3.48% (19/559) in the conventional prophylaxis group; RR 1.12 (CI 95% 0.61 - 2.06). There was no heterogeneity between the studies. We conclude that ETP with LMWH should be considered as a safe and useful strategy to prevent VTE in high-risk major abdominal surgery.

  18. Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle

    PubMed Central

    Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

    2016-01-01

    This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection. PMID:26789008

  19. Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

    PubMed Central

    Edwards, Ceiridwen J; Bollongino, Ruth; Scheu, Amelie; Chamberlain, Andrew; Tresset, Anne; Vigne, Jean-Denis; Baird, Jillian F; Larson, Greger; Ho, Simon Y.W; Heupink, Tim H; Shapiro, Beth; Freeman, Abigail R; Thomas, Mark G; Arbogast, Rose-Marie; Arndt, Betty; Bartosiewicz, László; Benecke, Norbert; Budja, Mihael; Chaix, Louis; Choyke, Alice M; Coqueugniot, Eric; Döhle, Hans-Jürgen; Göldner, Holger; Hartz, Sönke; Helmer, Daniel; Herzig, Barabara; Hongo, Hitomi; Mashkour, Marjan; Özdogan, Mehmet; Pucher, Erich; Roth, Georg; Schade-Lindig, Sabine; Schmölcke, Ulrich; Schulting, Rick J; Stephan, Elisabeth; Uerpmann, Hans-Peter; Vörös, István; Voytek, Barbara; Bradley, Daniel G; Burger, Joachim

    2007-01-01

    The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare. PMID

  20. Morphometric analysis of molars in a Middle Pleistocene population shows a mosaic of ‘modern’ and Neanderthal features

    PubMed Central

    Martinón-Torres, María; Spěváčková, Petra; Gracia-Téllez, Ana; Martínez, Ignacio; Bruner, Emiliano; Arsuaga, Juan Luis; Bermúdez de Castro, José María

    2013-01-01

    Previous studies of upper first molar (M1) crown shape have shown significant differences between Homo sapiens and Homo neanderthalensis that were already present in the European Middle Pleistocene populations, including the large dental sample from Atapuerca-Sima de los Huesos (SH). Analysis of other M1 features such as the total crown base area, cusp proportions, cusp angles and occlusal polygon have confirmed the differences between both lineages, becoming a useful tool for the taxonomic assignment of isolated teeth from Late Pleistocene sites. However, until now the pattern of expression of these variables has not been known for the SH sample. This fossil sample, the largest collection from the European Middle Pleistocene, is generally interpreted as being from the direct ancestors of Neanderthals, and thus is a reference sample for assessing the origin of the Neanderthal morphologies. Surprisingly, our study reveals that SH M1s present a unique mosaic of H. neanderthalensis and H. sapiens features. Regarding the cusp angles and the relative occlusal polygon area, SH matches the H. neanderthalensis pattern. However, regarding the total crown base area and relative cusps size, SH M1s are similar to H. sapiens, with a small crown area, a strong hypocone reduction and a protocone enlargement, although the protocone expansion in SH is significantly larger than in any other group studied. The SH dental sample calls into question the uniqueness of some so-called modern traits. Our study also sounds a note of caution on the use of M1 occlusal morphology for the alpha taxonomy of isolated M1s. PMID:23914934

  1. Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle.

    PubMed

    Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

    2016-01-01

    This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection.

  2. Morphometric analysis of molars in a Middle Pleistocene population shows a mosaic of 'modern' and Neanderthal features.

    PubMed

    Martinón-Torres, María; Spěváčková, Petra; Gracia-Téllez, Ana; Martínez, Ignacio; Bruner, Emiliano; Arsuaga, Juan Luis; Bermúdez de Castro, José María

    2013-10-01

    Previous studies of upper first molar (M1) crown shape have shown significant differences between Homo sapiens and Homo neanderthalensis that were already present in the European Middle Pleistocene populations, including the large dental sample from Atapuerca-Sima de los Huesos (SH). Analysis of other M1 features such as the total crown base area, cusp proportions, cusp angles and occlusal polygon have confirmed the differences between both lineages, becoming a useful tool for the taxonomic assignment of isolated teeth from Late Pleistocene sites. However, until now the pattern of expression of these variables has not been known for the SH sample. This fossil sample, the largest collection from the European Middle Pleistocene, is generally interpreted as being from the direct ancestors of Neanderthals, and thus is a reference sample for assessing the origin of the Neanderthal morphologies. Surprisingly, our study reveals that SH M(1) s present a unique mosaic of H. neanderthalensis and H. sapiens features. Regarding the cusp angles and the relative occlusal polygon area, SH matches the H. neanderthalensis pattern. However, regarding the total crown base area and relative cusps size, SH M(1) s are similar to H. sapiens, with a small crown area, a strong hypocone reduction and a protocone enlargement, although the protocone expansion in SH is significantly larger than in any other group studied. The SH dental sample calls into question the uniqueness of some so-called modern traits. Our study also sounds a note of caution on the use of M(1) occlusal morphology for the alpha taxonomy of isolated M(1) s.

  3. Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response.

    PubMed

    Vermeulen, C J; Sørensen, P; Kirilova Gagalova, K; Loeschcke, V

    2013-09-01

    In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds.

  4. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  5. An actuarial analysis shows that offering lung cancer screening as an insurance benefit would save lives at relatively low cost.

    PubMed

    Pyenson, Bruce S; Sander, Marcia S; Jiang, Yiding; Kahn, Howard; Mulshine, James L

    2012-04-01

    Lung cancer screening is not established as a public health practice, yet the results of a recent large randomized controlled trial showed that screening with low-dose spiral computed tomography reduces lung cancer mortality. Using actuarial models, this study estimated the costs and benefits of annual lung cancer screening offered as a commercial insurance benefit in the high-risk US population ages 50-64. Assuming current commercial reimbursement rates for treatment, we found that screening would cost about $1 per insured member per month in 2012 dollars. The cost per life-year saved would be below $19,000, an amount that compares favorably with screening for cervical, breast, and colorectal cancers. Our results suggest that commercial insurers should consider lung cancer screening of high-risk individuals to be high-value coverage and provide it as a benefit to people who are at least fifty years old and have a smoking history of thirty pack-years or more. We also believe that payers and patients should demand screening from high-quality, low-cost providers, thus helping set an example of efficient system innovation.

  6. Comparative analysis of zygotic developmental genes in Rhodnius prolixus genome shows conserved features on the tracheal developmental pathway.

    PubMed

    Lavore, A; Pascual, A; Salinas, F M; Esponda-Behrens, N; Martinez-Barnetche, J; Rodriguez, M; Rivera-Pomar, R

    2015-09-01

    Most of the in-depth studies on insect developmental genetic have been carried out in the fruit fly Drosophila melanogaster, an holometabolous insect, so much more still remains to be studied in hemimetabolous insects. Having Rhodnius prolixus sequenced genome available, we search for orthologue genes of zygotic signaling pathways, segmentation, and tracheogenesis in the R. prolixus genome and in three species of Triatoma genus transcriptomes, concluding that there is a high level of gene conservation. We also study the function of two genes required for tracheal system development in D. melanogaster - R. prolixus orthologues: trachealess (Rp-trh) and empty spiracles (Rp-ems). From that we see that Rp-trh is required for early tracheal development since Rp-trh RNAi shows that the primary tracheal branches fail to form. On the other hand, Rp-ems is implied in the proper formation of the posterior tracheal branches, in a similar way to D. melanogaster. These results represent the initial characterization of the genes involved in the tracheal development of an hemimetabolous insect building a bridge between the current genomic era and V. Wigglesworth's classical studies on insects' respiratory system physiology.

  7. Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products.

    PubMed

    Holloway, David M; Harrison, Lionel G; Kosman, David; Vanario-Alonso, Carlos E; Spirov, Alexander V

    2006-11-01

    We analyze the relation between maternal gradients and segmentation in Drosophila, by quantifying spatial precision in protein patterns. Segmentation is first seen in the striped expression patterns of the pair-rule genes, such as even-skipped (eve). We compare positional precision between Eve and the maternal gradients of Bicoid (Bcd) and Caudal (Cad) proteins, showing that Eve position could be initially specified by the maternal protein concentrations but that these do not have the precision to specify the mature striped pattern of Eve. By using spatial trends, we avoid possible complications in measuring single boundary precision (e.g., gap gene patterns) and can follow how precision changes in time. During nuclear cleavage cycles 13 and 14, we find that Eve becomes increasingly correlated with egg length, whereas Bcd does not. This finding suggests that the change in precision is part of a separation of segmentation from an absolute spatial measure, established by the maternal gradients, to one precise in relative (percent egg length) units.

  8. A Nationwide Analysis of Outcomes of Weekend Admissions for Intracerebral Hemorrhage Shows Disparities Based on Hospital Teaching Status

    PubMed Central

    Patel, Achint A.; Benjo, Alexandre; Pathak, Ambarish; Kar, Jitesh; Jani, Vishal B.; Annapureddy, Narender; Agarwal, Shiv Kumar; Sabharwal, Manpreet S.; Simoes, Priya K.; Konstantinidis, Ioannis; Yacoub, Rabi; Javed, Fahad; El Hayek, Georges; Menon, Madhav C.; Nadkarni, Girish N.

    2015-01-01

    Background and Purpose: With the “weekend effect” being well described, the Brain Attack Coalition released a set of “best practice” guidelines in 2005, with the goal to uniformly provide standard of care to patients with stroke. We attempted to define a “weekend effect” in outcomes among patients with intracranial hemorrhage (ICH) over the last decade, utilizing the Nationwide Inpatient Sample (NIS) data. We also attempted to analyze the trend of such an effect. Materials and Methods: We determined the association of ICH weekend admissions with hospital outcomes including mortality, adverse discharge, length of stay, and cost compared to weekday admissions using multivariable logistic regression. We extracted our study cohort from the NIS, the largest all-payer data set in the United States. Results: Of 485 329 ICH admissions from 2002 to 2011, 27.5% were weekend admissions. Overall, weekend admissions were associated with 11% higher odds of in-hospital mortality. When analyzed in 3-year groups, excess mortality of weekend admissions showed temporal decline. There was higher mortality with weekend admissions in nonteaching hospitals persisted (odds ratios 1.16, 1.13, and 1.09, respectively, for 3-year subgroups). Patients admitted during weekends were also 9% more likely to have an adverse discharge (odds ratio 1.09; 95% confidence interval: 1.07-1.11; P < .001) with no variation by hospital status. There was no effect of a weekend admission on either length of stay or cost of care. Conclusion: Nontraumatic ICH admissions on weekends have higher in-hospital mortality and adverse discharge. This demonstrates need for in-depth review for elucidating this discrepancy and stricter adherence to standard-of-care guidelines to ensure uniform care. PMID:27053981

  9. Transcriptome Analysis of Enterococcus faecalis during Mammalian Infection Shows Cells Undergo Adaptation and Exist in a Stringent Response State

    PubMed Central

    Frank, Kristi L.; Colomer-Winter, Cristina; Grindle, Suzanne M.; Lemos, José A.; Schlievert, Patrick M.; Dunny, Gary M.

    2014-01-01

    As both a commensal and a major cause of healthcare-associated infections in humans, Enterococcus faecalis is a remarkably adaptable organism. We investigated how E. faecalis adapts in a mammalian host as a pathogen by characterizing changes in the transcriptome during infection in a rabbit model of subdermal abscess formation using transcriptional microarrays. The microarray experiments detected 222 and 291 differentially regulated genes in E. faecalis OG1RF at two and eight hours after subdermal chamber inoculation, respectively. The profile of significantly regulated genes at two hours post-inoculation included genes involved in stress response, metabolism, nutrient acquisition, and cell surface components, suggesting genome-wide adaptation to growth in an altered environment. At eight hours post-inoculation, 88% of the differentially expressed genes were down-regulated and matched a transcriptional profile consistent with a (p)ppGpp-mediated stringent response. Subsequent subdermal abscess infections with E. faecalis mutants lacking the (p)ppGpp synthetase/hydrolase RSH, the small synthetase RelQ, or both enzymes, suggest that intracellular (p)ppGpp levels, but not stringent response activation, influence persistence in the model. The ability of cells to synthesize (p)ppGpp was also found to be important for growth in human serum and whole blood. The data presented in this report provide the first genome-wide insights on E. faecalis in vivo gene expression and regulation measured by transcriptional profiling during infection in a mammalian host and show that (p)ppGpp levels affect viability of E. faecalis in multiple conditions relevant to mammalian infection. The subdermal abscess model can serve as a novel experimental system for studying the E. faecalis stringent response in the context of the mammalian immune system. PMID:25545155

  10. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    PubMed Central

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-01-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air. PMID:26574164

  11. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    NASA Astrophysics Data System (ADS)

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-11-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  12. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging.

    PubMed

    Dukic, Maja; Adams, Jonathan D; Fantner, Georg E

    2015-11-17

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  13. Iron oxide mineral-water interface reactions studied by AFM

    SciTech Connect

    Hawley, M.E.; Rogers, P.S.Z.

    1994-07-01

    Natural iron mineral surfaces have been examined in air by atomic force (AFM) and scanning tunneling (STM) microscopies. A number of different surface features were found to be characteristic of the native surface. Even surfaces freshly exposed by crushing larger crystals were found to have a pebbly surface texture caused by the presence of thin coatings of what might be surface precipitates. This finding is interpreted as evidence for previous exposure to water, probably through an extensive network of microfractures. Surface reactions on the goethite crystals were studied by AFM at size resolutions ranging from microns to atomic resolution before, during, and after reaction with distilled water and 0.lN HCl. Immediate and extensive surface reconfiguration occurred on contact with water. In one case, after equilibration with water for 3 days, surface reprecipitation, etching and pitting were observed. Atomic resolution images taken under water were found to be disordered. The result of surface reaction was generally to increase the surface area substantially through the extension of surface platelet arrays, present prior to reaction. This work is being done in support of the site characterization project at Yucca Mountain.

  14. AFM nano-plough planar YBCO micro-bridges: critical currents and magnetic field effects.

    PubMed

    Elkaseh, A A O; Perold, W J; Srinivasu, V V

    2010-10-01

    The critical current (Ic) of YBa2Cu3O7-x (YBCO) AFM plough micro-constrictions is measured as a function of temperature, width and the magnetic flux density (B), which was applied perpendicular to the YBCO ab-plane and surface of the bridges. C-axis oriented thin films of YBa2Cu3O7-x were deposited on MgO substrates using an inverted cylindrical magnetron (ICM) sputtering technique. The films were then patterned into 8-10 micron size strips, using standard photolithography and dry etching processes. Micro-bridges with widths between 1.9 microm to 4.1 microm were fabricated by using atomic force microscope (AFM) nanolithography techniques. Critical current versus temperature data shows a straight-line behavior, which is typical of constriction type Josephson junctions. The Ic versus B characteristics exhibited a modulation, and a suppression of the critical current of up to 84%. It was also found that the critical current increases with increasing constriction width.

  15. Possible enhancements of AFM spin-fluctuations in high-TC cuprates

    NASA Astrophysics Data System (ADS)

    Jarlborg, Thomas

    2009-03-01

    Ab-initio band calculations for high-TC cuprates, together with modelling based of a free electron like band, show a strong interaction between anti-ferromagnetic (AFM) spin waves and periodic lattice distortions as for phonons, even though this type of spin-phonon coupling (SPC) is underestimated in calculations using the local density approximation. The SPC has a direct influence on the properties of the HTC cuprates and it can explain many observations. The strongest effects are seen for modulated waves in the CuO bond direction, and a band gap is formed near the X,Y points, but unusal band dispersion (like ``waterfalls'') might also be induced below the Fermi energy (EF) in the diagonal direction. The band results are used to propose different ways of increasing AFM spin-fluctuations locally, and to have a higher density-of-states (DOS) at EF. Static potential modulations, via periodic distribution of dopants or lattice distortions, can be tuned to increase the DOS. This opens for possibilities to enhance coupling for spin fluctuations (λsf) and superconductivity. The exchange enhancement is in general increased near a surface, which suggests a tendency towards static spin configurations. The sensivity of the band results to corrections of the local density potential are discussed.

  16. Comparison of CD measurements of an EUV photomask by EUV scatterometry and CD-AFM

    NASA Astrophysics Data System (ADS)

    Scholze, Frank; Soltwisch, Victor; Dai, Gaoliang; Henn, Mark-Alexander; Gross, Hermann

    2013-09-01

    EUV scatterometry is a potential high-throughput measurement method for the characterization of EUV photomask structures. We present a comparison of angle resolved extreme ultraviolet (EUV) scatterometry and critical dimension atomic force microscope (CD-AFM) as a reference metrology for measurements of geometrical parameters like line width (CD), height and sidewall angle of EUV photomask structures. The structures investigated are dense and semidense bright and dark lines with different nominal CDs between 140 nm and 540 nm. The results show excellent linearity of the critical dimension measured with both methods within a range of only 1.8 nm and an offset of the absolute values below 3 nm. A maximum likelihood estimation (MLE) method is used to reconstruct the shape parameters and to estimate their uncertainties from the measured scattering efficiencies. The newly developed CD-AFM at PTB allows versatile measurements of parameters such as height, CD, sidewall angle, line edge/width roughness, corner rounding, and pitch. It applies flared tips to probe steep and even undercut sidewalls and employs a new vector approaching probing (VAP) strategy which enables very low tip wear and high measurement flexibility. Its traceability is ensured by a set of calibrated step-height and reference CD standards.

  17. Investigation of geometrical effects in the carbon allotropes manipulation based on AFM: multiscale approach

    NASA Astrophysics Data System (ADS)

    Korayem, M. H.; Hefzabad, R. N.; Homayooni, A.; Aslani, H.

    2017-01-01

    Carbon allotropes are used as nanocarriers for drug and cell delivery. To obtain an accurate result in the nanoscale, it is important to use a precise model. In this paper, a multiscale approach is presented to investigate the manipulation process of carbon allotropes based on atomic force microscopy (AFM). For this purpose, the AFM setup is separated into two parts with different sizes as macro field (MF) and nano field (NF). Using Kirchhoff's plate model, the cantilever (the main part of MF) is modeled. The molecular dynamics method is applied to model the NF part, and then the MF and NF are coupled with the multiscale algorithm. With this model, by considering the effect of size and shape, the manipulation of carbon allotropes is carried out. The manipulations of armchair CNTs and fullerenes are performed to study the diameter changing effects. The result shows that the manipulation and friction force increases by increasing the diameter. The result of the indentation depth for the armchair CNTs indicates that decreasing the diameter causes the indentation depth to reduce. Moreover, the manipulations of four kinds of carbon allotropes with the same number of atoms have been studied to investigate the geometrical effects. The shapes of these nanoparticles change from sphere to cylinder. The results illustrate that the manipulation and the friction force decrease as the nanoparticle shape varies from sphere to cylinder. The Von-Mises results demonstrate that by changing the nanoparticle shape from the spherical to the cylindrical form, the stress increases, although the manipulation force reduces.

  18. AFM studies of cellular mechanics during osteogenic differentiation of human amniotic fluid-derived stem cells.

    PubMed

    Chen, Qian; Xiao, Pan; Chen, Jia-Nan; Cai, Ji-Ye; Cai, Xiao-Fang; Ding, Hui; Pan, Yun-Long

    2010-01-01

    Amniotic fluid-derived stem cells (AFSCs) are becoming an important source of cells for regenerative medicine given with apparent advantages of accessibility, renewal capacity and multipotentiality. In this study, the mechanical properties of human amniotic fluid-derived stem cells (hAFSCs), such as the average Young's modulus, were determined by atomic force microscopy (3.97 ± 0.53 kPa for hAFSCs vs. 1.52 ± 0.63 kPa for fully differentiated osteoblasts). These differences in cell elasticity result primarily from differential actin cytoskeleton organization in these two cell types. Furthermore, ultrastructures, nanostructural details on the surface of cell, were visualized by atomic force microscopy (AFM). It was clearly shown that surface of osteoblasts were covered by mineralized particles, and the histogram of particles size showed that most of the particles on the surface of osteoblasts distributed from 200 to 400 nm in diameter, while the diameter of hAFSCs particles ranged from 100 to 200 nm. In contrast, there were some dips on the surface of hAFSCs, and particles were smaller than that of osteoblasts. Additionally, as osteogenic differentiation of hAFSCs progressed, more and more stress fibers were replaced by a thinner actin network which is characteristic of mature osteoblasts. These results can improve our understanding of the mechanical properties of hAFSCs during osteogenic differentiation. AFM can be used as a powerful tool for detecting ultrastructures and mechanical properties.

  19. Investigation of the influence of UV irradiation on collagen thin films by AFM imaging.

    PubMed

    Stylianou, Andreas; Yova, Dido; Alexandratou, Eleni

    2014-12-01

    Collagen is the major fibrous extracellular matrix protein and due to its unique properties, it has been widely used as biomaterial, scaffold and cell-substrate. The aim of the paper was to use Atomic Force Microscopy (AFM) in order to investigate well-characterized collagen thin films after ultraviolet light (UV) irradiation. The films were also used as in vitro culturing substrates in order to investigate the UV-induced alterations to fibroblasts. A special attention was given in the alteration on collagen D-periodicity. For short irradiation times, spectroscopy (fluorescence/absorption) studies demonstrated that photodegradation took place and AFM imaging showed alterations in surface roughness. Also, it was highlighted that UV-irradiation had different effects when it was applied on collagen solution than on films. Concerning fibroblast culturing, it was shown that fibroblast behavior was affected after UV irradiation of both collagen solution and films. Furthermore, after a long irradiation time, collagen fibrils were deformed revealing that collagen fibrils are consisting of multiple shells and D-periodicity occurred on both outer and inner shells. The clarification of the effects of UV light on collagen and the induced modifications of cell behavior on UV-irradiated collagen-based surfaces will contribute to the better understanding of cell-matrix interactions in the nanoscale and will assist in the appropriate use of UV light for sterilizing and photo-cross-linking applications.

  20. AFM characterization of solid-supported lipid multilayers prepared by spin-coating.

    PubMed

    Pompeo, G; Girasole, M; Cricenti, A; Cattaruzza, F; Flamini, A; Prosperi, T; Generosi, J; Castellano, A Congiu

    2005-06-15

    Lipids are the principal components of biologically relevant structures as cellular membranes. They have been the subject of many studies due to their biological relevance and their potential applications. Different techniques, such as Langmuir-Blodgett and vesicle-fusion deposition, are available to deposit ordered lipid films on etched surfaces. Recently, a new technique of lipid film deposition has been proposed in which stacks of a small and well-controlled number of bilayers are prepared on a suitable substrate using a spin-coater. We studied the morphological properties of multi-layers made of cationic and neutral lipids (DOTAP and DOPC) and mixtures of them using dynamic mode atomic force microscopy (AFM). After adapting and optimizing, the spin-coating technique to deposit lipids on a chemically etched Silicon (1,0,0) substrate, a morphological nanometer-scale characterization of the aforementioned samples has been provided. The AFM study showed that an initial layer of ordered vesicles is formed and, afterward, depending on details of the spin-coating preparation protocol and to the dimension of the silicon substrate, vesicle fusion and structural rearrangements of the lipid layers may occur. The present data disclose the possibility to control the lipid's structures by acting on spin-coating parameters with promising perspectives for novel applications of lipid films.

  1. Dynamic response of AFM cantilevers to dissimilar functionalized silica surfaces in aqueous electrolyte solutions.

    PubMed

    Wu, Yan; Misra, Sambit; Karacor, M Basar; Prakash, Shaurya; Shannon, Mark A

    2010-11-16

    The dynamic response of an oscillating microcantilever with a gold-coated tip interacting with dissimilar functionalized silica surfaces was studied in electrolyte solutions with pH ranging from 4 to 9. Silica surfaces were chemically modified, yielding dissimilar surfaces with -Br, -NH(2), and -CH(3) functional group terminations. The relative hydrophobicity of the surfaces was characterized by contact angle measurements. The surface charge of the functionalized surfaces was first probed with commonly used static AFM measurements and serves as a reference to the dynamic response data. The amplitude and phase of the cantilever oscillation were monitored and used to calculate the effective interaction stiffness and damping coefficient, which relate to the electrical double layer interactions and also to distance-dependent hydrodynamic damping at the solid/water interface. The data for the dynamic response of the AFM over silica surfaces as a function of chemical functionalization and electrolyte pH show that the effective stiffness has a distinctive dependence on the surface charge of functionalized silica surfaces. The hydrodynamic damping also correlates strongly with the relative hydrophobicity of the surface. The data reported here indicate that interfacial properties can be strongly affected by changing the chemical composition of surfaces.

  2. AFM Studies on Liquid Superlubricity between Silica Surfaces Achieved with Surfactant Micelles.

    PubMed

    Li, Jinjin; Zhang, Chenhui; Cheng, Peng; Chen, Xinchun; Wang, Weiqi; Luo, Jianbin

    2016-06-07

    By using atomic force microscopy (AFM), we showed that the liquid superlubricity with a superlow friction coefficient of 0.0007 can be achieved between two silica surfaces lubricated by hexadecyltrimethylammonium bromide (C16TAB) solution. There exists a critical load that the lubrication state translates from superlow friction to high friction reversibly. To analyze the superlow friction mechanism and the factors influencing the critical load, we used AFM to measure the structure of adsorbed C16TAB molecules and the normal force between two silica surfaces. Experimental results indicate that the C16TAB molecules are firmly adsorbed on the two silica surfaces by electrostatic interaction, forming cylinder-like micelles. Meanwhile, the positively charged headgroups exposed to solution produce the hydration and double layer repulsion to bear the applied load. By controlling the concentration of C16TAB solution, it is confirmed that the critical load of superlow friction is determined by the maximal normal force produced by the hydration layer. Finally, the superlow friction mechanism was proposed that the adsorbed micellar layer forms the hydration layer, making the two friction surfaces be in the repulsive region and meanwhile providing excellent fluidity without adhesion between micelles.

  3. Morphological and Structural Changes on Human Dental Enamel After Er:YAG Laser Irradiation: AFM, SEM, and EDS Evaluation

    PubMed Central

    Rodríguez-Vilchis, Laura Emma; Olea-Mejìa, Oscar Fernando; Sánchez-Flores, Ignacio; Centeno-Pedraza, Claudia

    2011-01-01

    Abstract Objective: The purpose of this study was to evaluate, using atomic force microscopy (AFM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS), the morphological and structural changes of the enamel after irradiation with the Er:YAG laser. Background data: A previous study showed that subablative Er:YAG laser irradiation produced undesirable morphological changes on the enamel surface, such as craters and cracks; however, the enamel acid resistance was not increased. Methods: Fifty-two samples of human enamel were divided into four groups (n = 13): Group I was the control (no laser irradiation), whereas Groups II, III, and IV were irradiated with the Er:YAG 100 mJ (12.7 J/cm2), 100 mJ (7.5 J/cm2), and 150 mJ (11 J/cm2), respectively, at 10 Hz with water spray. The morphological changes were observed by AFM and SEM. The weight percentages (wt%) of calcium (Ca), phosphorus (P), oxygen (O) and chlorine (Cl) were determined in the resultant craters and their periphery using EDS. Kruskal–Wallis and Mann–Whitney U tests were performed (p ≤ 0.05) to distinguish significant differences among the groups. Results: The AFM images showed cracks with depths between 250 nm and 750 nm for Groups II and IV, respectively, and the widths of these cracks were 5.37 μm and 2.58 μm. The interior of the cracks showed a rough surface. The SEM micrographs revealed morphological changes. Significant differences were detected in Ca, P, and Cl in the crater and its periphery. Conclusions: AFM observations showed triangular-shaped cracks, whereas craters and cracks were evident by SEM in all irradiated samples. It was not possible to establish a characteristic chemical pattern in the craters. PMID:21417912

  4. Characterization of human ovarian teratoma hair by using AFM, FT-IR, and Raman spectroscopy.

    PubMed

    Kim, Kyung Sook; Lee, Jinwoo; Jung, Min-Hyung; Choi, Young Joon; Park, Hun-Kuk

    2011-12-01

    The structural, physical, and chemical properties of hair taken from an ovarian teratoma (teratoma hair) was first examined by atomic force microscopy (AFM), Fourier transform infrared (FT-IR), and Raman spectroscopy. The similarities and differences between the teratoma hair and scalp hair were also investigated. Teratoma hair showed a similar morphology and chemical composition to scalp hair. Teratoma hair was covered with a cuticle in the same manner as scalp hair and showed the same amide bonding modes as scalp hair according to FT-IR and Raman spectroscopy. On the other hand, teratoma hair showed different physical properties and cysteic acid bands from scalp hair: the surface was rougher and the adhesive force was lower than the scalp hair. The cystine oxides modes did not change with the position unlike scalp hair. These differences can be understood by environmental effects not by the intrinsic properties of the teratoma hair.

  5. Intrinsically High-Q Dynamic AFM Imaging in Liquid with a Significantly Extended Needle Tip

    PubMed Central

    Minary-Jolandan, Majid; Tajik, Arash; Wang, Ning; Yu, Min-Feng

    2012-01-01

    Atomic force microscope (AFM) probe with a long and rigid needle tip was fabricated and studied for high Q factor dynamic (tapping mode) AFM imaging of samples submersed in liquid. The extended needle tip over a regular commercially-available tapping mode AFM cantilever was sufficiently long to keep the AFM cantilever from submersed in liquid, which significantly minimized the hydrodynamic damping involved in dynamic AFM imaging of samples in liquid. Dynamic AFM imaging of samples in liquid at an intrinsic Q factor of over 100 and an operation frequency of over 200 kHz was demonstrated. The method has the potential to be extended to acquire viscoelastic materials properties and provide truly gentle imaging of soft biological samples in physiological environments. PMID:22595833

  6. AFM visualization of sub-50nm polyplex disposition to the nuclear pore complex without compromising the integrity of the nuclear envelope.

    PubMed

    Andersen, Helene; Parhamifar, Ladan; Hunter, A Christy; Shahin, Victor; Moghimi, S Moein

    2016-12-28

    It has been questioned as to whether polyplexes in the cytoplasm can reach the nuclear compartment and if so in what form. By applying atomic force microscopy (AFM) to the nuclear envelope and the nuclear pore complexes, we demonstrate that disposition of polyethylenimine (PEI)/DNA polyplexes that were microinjected into the oocytes of Xenopus laevis, as an example of a non-dividing cell, is exclusive to the nuclear pore complex (NPC). AFM images show NPCs clogged only with sub-50nm polyplexes. This mode of disposition neither altered the morphology/integrity of the nuclear membrane nor the NPC. AFM images further show polyplexes on the nucleoplasmic side of the envelope, presumably indicating species in transit. Transmission electron microscopy studies of ruptured nuclei from transfected human cell lines demonstrate the presence of sub-50nm particles resembling polyplexes in morphology compared with control preparations.

  7. In situ Electrochemical-AFM Study of LiFePO4 Thin Film in Aqueous Electrolyte.

    PubMed

    Wu, Jiaxiong; Cai, Wei; Shang, Guangyi

    2016-12-01

    Lithium-ion (Li-ion) batteries have been widely used in various kinds of electronic devices in our daily life. The use of aqueous electrolyte in Li-ion battery would be an alternative way to develop low cost and environmentally friendly batteries. In this paper, the lithium iron phosphate (LiFePO4) thin film cathode for the aqueous rechargeable Li-ion battery is prepared by radio frequency magnetron sputtering deposition method. The XRD, SEM, and AFM results show that the film is composed of LiFePO4 grains with olivine structure and the average size of 100 nm. Charge-discharge measurements at current density of 10 μAh cm(-2) between 0 and 1 V show that the LiFePO4 thin film electrode is able to deliver an initial discharge capacity of 113 mAh g(-1). Specially, the morphological changes of the LiFePO4 film electrode during charge and discharge processes were investigated in aqueous environment by in situ EC-AFM, which is combined AFM with chronopotentiometry method. The changes in grain area are measured, and the results show that the size of the grains decreases and increases during the charge and discharge, respectively; the relevant mechanism is discussed.

  8. In situ Electrochemical-AFM Study of LiFePO4 Thin Film in Aqueous Electrolyte

    NASA Astrophysics Data System (ADS)

    Wu, Jiaxiong; Cai, Wei; Shang, Guangyi

    2016-04-01

    Lithium-ion (Li-ion) batteries have been widely used in various kinds of electronic devices in our daily life. The use of aqueous electrolyte in Li-ion battery would be an alternative way to develop low cost and environmentally friendly batteries. In this paper, the lithium iron phosphate (LiFePO4) thin film cathode for the aqueous rechargeable Li-ion battery is prepared by radio frequency magnetron sputtering deposition method. The XRD, SEM, and AFM results show that the film is composed of LiFePO4 grains with olivine structure and the average size of 100 nm. Charge-discharge measurements at current density of 10 μAh cm-2 between 0 and 1 V show that the LiFePO4 thin film electrode is able to deliver an initial discharge capacity of 113 mAh g-1. Specially, the morphological changes of the LiFePO4 film electrode during charge and discharge processes were investigated in aqueous environment by in situ EC-AFM, which is combined AFM with chronopotentiometry method. The changes in grain area are measured, and the results show that the size of the grains decreases and increases during the charge and discharge, respectively; the relevant mechanism is discussed.

  9. Device level 3D characterization using PeakForce AFM

    NASA Astrophysics Data System (ADS)

    Timoney, Padraig; Zhang, Xiaoxiao; Vaid, Alok; Hand, Sean; Osborne, Jason; Milligan, Eric; Feinstein, Adam

    2016-03-01

    Traditional metrology solutions face a range of challenges at the 1X node such as three dimensional (3D) measurement capabilities, shrinking overlay and critical dimension (CD) error budgets driven by multi-patterning and via in trench CD measurements. With advent of advanced technology nodes and 3D processing, an increasing need is emerging for in-die metrology including across-structure and structure-to-structure characterization. A myriad of work has emerged in the past few years intending to address these challenges from various aspects; in-die OCD with reduced spot size and tilt beam on traditional critical dimension scanning electron microscopy (CDSEM) for height measurements. This paper explores the latest capability offered by PeakForceTM Tapping Atomic Force Microscopy (PFT-AFM). The use of traditional harmonic tapping mode for scanning high aspect ratio, and complex "3D" wafer structures, results in limited depth probing capability as well as excessive tip wear. These limitations arise due to the large tip-sample interaction volume in such confined spaces. PeakForce Tapping eliminates these limitations through direct real time control of the tip-sample interaction contact force. The ability of PeakForce to measure, and respond directly to tip- sample interaction forces results in more detailed feature resolution, reduced tip wear, and improved depth capability. In this work, the PFT-AFM tool was applied for multiple applications, including the 14nm fin and replacement metal gate (RMG) applications outlined below. Results from DOE wafers, detailed measurement precision studies and correlation to reference metrology are presented for validation of this methodology. With the fin application, precision of 0.3nm is demonstrated by measuring 5 dies with 10 consecutive runs. Capability to resolve within-die and localized within-macro height variation is also demonstrated. Results obtained from the fin measurements support the increasing trend that measurements

  10. Dispersion and Fixation of Adeno-Associated Virus with Glutaraldehyde for Afm Studies

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Wang, Xinyan; Yang, Haijun; Lü, Junhong

    Sample preparation is an important procedure for atomic force microscope (AFM) studies. However, flexible virus particles have a tendency to aggregate together and are easily compressed during sample preparation or by AFM tip that subsequently hamper studying of virus by AFM. Herein, low concentration chemical reagent of glutaraldehyde (2%, v/v) is pre-mixed in virus suspension that facilitates the dispersion and observation of recombinant serotype 2 adeno-associated virus particles deposited on mica surface with little deformation.

  11. Acquisition of a Modular, Multi-laser, Raman-AFM Instrument for Multdisciplinary Research

    DTIC Science & Technology

    2015-04-28

    vapor deposition on copper foils. The four lasers range from the blue to 785 nm and provides a unique handle to determine excitation dependence of...Acquisition of a Modular, Multi- laser , Raman- AFM Instrument for Multdisciplinary Research A four- laser , confocal Raman/Atomic Force Scanning... laser , Raman-AFM Instrument for Multdisciplinary Research Report Title A four- laser , confocal Raman/Atomic Force Scanning microscope (Raman-AFM

  12. Interlayer formation of diamond-like carbon coatings on industrial polyethylene: Thickness dependent surface characterization by SEM, AFM and NEXAFS

    NASA Astrophysics Data System (ADS)

    Fischer, Christian B.; Rohrbeck, Magdalena; Wehner, Stefan; Richter, Matthias; Schmeißer, Dieter

    2013-04-01

    The coating of materials with diamond-like carbon (DLC) is a very common way to change and improve their basic characteristics. Although DLC is used on several substrates, the chemical and physical properties throughout the coating process on plastics are yet sparsely investigated. Two types of protective coatings one sp3-enriched (robust, r-type) and one with more sp2-centers (flexible, f-type) have been realized on polyethylene by PECVD deposition. SEM and AFM analysis of coated samples of DLC types revealed diverse surface topographies on different scales and images appeared even differently smoothed by the carbonaceous deposits. Grains of both DLC types are platelet-shaped and nearly double in size for the robust type indicating fundamental differences in the epitaxial DLC growth. NEXAFS spectroscopy showed significant details of carbon centers in chemically different neighborhood displaying a characteristic fingerprint behavior. Comparison of deposition models revealed a mechanism of interlayer formation which is discussed in detail. Interlayer formation is clearly the appropriate explanation of the process for the current carbon deposition between these two unequal materials. An improved understanding of hard DLC and soft polyethylene assembly is given in the presented work.

  13. Bubble colloidal AFM probes formed from ultrasonically generated bubbles.

    PubMed

    Vakarelski, Ivan U; Lee, Judy; Dagastine, Raymond R; Chan, Derek Y C; Stevens, Geoffrey W; Grieser, Franz

    2008-02-05

    Here we introduce a simple and effective experimental approach to measuring the interaction forces between two small bubbles (approximately 80-140 microm) in aqueous solution during controlled collisions on the scale of micrometers to nanometers. The colloidal probe technique using atomic force microscopy (AFM) was extended to measure interaction forces between a cantilever-attached bubble and surface-attached bubbles of various sizes. By using an ultrasonic source, we generated numerous small bubbles on a mildly hydrophobic surface of a glass slide. A single bubble picked up with a strongly hydrophobized V-shaped cantilever was used as the colloidal probe. Sample force measurements were used to evaluate the pure water bubble cleanliness and the general consistency of the measurements.

  14. BOREAS AFM-04 Twin Otter Aircraft Sounding Data

    NASA Technical Reports Server (NTRS)

    MacPherson, J. Ian; Desjardins, Raymond L.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-4 team used the National Research Council, Canada (NRC) Twin Otter aircraft to make sounding measurements through the boundary layer. These measurements included concentrations of carbon dioxide and ozone, atmospheric pressure, dry bulb temperature, potential temperature, dewpoint temperature, calculated mixing ratio, and wind speed and direction. Aircraft position, heading, and altitude were also recorded. Data were collected at both the Northern Study Area (NSA) and the Southern Study Area (SSA) in 1994 and 1996. These data are stored in tabular ASCII files. The Twin Otter aircraft sounding data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files also are available on a CD-ROM (see document number 20010000884).

  15. Examination of Humidity Effects on Measured Thickness and Interfacial Phenomena of Exfoliated Graphene on SiO2 via AC-AFM

    NASA Astrophysics Data System (ADS)

    Jinkins, Katherine; Camacho, Jorge; Farina, Lee; Wu, Yan

    2015-03-01

    Tapping (AC) mode Atomic Force Microscopy (AFM) is commonly used to determine the thickness of graphene samples. However, AFM measurements have been shown to be sensitive to environmental conditions such as adsorbed water, in turn dependent on relative humidity (RH). In the present study, AC-AFM is used to measure the thickness and loss tangent of exfoliated graphene on silicon dioxide (SiO2) as RH is increased from 10% to 80%. We show that the measured thickness of graphene is dependent on RH. Loss tangent is an AFM imaging technique that interprets the phase information as a relationship between the stored and dissipated energy in the tip-sample interaction. This study demonstrates the loss tangent of the graphene and oxide regions are both affected by humidity, with generally higher loss tangent for graphene than SiO2. As RH increases, we observe the loss tangent of both materials approaches the same value. We hypothesize that there is a layer of water trapped between the graphene and SiO2 substrate to explain this observation. Using this interpretation, the loss tangent images also indicate movement and change in this trapped water layer as RH increases, which impacts the measured thickness of graphene using AC-AFM.

  16. In-plane information from tapping mode AFM images

    NASA Astrophysics Data System (ADS)

    Marcus, Matthew

    2003-03-01

    Phase contrast in intermittent-contact atomic force microscopy is shown to reveal in-plane structural and mechanical properties of poly(diacetylene) monolayer films. This is surprising because measurements of in-plane properties typically require a contact mode of microscopy. Such measurements are possible because the tilt in the oscillating cantilever provides components of motion not just perpendicular to the surface, but also parallel to the sample surface. Lateral tip displacement is virtually universal in AFM, implying that any oscillating tip-AFM technique is sensitive to in-plane material properties. Although the tilt in the cantilever is small ( 10^o) it produces a component of motion that is 20% of the total tip displacement, and this motion accounts for 5-10% of dissipated energy through the tip-sample interaction[1]. The data is used in conjunction with a numerical model to extract in-plane material parameters. The effect of the cantilever tilt on phase measurements is directly verified through measurements on silicon samples tilted at a variety of angles with respect to the cantilever. The lateral tip displacement we make use of allows measurements of in-plane properties of soft samples such as polymer and biological samples. This work was done in collaboration with M. D'Amato, R.W. Carpick, and M.A. Eriksson, and was supported by the NSF CAREER and MRSEC programs and the Research Corporation. 1. M.S. Marcus, R.W. Carpick, D.Y. Sasaki, M.A. Eriksson, Phys. Rev. Lett. 88, 226103 (2002)

  17. AFM and SEM study of the effects of etching on IPS-Empress 2 TM dental ceramic

    NASA Astrophysics Data System (ADS)

    Luo, X.-P.; Silikas, N.; Allaf, M.; Wilson, N. H. F.; Watts, D. C.

    2001-10-01

    The aim of this study was to investigate the effects of increasing etching time on the surface of the new dental material, IPS-Empress 2 TM glass ceramic. Twenty one IPS-Empress 2 TM glass ceramic samples were made from IPS-Empress 2 TM ingots through lost-wax, hot-pressed ceramic fabrication technology. All samples were highly polished and cleaned ultrasonically for 5 min in acetone before and after etching with 9.6% hydrofluoric acid gel. The etching times were 0, 10, 20, 30, 60, 90 and 120 s respectively. Microstructure was analysed by scanning electron microscopy (SEM) and atomic force microscopy (AFM) was used to evaluate the surface roughness and topography. Observations with SEM showed that etching with hydrofluoric acid resulted in preferential dissolution of glass matrix, and that partially supported crystals within the glass matrix were lost with increasing etching time. AFM measurements indicated that etching increased the surface roughness of the glass-ceramic. A simple least-squares linear regression was used to establish a relationship between surface roughness parameters ( Ra, RMS), and etching time, for which r2>0.94. This study demonstrates the benefits of combining two microscopic methods for a better understanding of the surface. SEM showed the mode of action of hydrofluoric acid on the ceramic and AFM provided valuable data regarding the extent of surface degradation relative to etching time.

  18. Multiparametric AFM reveals turgor-responsive net-like peptidoglycan architecture in live streptococci

    NASA Astrophysics Data System (ADS)

    Saar Dover, Ron; Bitler, Arkady; Shimoni, Eyal; Trieu-Cuot, Patrick; Shai, Yechiel

    2015-05-01

    Cell-wall peptidoglycan (PG) of Gram-positive bacteria is a strong and elastic multi-layer designed to resist turgor pressure and determine the cell shape and growth. Despite its crucial role, its architecture remains largely unknown. Here using high-resolution multiparametric atomic force microscopy (AFM), we studied how the structure and elasticity of PG change when subjected to increasing turgor pressure in live Group B Streptococcus. We show a new net-like arrangement of PG, which stretches and stiffens following osmotic challenge. The same structure also exists in isogenic mutants lacking surface appendages. Cell aging does not alter the elasticity of the cell wall, yet destroys the net architecture and exposes single segmented strands with the same circumferential orientation as predicted for intact glycans. Together, we show a new functional PG architecture in live Gram-positive bacteria.

  19. Investigation of Oxidation Profile in PMR-15 Polyimide using Atomic Microscope (AFM)

    NASA Technical Reports Server (NTRS)

    Meador, Mary Ann B.; Johnson, Lili L.; Eby, R. K.

    2002-01-01

    Nanoindentation measurements are made on thermosetting materials using cantiever deflection vs. piezoelectric scanner position behavior determined by AFM. The spring model is used to determine mechanical properties of materials. The generalized Sneddon's equation is utilized to calculate Young's moduli for thermosetting materials at ambient conditions. Our investigations show that the force-penetration depth curves during unloading in these materials can be described accurately by a power law relationship. The results show that the accuracy of the measurements can be controlled within 7%. The above method is used to study oxidation profiles in Pl\\1R-15 polyimide. The thermo-mechanical profiles ofPNIR-15 indicate that the elastic modulus at the surface portion of the specimen is different from that at the interior of the material. It is also shown that there are two zones within the oxidized portion of the samples. Results confirm that the surface layer and the core material have substantially different properties.

  20. AFM study of the effects of laser surface remelting on the morphology of Al-Fe aerospace alloys

    SciTech Connect

    Pariona, Moises Meza; Teleginski, Viviane; Santos, Kelly dos; Leandro Ribeiro dos Santos, Everton; Aparecida de Oliveira Camargo de Lima, Angela; Riva, Rudimar

    2012-12-15

    Laser beam welding has recently been incorporated into the fabrication process of aircraft and automobile structures. Surface roughness is an important parameter of product quality that strongly affects the performance of mechanical parts, as well as production costs. This parameter influences the mechanical properties such as fatigue behavior, corrosion resistance, creep life, etc., and other functional characteristics such as friction, wear, light reflection, heat transmission, lubrification, electrical conductivity, etc. The effects of laser surface remelting (LSR) on the morphology of Al-Fe aerospace alloys were examined before and after surface treatments, using optical microscopy (OM), scanning electron microscopy (SEM), low-angle X-ray diffraction (LA-XRD), atomic force microscopy (AFM), microhardness measurements (Vickers hardness), and cyclic voltammetry. This analysis was performed on both laser-treated and untreated sanded surfaces, revealing significant differences. The LA-XRD analysis revealed the presence of alumina, simple metals and metastable intermetallic phases, which considerably improved the microhardness of laser-remelted surfaces. The morphology produced by laser surface remelting enhanced the microstructure of the Al-Fe alloys by reducing their roughness and increasing their hardness. The treated surfaces showed passivity and stability characteristics in the electrolytic medium employed in this study. - Highlights: Black-Right-Pointing-Pointer The samples laser-treated and untreated showed significant differences. Black-Right-Pointing-Pointer The La-XRD revealed the presence of alumina in Al-1.5 wt.% Fe. Black-Right-Pointing-Pointer The laser-treated reducing the roughness and increasing the hardness. Black-Right-Pointing-Pointer The laser-treated surfaces showed characteristic passive in the electrolytic medium. Black-Right-Pointing-Pointer The laser-treated is a promising technique for applications technological.

  1. Data fusion for CD metrology: heterogeneous hybridization of scatterometry, CDSEM, and AFM data

    NASA Astrophysics Data System (ADS)

    Hazart, J.; Chesneau, N.; Evin, G.; Largent, A.; Derville, A.; Thérèse, R.; Bos, S.; Bouyssou, R.; Dezauzier, C.; Foucher, J.

    2014-04-01

    The manufacturing of next generation semiconductor devices forces metrology tool providers for an exceptional effort in order to meet the requirements for precision, accuracy and throughput stated in the ITRS. In the past years hybrid metrology (based on data fusion theories) has been investigated as a new methodology for advanced metrology [1][2][3]. This paper provides a new point of view of data fusion for metrology through some experiments and simulations. The techniques are presented concretely in terms of equations to be solved. The first point of view is High Level Fusion which is the use of simple numbers with their associated uncertainty postprocessed by tools. In this paper, it is divided into two stages: one for calibration to reach accuracy, the second to reach precision thanks to Bayesian Fusion. From our perspective, the first stage is mandatory before applying the second stage which is commonly presented [1]. However a reference metrology system is necessary for this fusion. So, precision can be improved if and only if the tools to be fused are perfectly matched at least for some parameters. We provide a methodology similar to a multidimensional TMU able to perform this matching exercise. It is demonstrated on a 28 nm node backend lithography case. The second point of view is Deep Level Fusion which works on the contrary with raw data and their combination. In the approach presented here, the analysis of each raw data is based on a parametric model and connections between the parameters of each tool. In order to allow OCD/SEM Deep Level Fusion, a SEM Compact Model derived from [4] has been developed and compared to AFM. As far as we know, this is the first time such techniques have been coupled at Deep Level. A numerical study on the case of a simple stack for lithography is performed. We show strict equivalence of Deep Level Fusion and High Level Fusion when tools are sensitive and models are perfect. When one of the tools can be considered as a

  2. Supramolecular self-assembly of linear oligosilsesquioxanes on mica--AFM surface imaging and hydrophilicity studies.

    PubMed

    Kowalewska, Anna; Nowacka, Maria; Tracz, Adam; Makowski, Tomasz

    2015-06-28

    Linear oligomeric [2-(carboxymethylthio)ethylsilsesquioxanes] (LPSQ-COOH) adsorb spontaneously on muscovite mica and form smooth, well-ordered lamellar structures at the liquid-solid interface. Side carboxylic groups, having donor-acceptor character with regard to hydrogen bonds, are engaged both in multipoint molecule-to-substrate interactions and intermolecular cross-linking. The unique arrangement of silsesquioxane macromolecules, with COOH groups situated at the interface with air, produces highly hydrophilic surfaces of good thermal and solvolytic stability. Supramolecular assemblies of LPSQ-COOH were studied using atomic force microscopy (AFM), angle-resolved X-ray photoelectron spectroscopy (ARXPS) and attenuated total reflectance (ATR) FTIR spectroscopy. Comparative height profile analysis combined with ATR-FTIR studies of the spectral regions characteristic of carboxylic groups and C1s core level envelope by XPS confirmed specific interactions between LPSQ-COOH and mica.

  3. Measurement of a CD and sidewall angle artifact with two-dimensional CD AFM metrology

    NASA Astrophysics Data System (ADS)

    Dixson, Ronald G.; Sullivan, Neal T.; Schneir, Jason; McWaid, Thomas H.; Tsai, Vincent W.; Prochazka, Jerry; Young, Michael

    1996-05-01

    Despite the widespread acceptance of SEM metrology in semiconductor manufacturing, there is no SEM CD standard currently available. Producing such a standard is challenging because SEM CD measurements are not only a function of the linewidth, but also dependent on the line material, sidewall roughness, sidewall angle, line height, substrate material, and the proximity of other objects. As the presence of AFM metrology in semiconductor manufacturing increases, the history of SEM CD metrology raises a number of questions about the prospect of AFM CD artifacts. Is an AFM CD artifact possible? What role would it play in the manufacturing environment? Although AFM has some important advantages over SEM, such as relative insensitivity to material differences, the throughput and reliability of most AFM instruments is not yet at the level necessary to support in-line CD metrology requirements. What, then, is the most useful relationship between AFM and SEM metrology? As a means of addressing some of these questions, we have measured the CD and sidewall angle of 1.2 micrometer oxy-nitride line on Si using three different techniques: optical microscopy (with modeling), AFM, and cross sectional TEM. Systematic errors in the AFM angle measurements were reduced by using a rotational averaging technique that we describe. We found good agreement with uncertainties below 30 nm (2 sigma) for the CD measurement and 1.0 degrees (2 sigma) for the sidewall angles. Based upon these results we suggest a measurement procedure which will yield useful AFM CD artifacts. We consider the possibility that AFMs, especially when used with suitable CD artifacts, can effectively support SEM CD metrology. This synergistic relationship between the AFM and SEM represents an emerging paradigm that has also been suggested by a number of others.

  4. Probing the role of metal cations on the aggregation behavior of amyloid β-peptide at a single molecule level by AFM

    NASA Astrophysics Data System (ADS)

    Xie, Yang; Wang, Jianhua; Liu, Chundong

    2016-09-01

    With the development of nanotechnology, understanding of intermolecular interactions on a single molecule level by atomic force spectroscopy (AFM) has played an important role in molecular biology and biomedical science. In recent years, some research suggested that the presence of metal cations is an important regulator in the processes of misfolding and aggregation of the amyloid β-protein (Aβ), which may be an important etiological factor of Alzheimer's disease. However, the knowledge on the principle of interactions between Aβ and metal cations at the single molecule level is still poor understood. In this paper, the amyloid β-protein (Aβ) was fabricated on substrate of mixed thiol-modified gold nanoparticles using self-assembled monolayer method and the adhesion force in the longitudinal direction between metal cations and Aβ42 were investigated by AFM. The role of metal ions on Aβ aggregation is discussed from the perspective of single molecular force. The force results showed that the specific adhesion force F i and the nonspecific force F 0 between a single Aβ-Aβ pair in control experiment were calculated as 42 ± 3 and 80 pN, respectively. However, F i between a single Aβ-Aβ pair in the presence of Cu2+, Zn2+, Ca2+ and Al3+ increased dramatically to 84 ± 6, 89 ± 3, 73 ± 5, 95 ± 5 pN successively, which indicated that unbinding between Aβ proteins is accelerated in the presence of metal cations. What is more, the imaging results showed that substoichiometric copper cations accelerate the formation of fibrils within 3 days. The combined atomic force spectroscopy and imaging analysis indicate that metal cations play a role in promoting the aggregating behavior of Aβ42.

  5. Mechanical properties of in situ demineralised human enamel measured by AFM nanoindentation

    NASA Astrophysics Data System (ADS)

    Finke, Manuela; Hughes, Julie A.; Parker, David M.; Jandt, Klaus D.

    2001-10-01

    Diet-induced demineralisation is one of the key factors in surface changes of tooth enamel, with soft drinks being a significant etiological agent. The first step in this dissolution process is characterised by a change in the mechanical properties of the enamel and a roughening of the surface. The objective of this pilot study was to measure early stages of in situ induced hardness changes of polished human enamel surfaces with high accuracy using a nanoindenter attached to an atomic force microscope (AFM). Human unerupted third molars were cleaned, sterilised with sodium hypochlorite, sectioned and embedded in epoxy resin. The outer enamel surface was polished and the samples partly covered with a tape, allowing a 2-mm-wide zone to be exposed to the oral environment. Samples were fitted in an intra-oral appliance, which was worn from 9 a.m. to 5 p.m. for one day. During this time the volunteer sipped 250 ml of a drink over 10 min periods at 9.00, 11.00, 13.00 and 15.00 h. Three different drinks, mineral water, orange juice and the prototype of a blackcurrant drink with low demineralisation potential were used in this study. At the end of the experiment the samples were detached from the appliance, the tape removed and the surfaces chemically cleaned. The surface hardness and reduced Young's modulus of the exposed and unexposed areas of each sample were determined. In addition, high resolution topographical AFM images were obtained. This study shows that by determining the hardness and reduced Young's modulus, the difference in demineralisation caused by the drinks can be detected and quantified before statistically significant changes in surface topography could be observed with the AFM. The maximum decrease in surface hardness and Young's modulus occurred in the samples exposed to orange juice, followed by those exposed to the blackcurrant drink, while exposure to water led to the same values as unexposed areas. A one-way ANOVA showed a statistically significant

  6. Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup

    PubMed Central

    Leitner, Michael; Fantner, Georg E.; Fantner, Ernest J.; Ivanova, Katerina; Ivanov, Tzvetan; Rangelow, Ivo; Ebner, Andreas; Rangl, Martina; Tang, Jilin; Hinterdorfer, Peter

    2012-01-01

    In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46 μm, a width of about 11 μm, and a thickness between 150 and 600 nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants. PMID:22721963

  7. Atomic force microscopy for analyzing metaphase chromosomes: comparison of AFM images with fluorescence labeling images of banding patterns.

    PubMed

    Hoshi, Osamu; Ushiki, Tatsuo

    2014-01-01

    The combined use of fluorescence microscopy with atomic force microscopy (AFM) has been introduced to analyze the replication-banding patterns of human chromosomes. Human lymphocytes synchronized with excess thymidine are treated with 5-ethynyl-2'-deoxyuridine (EdU) during the late S phase. EdU-labeled DNA is detected in metaphase chromosomes using Alexa Fluor 488(®) azide, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acetylene group of EdU. Chromosomes with EdU incorporated during the late S phase show a banding pattern similar to the G-banding pattern of normal human chromosomes. The comparison between the fluorescence and AFM image of the same chromosome indicates the presence of ridges and grooves in the chromatid arms, which correspond to G-positive and G-negative bands, respectively. This technique of EdU-labeled replication bands combined with AFM is useful to analyze the structure of chromosomes in relation to the banding pattern.

  8. AFM-based study of fullerenol (C60(OH)24)-induced changes of elasticity in living SMCC-7721 cells.

    PubMed

    Liu, Yang; Wang, Zuobin; Wang, Xinyue

    2015-05-01

    In this study, the alterations of the morphology and biomechanical properties of living SMCC-7721 cancer cells treated with fullerenol (C60(OH)24) for 24, 48, and 72h were investigated using an atomic force microscope (AFM). Comparative analyses show that the elastic moduli of the SMCC-7721 cells exposed to fullerenol decrease significantly with the increase of the treatment periods. Furthermore, in different phases of the treatment, a global decrease in elasticity is accompanied by cellular morphological changes, and the time-dependent effect of the fullerenol can be observed using AFM and optical microscope. In addition, as the treatment duration increases, the indentation force and depth penetrated into the cell membrane by the AFM tip are in a declining trend. The reduction in the stiffness of the cells exposed to fullerenol could be associated with the disruption of the cellular cytoskeleton network. The investigation indicates that the elastic modulus of single living cells can be a useful biomarker to evaluate the effects of fullerenol or other anticancer agents on the cells and reveal instructive information for cellular dynamic behaviors.

  9. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction.

    PubMed

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-07-25

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.

  10. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

    NASA Astrophysics Data System (ADS)

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-07-01

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.

  11. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

    PubMed Central

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-01-01

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation. PMID:27452115

  12. Proceedings of the 2010 AFMS Medical Research Symposium. Volume 5. Nursing Track: Abstracts and Presentations

    DTIC Science & Technology

    2011-03-15

    will include hematocrit, hemoglobin , mean corpuscle volume, iron , total iron binding capacity, Ferritin , and soluble transferring receptor. The...Iraq/Afghanistan ........ 2  Iron Status of Deployed Military Members...2010 AFMS Medical Research Symposium Volume 5 Nursing 8 Proceedings of the 2010 AFMS Medical Research Symposium Volume 5 Nursing 9 Iron

  13. Fabrication of YBCO-LSMO-YBCO Lateral Structure with AFM Lithography

    NASA Astrophysics Data System (ADS)

    Ishii, K.; Tachiki, M.; Ooi, S.; Hirata, K.

    We have tried to make the superconductor/half metal/superconductor (SC/HF/SC) Josephson junction to make clear a long range proximity effect. The structure was consisted of high-Tc superconductor YBa2Cu3O7-x and half metallic ferromagnet La0.7Sr0.3MnO3 thin films deposited by pulse laser deposition on SrTiO3(100) single crystal substrates. The SC/HF/SC lateral structure was made by scratching with the atomic force microscope (AFM) probe. We could cut the ditch which has 30 nm width and 50 nm depth. We have investigated the I-V and R-T measurements of the structure. The structure after the fabrication did not show the superconducting state and we could not find the Josephson current.

  14. BOREAS AFM-6 NOAA/ETL 35 GHz Cloud/Turbulence Radar GIF Images

    NASA Technical Reports Server (NTRS)

    Martner, Brooks E.; Newcomer, Jeffrey A. (Editor); Hall, Forrest G.; Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Administration/Environment Technology Laboratory (NOAA/ETL) operated a 35-GHz cloud-sensing radar in the Northern Study Area (NSA) near the Old Jack Pine (OJP) tower from 16 Jul 1994 to 08 Aug 1994. This data set contains a time series of GIF images that show the structure of the lower atmosphere. The NOAA/ETL 35-GHz cloud/turbulence radar GIF images are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  15. Hot-Fire Testing of a 1N AF-M315E Thruster

    NASA Technical Reports Server (NTRS)

    Burnside, Christopher G.; Pedersen, Kevin; Pierce, Charles W.

    2015-01-01

    This hot-fire test continues NASA investigation of green propellant technologies for future missions. To show the potential for green propellants to replace some hydrazine systems in future spacecraft, NASA Marshall Space Flight Center (MSFC) is continuing to embark on hot-fire test campaigns with various green propellant blends. NASA completed a hot-fire test of a 1N AF-M315E monopropellant thruster at the Marshall Space Flight Center in the small altitude test stand located in building 4205. The thruster is a ground test article used for basic performance determination and catalyst studies. The purpose of the hot-fire testing was for performance determination of a 1N size thruster and form a baseline from which to study catalyst performance and life with follow-on testing to be conducted at a later date. The thruster performed as expected. The result of the hot-fire testing are presented in this paper and presentation.

  16. Sensitivity analysis of rectangular atomic force microscope cantilevers immersed in liquids based on the modified couple stress theory.

    PubMed

    Lee, Haw-Long; Chang, Win-Jin

    2016-01-01

    The modified couple stress theory is adopted to study the sensitivity of a rectangular atomic force microscope (AFM) cantilever immersed in acetone, water, carbon tetrachloride (CCl4), and 1-butanol. The theory contains a material length scale parameter and considers the size effect in the analysis. However, this parameter is difficult to obtain via experimental measurements. In this study, a conjugate gradient method for the parameter estimation of the frequency equation is presented. The optimal method provides a quantitative approach for estimating the material length scale parameter based on the modified couple stress theory. The results show that the material length scale parameter of the AFM cantilever immersed in acetone, CCl4, water, and 1-butanol is 0, 25, 116.3, and 471 nm, respectively. In addition, the vibration sensitivities of the AFM cantilever immersed in these liquids are investigated. The results are useful for the design of AFM cantilevers immersed in liquids.

  17. Characterization of mineral-associated organic matter: a combined approach of AFM and NanoSIMS

    NASA Astrophysics Data System (ADS)

    Pohl, Lydia; Schurig, Christian; Eusterhues, Karin; Mueller, Carsten W.; Höschen, Carmen; Totsche, Kai-Uwe; Kögel-Knabner, Ingrid

    2016-04-01

    The heterogeneous spatial distribution and amount of organic matter (OM) in soils, especially at the micro- or submicron-scale, has major consequences for the soil microstructure and for the accessibility of OM to decomposing microbial communities. Processes occurring at the microscale control soil properties and processes at larger scales, such as macro-aggregation and carbon turnover. Since OM acts as substrate and most important driver for biogeochemical processes, particular attention should be paid to its spatial interaction with soil minerals. In contrast to bulk analysis, Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) offers the possibility to examine the composition and spatial distribution of OM within the intact organo-mineral matrix. Nevertheless, the yield of secondary electrons is influenced by the individual topography of the analysed particles, which aggravated the quantitative interpretation of the data. A combination of NanoSIMS and Atomic Force Microscopy (AFM), enabled us to visualize and quantify the topographical features of individual particles and correct the NanoSIMS data for this effect. We performed adsorption experiments with water-soluble soil OM in 6 concentration steps, which was extracted from forest floor layer of a Podzol, and adsorbed to illite. Upon the end of the sorption experiments the liquid phase and the solid phase were separated and the carbon content was analysed with TOC- and C/N-measurement, respectively. For the spatially resolved analyses, the samples were applied as thin layers onto silicon wafers and individual particles were chosen by means of the AFM. Subsequently, the identical particles were analysed with NanoSIMS to investigate the distribution of C, N, O, Si, P and Al. The recorded data were analysed for differences in elemental distribution between the different concentration steps. Additionally, we performed a correlation of the detectable counts with the topography of the particle within one

  18. BOREAS AFM-03-NCAR Electra 1994 Aircraft Sounding Data

    NASA Technical Reports Server (NTRS)

    Lenschow, Donald H.; Oncley, Steven P.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-3 team used the National Center for Atmospheric Research's (NCAR) Electra aircraft to make sounding measurements to study the planetary boundary layer using in situ and remote-sensing measurements. Measurements were made of wind speed and direction, air pressure and temperature, potential temperature, dewpoint, mixing ratio of H, O, CO, concentration, and ozone concentration. Twenty-five research missions were flown over the Northern Study Area (NSA), Southern Study Area (SSA), and the transect during BOREAS Intensive Field Campaigns (IFCs) 1, 2, and 3 during 1994. All missions had from four to ten soundings through the top of the planetary boundary layer. This sounding data set contains all of the in situ vertical profiles through the boundary layer top that were made (with the exception of 'porpoise' maneuvers). Data were recorded in one-second time intervals. These data are stored in tabular ASCII files. The NCAR Electra 1994 aircraft sounding data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  19. BOREAS AFM-2 Wyoming King Air 1994 Aircraft Sounding Data

    NASA Technical Reports Server (NTRS)

    Kelly, Robert D.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS AFM-2 team used the University of Wyoming King Air aircraft during IFCs 1, 2, and 3 in 1994 to collected pass-by-pass fluxes (and many other statistics) for the large number of level (constant altitude), straight-line passes used in a variety of flight patterns over the SSA and NSA and areas along the transect between these study areas. The data described here form a second set, namely soundings that were incorporated into nearly every research flight by the King Air in 1994. These soundings generally went from near the surface to above the inversion layer. Most were flown immediately after takeoff or immediately after finishing the last flux pattern of that particular day's flights. The parameters that were measured include wind direction, wind speed, west wind component (u), south wind component (v), static pressure, air dry bulb temperature, potential temperature, dewpoint, temperature, water vapor mixing ratio, and CO2 concentration. Data on the aircraft's location, attitude, and altitude during data collection are also provided. These data are stored in tabular ASCH files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  20. PREFACE: NC-AFM 2005: Proceedings of the 8th International Conference on Non-Contact Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Reichling, M.; Mikosch, W.

    2006-04-01

    The 8th International Conference on Non-Contact Atomic Force Microscopy, held in Bad Essen, Germany, from 15 18th August 2005, attracted a record breaking number of participants presenting excellent contributions from a variety of scientific fields. This clearly demonstrated the high level of activity and innovation present in the community of NC-AFM researchers and the continuous growth of the field. The strongest ever participation of companies for a NC-AFM meeting is a sign for the emergence of new markets for the growing NC-AFM community; and the high standard of the products presented at the exhibition, many of them brand-new developments, reflected the unbroken progress in technology. The development of novel technologies and the sophistication of known techniques in research laboratories and their subsequent commercialization is still a major driving force for progress in this area of nanoscience. The conference was a perfect demonstration of how progress in the development of enabling technologies can readily be transcribed into basic research yielding fundamental insight with an impact across disciplines. The NC-AFM 2005 scientific programme was based on five cornerstones, each representing an area of vivid research and scientific progress. Atomic resolution imaging on oxide surfaces, which has long been a vision for the catalysis community, appears to be routine in several laboratories and after a period of demonstrative experiments NC-AFM now makes unique contributions to the understanding of processes in surface chemistry. These capabilities also open up new routes for the analysis of clusters and molecules deposited on dielectric surfaces where resolution limits are pushed towards the single atom level. Atomic precision manipulation with the dynamic AFM left the cradle of its infancy and flourishes in the family of bottom-up fabrication nanotechnologies. The systematic development of established and the introduction of new concepts of contrast

  1. An AFM study of the chlorite-fluid interface. [Atomic Force Microscopy

    SciTech Connect

    Vrdoljak, G.A.; Henderson, G.S.; Fawcett, J.J. . Dept. of Geology)

    1992-01-01

    Chlorite is a ubiquitous mineral in many geologic environments and plays an important role in elemental adsorption and retention in soils. Chlorite has a 2:1 layer structure consisting of two tetrahedral sheets with an octahedral sheet between them (talc-like layer). The 2:1 layer is charge balanced and hydrogen-bonded by an interlayer of MgOH[sub 6] octahedra (brucite-like layer). The nature of chlorite's structure, its ease of imaging, and perfect 001 cleavage, make this mineral an ideal substrate for use in elemental adsorption studies in solution, with the AFM. The 001 cleavage plane of a 2b polytype with composition (Mg[sub 4.4]Fe[sub 0.6]Al[sub 1.0])[(Si[sub 2.9]Al[sub 1.1])]O[sub 10](OH)[sub g] has been imaged in air, water, and oil by atomic force microscopy. Dissolution features are observed in water, showing sub-micron features dissolving in real-time. Atomic resolution of both the talc-like and brucite-like layers has been obtained in air. However, only the tetrahedral sheet of the talc-like layer has been imaged at atomic resolution in oil and water, which may indicate a structural instability of the brucite-like surface in solution. Measurements of the unit-cell dimensions (a and b) for the talc-like layer in the three different media indicate a structural expansion of the mineral surface in solution. The a unit cell dimension expands by 7.4 [+-] 0.1% when in water; conversely, the b dimension varies greatly when in oil ([minus]10% to +20%), relative to air. The effects of these solution media on the structure of chlorite are revealed by characterization with the AFM. This information should prove useful in future studies of adsorption onto layer silicates.

  2. GaN nanowire tip for high aspect ratio nano-scale AFM metrology (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Behzadirad, Mahmoud; Dawson, Noel; Nami, Mohsen; Rishinaramangalam, Ashwin K.; Feezell, Daniel F.; Busani, Tito L.

    2016-09-01

    In this study we introduce Gallium Nitride (GaN) nanowire (NW) as high aspect ratio tip with excellent durability for nano-scale metrology. GaN NWs have superior mechanical property and young modulus compare to commercial Si and Carbon tips which results in having less bending issue during measurement. The GaN NWs are prepared via two different methods: i) Catalyst-free selected area growth, using Metal Organic Chemical Vapor Deposition (MOCVD), ii) top-down approach by employing Au nanoparticles as the mask material in dry-etch process. To achieve small diameter tips, the semipolar planes of the NWs grown by MOCVD are etched using AZ400k. The diameter of the NWs fabricated using the top down process is controlled by using different size of nanoparticles and by Inductively Coupled Plasma etching. NWs with various diameters were manipulated on Si cantilevers using Focus Ion Beam (FIB) to make tips for AFM measurement. A Si (110) substrate containing nano-scale grooves with vertical 900 walls were used as a sample for inspection. AFM measurements were carried out in tapping modes for both types of nanowires (top-down and bottom-up grown nanowires) and results are compared with conventional Si and carbon nanotube tips. It is shown our fabricated tips are robust and have improved edge resolution over conventional Si tips. GaN tips made with NW's fabricated using our top down method are also shown to retain the gold nanoparticle at tip, which showed enhanced field effects in Raman spectroscopy.

  3. PREFACE: NC-AFM 2006: Proceedings of the 9th International Conference on Non-contact Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Tomitori, Masahiko; Onishi, Hiroshi

    2007-02-01

    The advent of scanning probe microscopy (SPM) in the 1980s has significantly promoted nanoscience and nanotechnology. In particular, non-contact atomic force microscopy (NC-AFM), one of the SPM family, has unique capabilities with high spatial resolution for nanoscale measurements in vacuum, air and liquids. In the last decade we have witnessed the rapid progress of NC-AFM with improved performance and increasing applications. A series of NC-AFM international conferences have greatly contributed to this field. Initiated in Osaka in 1998, the NC-AFM meeting has been followed by annual conferences at Pontresina, Hamburg, Kyoto, Montreal, Dingle, Seattle and Bad Essen. The 9th conference was held in Kobe, Japan, 16-20 July 2006. This special issue of Nanotechnology contains the outstanding contributions of the conference. During the meeting delegates learnt about a number of significant advances. Topics covered atomic resolution imaging of metals, semiconductors, insulators, ionic crystals, oxides, molecular systems, imaging of biological materials in various environments and novel instrumentation. Work also included the characterization of electronic and magnetic properties, tip and cantilever fabrication and characterization, atomic distinction based on analysis of tip-sample interaction, atomic scale manipulation, fabrication of nanostructures using NC-AFM, and related theories and simulations. We are greatly impressed by the increasing number of applications, and convinced that NC-AFM and related techniques are building a bridge to a future nano world, where quantum phenomena will dominate and nano devices will be realized. In addition, a special session on SPM road maps was held as a first trial in the field, where the future prospects of SPM were discussed enthusiastically. The overall success of the NC-AFM 2006 conference was due to the efforts of many individuals and groups with respect to scientific and technological progress, as well as the international

  4. Spatial dependence of polycrystalline FTO’s conductance analyzed by conductive atomic force microscope (C-AFM)

    SciTech Connect

    Peixoto, Alexandre Pessoa; Costa, J. C. da

    2014-05-15

    Fluorine-doped Tin oxide (FTO) is a highly transparent, electrically conductive polycrystalline material frequently used as an electrode in organic solar cells and optical-electronic devices [1–2]. In this work a spatial analysis of the conductive behavior of FTO was carried out by Conductive-mode Atomic Force Microscopy (C-AFM). Rare highly oriented grains sample give us an opportunity to analyze the top portion of polycrystalline FTO and compare with the border one. It is shown that the current flow essentially takes place through the polycrystalline edge at grain boundaries.

  5. AF-M315E Propulsion System Advances and Improvements

    NASA Technical Reports Server (NTRS)

    Masse, Robert K.; Allen, May; Driscoll, Elizabeth; Spores, Ronald A.; Arrington, Lynn A.; Schneider, Steven J.; Vasek, Thomas E.

    2016-01-01

    Even as for the GR-1 awaits its first on-orbit demonstration on the planned 2017 launch of NASA's Green Propulsion Infusion Mission (GPIM) program, ongoing efforts continue to advance the technical state-of-the-art through improvements in the performance, life capability, and affordability of both Aerojet Rocketdyne's 1-N-class GR-1 and 20-N-class GR-22 green monopropellant thrusters. Hot-fire testing of a design upgrade of the GR-22 thruster successfully demonstrated resolution of a life-limiting thermo-structural issue encountered during prototype testing on the GPIM program, yielding both an approximately 2x increase in demonstrating life capability, as well as fundamental insights relating to how ionic liquid thrusters operate, thruster scaling, and operational factors affecting catalyst bed life. Further, a number of producibility improvements, related to both materials and processes and promising up to 50% unit cost reduction, have been identified through a comprehensive Design for Manufacturing and Assembly (DFMA) assessment activity recently completed at Aerojet Rocketdyne. Focused specifically on the GR-1 but applicable to the common-core architecture of both thrusters, ongoing laboratory (heavyweight) thruster testing being conducted under a Space Act Agreement at NASA Glenn Research Center has already validated a number of these proposed manufacturability upgrades, additionally achieving a greater than 40% increase in thruster life. In parallel with technical advancements relevant to conventional large spacecraft, a joint effort between NASA and Aerojet Rocketdyne is underway to prepare 1-U CubeSat AF-M315E propulsion module for first flight demonstration in 2018.

  6. The formation of liquid bridge in different operating modes of AFM

    NASA Astrophysics Data System (ADS)

    Wei, Zheng; Sun, Yan; Ding, WenXuan; Wang, ZaiRan

    2016-09-01

    The liquid bridge is one of the principal factors that cause artifacts in ambient-pressure atomic force microscope (AFM) images. Additionally, it is the main component of the adhesion force in ambient conditions. To understand the AFM imaging mechanism and the sample characteristics, it is essential to study the liquid bridge. This study interprets the physical mechanism involved in liquid bridge formation, which is composed of three different physical processes: the squeezing process, capillary condensation, and liquid film flow. We discuss the contributions of these three mechanisms to the volume and the capillary force of the liquid bridge in different AFM operation modes.

  7. Wetting properties of AFM probes by means of contact angle measurement

    NASA Astrophysics Data System (ADS)

    Tao, Zhenhua; Bhushan, Bharat

    2006-09-01

    An atomic force microscopy (AFM) based technique was developed to measure the wetting properties of probe tips. By advancing and receding the AFM tip across the water surface, the meniscus force between the tip and the liquid was measured at the tip-water separation. The water contact angle was determined from the meniscus force. The obtained contact angle results were compared with that by the sessile drop method. It was found that the AFM based technique provided higher contact angle values than the sessile drop method. The mechanisms responsible for the difference are discussed.

  8. Metabolic control analysis of developing oilseed rape (Brassica napus cv Westar) embryos shows that lipid assembly exerts significant control over oil accumulation.

    PubMed

    Tang, Mingguo; Guschina, Irina A; O'Hara, Paul; Slabas, Antoni R; Quant, Patti A; Fawcett, Tony; Harwood, John L

    2012-10-01

    Metabolic control analysis allows the study of metabolic regulation. We applied both single- and double-manipulation top-down control analysis to examine the control of lipid accumulation in developing oilseed rape (Brassica napus) embryos. The biosynthetic pathway was conceptually divided into two blocks of reactions (fatty acid biosynthesis (Block A), lipid assembly (Block B)) connected by a single system intermediate, the acyl-coenzyme A (acyl-CoA) pool. Single manipulation used exogenous oleate. Triclosan was used to inhibit specifically Block A, whereas diazepam selectively manipulated flux through Block B. Exogenous oleate inhibited the radiolabelling of fatty acids from [1-(14)C]acetate, but stimulated that from [U-14C]glycerol into acyl lipids. The calculation of group flux control coefficients showed that c. 70% of the metabolic control was in the lipid assembly block of reactions. Monte Carlo simulations gave an estimation of the error of the resulting group flux control coefficients as 0.27±0.06 for Block A and 0.73±0.06 for Block B. The two methods of control analysis gave very similar results and showed that Block B reactions were more important under our conditions. This contrasts notably with data from oil palm or olive fruit cultures and is important for efforts to increase oilseed rape lipid yields.

  9. Contrast mechanisms on nanoscale subsurface imaging in ultrasonic AFM: scattering of ultrasonic waves and contact stiffness of the tip-sample.

    PubMed

    Sharahi, Hossein Jiryaei; Shekhawat, Gajendra; Dravid, Vinayak; Park, Simon; Egberts, Philip; Kim, Seonghwan

    2017-02-09

    Ultrasonic atomic force microscopy (AFM) and its associated derivatives are nondestructive techniques that can elucidate subsurface nanoscale structures and properties. Despite the usefulness of these techniques, the physical contrast mechanisms responsible for the reported subsurface features observed in ultrasonic AFM are not well defined. In this study, we present a comprehensive model combining ultrasonic wave scattering and tip-sample contact stiffness to better reproduce the experimentally measured phase variations over subsurface features in two model systems. These model systems represent the two extreme sample types typically imaged by ultrasonic AFM, one being a hard material and the other a soft polymeric material. The theoretical analysis presented and associated comparisons with experimental results suggest that the image contrast depends on the combination of two contrast mechanisms: the perturbation of the scattered ultrasonic waves and the local variation of the contact stiffness at the tip-sample contact. The results of this study open up a new door for the depth estimation of buried nanoscale features into hard (engineering structures) and soft (polymers and biological structures) materials, and eventually lead to non-invasive, high-resolution 3D nano-tomography by ultrasonic AFM.

  10. Direct electrochemical and AFM detection of amyloid-β peptide aggregation on basal plane HOPG

    NASA Astrophysics Data System (ADS)

    Lopes, Paula; Xu, Meng; Zhang, Min; Zhou, Ting; Yang, Yanlian; Wang, Chen; Ferapontova, Elena E.

    2014-06-01

    Amyloidogenesis is associated with more than 30 human diseases, including Alzheimer's which is related to aggregation of β-amyloid peptide (Aβ). Here, consecutive stages of Aβ42 aggregation and amyloid fibril formation were followed electrochemically via oxidation of tyrosines in Aβ42 adsorbed on the basal plane graphite electrode and directly correlated with Aβ42 morphological changes observed by atomic force microscopy of the same substrate. The results offer new tools for analysis of mechanisms of Aβ aggregation.Amyloidogenesis is associated with more than 30 human diseases, including Alzheimer's which is related to aggregation of β-amyloid peptide (Aβ). Here, consecutive stages of Aβ42 aggregation and amyloid fibril formation were followed electrochemically via oxidation of tyrosines in Aβ42 adsorbed on the basal plane graphite electrode and directly correlated with Aβ42 morphological changes observed by atomic force microscopy of the same substrate. The results offer new tools for analysis of mechanisms of Aβ aggregation. Electronic supplementary information (ESI) available: Experimental details: procedures for Aβ42 aggregation and electrode modification, DPV/AFM measurements and analysis. See DOI: 10.1039/c4nr02413c

  11. Comparative analysis of multilineage properties of mesenchymal stromal cells derived from fetal sources shows an advantage of mesenchymal stromal cells isolated from cord blood in chondrogenic differentiation potential

    PubMed Central

    Pievani, Alice; Scagliotti, Valeria; Russo, Francesca Maria; Azario, Isabella; Rambaldi, Benedetta; Sacchetti, Benedetto; Marzorati, Simona; Erba, Eugenio; Giudici, Giovanni; Riminucci, Mara; Biondi, Andrea; Vergani, Patrizia; Serafini, Marta

    2014-01-01

    Background aims Cord blood (CB) and amniotic fluid (AF) could represent new and attractive mesenchymal stromal cell (MSC) sources, but their potential therapeutic applications are still limited by lack of standardized protocols for isolation and differentiation. In particular, chondrogenic differentiation has never been deeply investigated. Methods MSCs were obtained from CB and AF samples collected during cesarean sections at term and compared for their biological and differentiation properties, with particular interest in cartilage differentiation, in which quantitative real-time polymerase chain reaction and immunohistochemical analyses were performed to evaluate the expression of type 2 collagen, type 10 collagen, SRY-box9 and aggrecan. Results We were able to isolate MSCs from 12 of 30 (40%) and 5 of 20 (25%) CB and AF units, respectively. Fluorescence in situ hybridization analysis indicated the fetal origin of isolated MSC strains. Both populations expressed mesenchymal but not endothelial and hematopoietic markers, even though we observed a lower expression of human leukocyte antigen (HLA) I in CB-MSCs. No differences in proliferation rate and cell cycle analysis could be detected. After osteogenic induction, both populations showed matrix mineralization and typical marker expression. Under chondrogenic conditions, pellets derived from CB-MSCs, in contrast with AF-MSCs pellets, were significantly larger, showed cartilage-like morphology and resulted positive for chondrocyte-associated markers, such as type 2 collagen, type 10 collagen, SRY-box9 and aggrecan. Conclusions Our results show that CB-MSCs and AF-MSCs collected at term differ from each other in their biological and differentiation properties. In particular, only CB-MSCs showed a clear chondrogenic potential and thus could represent an ideal candidate for cartilage-tissue engineering. PMID:24794181

  12. Adiabatic Compression Sensitivity of AF-M315E (Briefing Charts)

    DTIC Science & Technology

    2015-07-27

    dynamic response • Waterhammer effect Distribution A: Approved for public release; distribution unlimited Hydroxyethylhydrazinium Nitrate ...Hydroxylammonium Nitrate (HEHN) (HAN) [ ]-NO3 + [ ]HOCH2CH2N2H4 [ ]-+[ ]NH3OH NO3 AF-M315E

  13. Quantitative Measurements of Elastic Properties with Ultrasonic-Based AFM and Conventional Techniques

    NASA Astrophysics Data System (ADS)

    Hurley, D. C.

    A prime motivation for the original development of ultrasonic-based AFM methods was to enable measurements of elastic properties with nanoscale spatial resolution. In this chapter, we discuss the quantitative measurement of elastic modulus with ultrasonic-based AFM methods and compare it to measurement by more conventional or established techniques. First, we present the basic principles of modulus measurement with methods that involve contact resonance spectroscopy, such as atomic force acoustic microscopy (AFAM) and ultrasonic AFM (U-AFM). Fundamental concepts of modulus measurement with more established approaches, especially instrumented (nano-) indentation (NI) and surface acoustic wave spectroscopy (SAWS), are then discussed. We consider the relative strengths and limitations of various approaches, for example measurement accuracy, spatial resolution, and applicability to different materials. Example results for specific material systems are given with an emphasis on studies involving direct intercomparison of different techniques. Finally, current research in this area and opportunities for future work are described.

  14. AFM imaging of ligand binding to platelet integrin alphaIIbbeta3 receptors reconstituted into planar lipid bilayers.

    PubMed

    Hussain, Mohammad A; Agnihotri, Aashiish; Siedlecki, Christopher A

    2005-07-19

    The platelet integrin alphaIIbbeta3 plays a key role in platelet adhesion, activation, and aggregation at the subendothelium and at protein-coated synthetic biomaterials. In this study, interactions between alphaIIbbeta3 and both protein and peptide ligands for the receptor were imaged under physiological conditions by high-resolution atomic force microscopy (AFM). To directly image the ligand-receptor interactions, alphaIIbbeta3 receptors were reconstituted into a supported lipid bilayer formed on a mica surface in the AFM fluid cell assembly and subsequently activated with Mn2+. Fibrinogen, the natural protein ligand for the integrin, as well as a nanogold-labeled peptide ligand (an RGD-containing heptamer) were infused into the AFM fluid cell, incubated with the reconstituted and activated receptors, and imaged under buffer. Height images illustrating topographical features showed the integrin reconstituted in the bilayer. Fibrinogen molecules binding to the receptors were easily observed in the height images, with fibrinogen showing its characteristic trinodular structure and occasionally bridging integrin receptors. Fibrinogen was observed to bind to integrins at the D-domain consistent with the location of the gamma-chain dodecapeptide, while fibrinogen bridging integrins bound to receptors on opposite sides of the protein consistent with a 2-fold axis of symmetry. Peptide ligands were not visible in height images; however, phase images that map the mechanical properties detected the nanogold labels and demonstrated the presence of peptide ligands bound to the receptors. The results demonstrate the ability of this high-resolution microscopy technique to directly visualize single ligand/receptor interactions in a dynamic and physiologically relevant environment, and establish a framework for future fundamental studies of single protein/receptor interactions during normal pathological processes as well as biomaterial surface-induced thrombosis.

  15. Leveraging Air Force Medical Service (AFMS) Senior Leadership Corps Diversity to Improve Efficiency

    DTIC Science & Technology

    2013-04-01

    commanders and AFMS senior leadership; • Set a single PME standard for AFMS officers; • Shift provider billets to patient care roles and establish...single PME standard, and by realigning human resources to increase clinical currency, medical readiness and resource efficiency. Some structural...organizational entity. Like running a surgical service or a medical service. . . . It’s much bigger than that, because you’re dealing with finance and

  16. Attaching single biomolecules selectively to the apex of AFM tips for measuring specific interactions.

    PubMed

    Gu, Jianhua; Xiao, Zhongdang; Yam, Chi-Ming; Qin, Guoting; Deluge, Maxence; Boutet, Sabine; Cai, Chengzhi

    2005-11-01

    We present a general approach for preparing well-defined AFM tips for probing single target molecules. We demonstrated that carboxylic acid groups could be generated by electrochemical oxidation selectively at the apex of an AFM tip that is coated with a monolayer of oligo(ethylene glycol) derivatives for resisting nonspecific interactions. These carboxylic acid groups were used as handles to tether only one ligand molecule, such as biotin, to the tip apex for measurement of specific interactions with biomolecules.

  17. Using XAFS, EDAX and AFM in comparative study of various natural and synthetic emeralds

    NASA Astrophysics Data System (ADS)

    Parikh, P.; Saini, N. L.; Dalela, S.; Bhardwaj, D. M.; Fernandes, S.; Gupta, R. P.; Garg, K. B.

    2003-01-01

    We have performed XAFS, EDAX and AFM studies on some natural and synthetic emeralds. While the XAFS results yield information on changes in the valence of the Cr ion and the n-n distance the AFM is used to determine the areal atomic density on surface of the crystals. It is a pilot study to explore if the three techniques can offer a possible way of distinguishing between the natural and synthetic emeralds and the results are promising.

  18. Measuring the viscoelastic creep of soft samples by step response AFM.

    PubMed

    Yango, Achu; Schäpe, Jens; Rianna, Carmela; Doschke, Holger; Radmacher, Manfred

    2016-10-12

    We have measured the creep response of soft gels and cells after applying a step in loading force with atomic force microscopy (AFM). By analysing the creep response data using the standard linear solid model, we can quantify the viscous and elastic properties of these soft samples independently. Cells, in comparison with gels of similar softness, are much more viscous, as has been qualitatively observed in conventional force curve data before. Here, we quantify the spring constant and the viscous damping coefficient from the creep response data. We propose two different modes for applying a force step: (1) indirectly by increasing the sample height or (2) directly by employing magnetic cantilevers. Both lead to similar results, whereas the latter seems to be better defined since it resembles closely a constant strain mode. The former is easier to implement in most instruments, and thus may be preferable from a practical point of view. Creep analysis by step response is much more appropriate to analyse the viscoelastic response of soft samples like cells than the usually used force curve analysis.

  19. Investigating the Photocatalytic Degradation of Oil Paint using ATR-IR and AFM-IR.

    PubMed

    Morsch, Suzanne; van Driel, Birgit A; van den Berg, Klaas Jan; Dik, Joris

    2017-03-22

    As linseed oil has a longstanding and continuing history of use as a binder in artistic paints, developing an understanding of its degradation mechanism is critical to conservation efforts. At present, little can be done to detect the early stages of oil paint deterioration due to the complex chemical composition of degrading paints. In this work, we use advanced infrared analysis techniques to investigate the UV-induced deterioration of model linseed oil paints in detail. Subdiffraction limit infrared analysis (AFM-IR) is applied to identify and map accelerated degradation in the presence of two different grades of titanium white pigment particles (rutile or anatase TiO2). Differentiation between the degradation of these two formulations demonstrates the sensitivity of this approach. The identification of characteristic peaks and transient species residing at the paint surface allows infrared absorbance peaks related to degradation deeper in the film to be extricated from conventional ATR-FTIR spectra, potentially opening up a new approach to degradation monitoring.

  20. Analysis of the surface structure of HFCVD diamond films

    SciTech Connect

    Mehta, P.; Feigerle, C.S.; Clausing, R.E.; Heatherly, L.; Thundat, T.

    1995-07-01

    Structure analysis was carried out on various surface features of diamond films using scanning electron microscopy (SEM) and atomic force microscopy (AFM). The films were grown via hot filament assisted chemical vapor deposition (HFCVD) in methane and hydrogen gas mixtures. The authors investigated the surfaces of films grown under parameters selected to produce certain textures or surface features such as penetration twins or hopper shaped faces. The SEM images of these films show that the {l_brace}100{r_brace} planes are usually flatter than the {l_brace}111{r_brace}. The {l_brace}111{r_brace} planes show interesting growth features. The ``hopper`` shaped structures were imaged in the tapping mode of the AFM, and the angles between planes and their orientations have been determined. These AFM and SEM images are presented with quantitative analyses of the exposed surfaces. Detailed quantitative information will be useful in understanding the growth of these films.

  1. Surface characterisation of two strains of Staphylococcus epidermidis with different slime-production by AFM

    NASA Astrophysics Data System (ADS)

    Méndez-Vilas, A.; Gallardo-Moreno, A. M.; González-Martín, M. L.; Calzado-Montero, R.; Nuevo, M. J.; Bruque, J. M.; Pérez-Giraldo, C.

    2004-11-01

    Slime-producer Staphylococcus epidermidis is one opportunistic bacteria directly related to biomaterial infections inside the human body. The characterisation of the bacterial surface is crucial when trying to control its adhesion process and prevent the biofilm formation. This work aims to analyse the microscopic and submicroscopic surface structure of two strains of S. epidermidis with different slime production, as well as mapping the surface interaction forces. Atomic force microscopy (AFM) shows that S. epidermidis ATCC35984 is covered by a granular-like film, highly compacted with the presence of repeated "holes". However, S. epidermidis ATCC35983 only shows a partial coverage by a less compacted granular-like film, mainly located in the inter-cellular zones. Both films are related to the slime of the two strains studied. As regards to the adhesion forces, results show a greater adhesion of the tip to the slime covering S. epidermidis ATCC35984, than that covering the surface of S. epidermidis ATCC35983. In addition, the adhesion to the free-slime zones of the last strain was higher than to the slime-covered parts.

  2. Probing ternary solvent effect in high Voc polymer solar cells using advanced AFM techniques

    DOE PAGES

    Li, Chao; Soleman, Mikhael; Lorenzo, Josie; ...

    2016-01-25

    This work describes a simple method to develop a high Voc low band gap PSCs. In addition, two new atomic force microscopy (AFM)-based nanoscale characterization techniques to study the surface morphology and physical properties of the structured active layer are introduced. With the help of ternary solvent processing of the active layer and C60 buffer layer, a bulk heterojunction PSC with Voc more than 0.9 V and conversion efficiency 7.5% is developed. In order to understand the fundamental properties of the materials ruling the performance of the PSCs tested, AFM-based nanoscale characterization techniques including Pulsed-Force-Mode AFM (PFM-AFM) and Mode-Synthesizing AFMmore » (MSAFM) are introduced. Interestingly, MSAFM exhibits high sensitivity for direct visualization of the donor–acceptor phases in the active layer of the PSCs. Lastly, conductive-AFM (cAFM) studies reveal local variations in conductivity in the donor and acceptor phases as well as a significant increase in photocurrent in the PTB7:ICBA sample obtained with the ternary solvent processing.« less

  3. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    PubMed Central

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; Norton, Malgorzata G.; Teckman, Jeffrey H.; Marszal, Ewa; Osmulski, Pawel A.

    2016-01-01

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found in WT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo

  4. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    DOE PAGES

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; ...

    2016-03-23

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemicalmore » data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo

  5. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    SciTech Connect

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; Norton, Malgorzata G.; Teckman, Jeffrey H.; Marszal, Ewa; Osmulski, Pawel A.

    2016-03-23

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in

  6. Electrical characterization of FIB processed metal layers for reliable conductive-AFM on ZnO microstructures

    NASA Astrophysics Data System (ADS)

    Pea, M.; Maiolo, L.; Giovine, E.; Rinaldi, A.; Araneo, R.; Notargiacomo, A.

    2016-05-01

    We report on the conductive-atomic force microscopy (C-AFM) study of metallic layers in order to find the most suitable configuration for electrical characterization of individual ZnO micro-pillars fabricated by focused ion beam (FIB). The electrical resistance between the probe tip and both as deposited and FIB processed metal layers (namely, Cr, Ti, Au and Al) has been investigated. Both chromium and titanium evidenced a non homogenous and non ohmic behaviour, non negligible scanning probe induced anodic oxidation associated to electrical measurements, and after FIB milling they exhibited significantly higher tip-sample resistance. Aluminium had generally a more apparent non conductive behaviour. Conversely, gold films showed very good tip-sample conduction properties being less sensitive to FIB processing than the other investigated metals. We found that a reliable C-AFM electrical characterization of ZnO microstructures obtained by FIB machining is feasible by using a combination of metal films as top contact layer. An Au/Ti bilayer on top of ZnO was capable to sustain the FIB fabrication process and to form a suitable ohmic contact to the semiconductor, allowing for reliable C-AFM measurement. To validate the consistency of this approach, we measured the resistance of ZnO micropillars finding a linear dependence on the pillar height, as expected for an ohmic conductor, and evaluated the resistivity of the material. This procedure has the potential to be downscaled to nanometer size structures by a proper choice of metal films type and thickness.

  7. RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

    PubMed

    Liu, Ren-Hu; Meng, Jin-Ling

    2006-09-01

    Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

  8. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  9. A propensity score analysis shows that empirical treatment with linezolid does not increase the thirty-day mortality rate in patients with Gram-negative bacteremia.

    PubMed

    Ternavasio-de la Vega, Hugo-Guillermo; Mateos-Díaz, Ana-María; Martinez, Jose-Antonio; Almela, Manel; Cobos-Trigueros, Nazaret; Morata, Laura; De-la-Calle, Cristina; Sala, Marta; Mensa, Josep; Marcos, Miguel; Soriano, Alex

    2014-12-01

    The role of linezolid in empirical therapy of suspected bacteremia remains unclear. The aim of this study was to evaluate the influence of empirical use of linezolid or glycopeptides in addition to other antibiotics on the 30-day mortality rates in patients with Gram-negative bacteremia. For this purpose, 1,126 patients with Gram-negative bacteremia in the Hospital Clinic of Barcelona from 2000 to 2012 were included in this study. In order to compare the mortality rates between patients who received linezolid or glycopeptides, the propensity scores on baseline variables were used to balance the treatment groups, and both propensity score matching and propensity-adjusted logistic regression were used to compare the 30-day mortality rates between the groups. The overall 30-day mortality rate was 16.0% during the study period. Sixty-eight patients received empirical treatment with linezolid, and 1,058 received glycopeptides. The propensity score matching included 64 patients in each treatment group. After matching, the mortality rates were 14.1% (9/64) in patients who received glycopeptides and 21.9% (14/64) in those who received linezolid, and a nonsignificant association between empirical linezolid treatment and mortality rate (odds ratio [OR], 1.63; 95% confidence interval [CI], 0.69 to 3.82; P = 0.275, McNemar's test) was found. This association remained nonsignificant when variables that remained unbalanced after matching were included in a conditional logistic regression model. Further, the stratified propensity score analysis did not show any significant relationship between empirical linezolid treatment and the mortality rate after adjustment by propensity score quintiles or other variables potentially associated with mortality. In conclusion, the propensity score analysis showed that empirical treatment with linezolid compared with that with glycopeptides was not associated with 30-day mortality rates in patients with Gram-negative bacteremia.

  10. Television Quiz Show Simulation

    ERIC Educational Resources Information Center

    Hill, Jonnie Lynn

    2007-01-01

    This article explores the simulation of four television quiz shows for students in China studying English as a foreign language (EFL). It discusses the adaptation and implementation of television quiz shows and how the students reacted to them.

  11. Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance.

    PubMed

    Yu, Guohua; Cui, Zhenling; Sun, Xian; Peng, Jinfu; Jiang, Jun; Wu, Wei; Huang, Wenhua; Chu, Kaili; Zhang, Lu; Ge, Baoxue; Li, Yao

    2015-05-01

    Global analysis of expression profiles using DNA microarrays was performed between a reference strain H37Rv and two clinical extensively drug-resistant isolates in response to three anti-tuberculosis drug exposures (isoniazid, capreomycin, and rifampicin). A deep analysis was then conducted using a combination of genome sequences of the resistant isolates, resistance information, and related public microarray data. Certain known resistance-associated gene sets were significantly overrepresented in upregulated genes in the resistant isolates relative to that observed in H37Rv, which suggested a link between resistance and expression levels of particular genes. In addition, isoniazid and capreomycin response genes, but not rifampicin, either obtained from published works or our data, were highly consistent with the differentially expressed genes of resistant isolates compared to those of H37Rv, indicating a strong association between drug resistance of the isolates and genes differentially regulated by isoniazid and capreomycin exposures. Based on these results, 92 genes of the studied isolates were identified as candidate resistance genes, 10 of which are known resistance-related genes. Regulatory network analysis of candidate resistance genes using published networks and literature mining showed that three two-component regulatory systems and regulator CRP play significant roles in the resistance of the isolates by mediating the production of essential envelope components. Finally, drug sensitivity testing indicated strong correlations between expression levels of these regulatory genes and sensitivity to multiple anti-tuberculosis drugs in Mycobacterium tuberculosis. These findings may provide novel insights into the mechanism underlying the emergence and development of drug resistance in resistant tuberculosis isolates and useful clues for further studies on this issue.

  12. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.

    PubMed

    Pánek, Tomáš; Zadrobílková, Eliška; Walker, Giselle; Brown, Matthew W; Gentekaki, Eleni; Hroudová, Miluše; Kang, Seungho; Roger, Andrew J; Tice, Alexander K; Vlček, Čestmír; Čepička, Ivan

    2016-05-01

    Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.

  13. Molecular analysis of transgenic melon plants showing virus resistance conferred by direct repeat of movement gene of Cucumber green mottle mosaic virus.

    PubMed

    Ali, Emran Md; Emran, Ali; Tabei, Yutaka; Kobayashi, Kappei; Yamaoka, Naoto; Nishiguchi, Masamichi

    2012-08-01

    Cucumber green mottle mosaic virus (CGMMV) is a major limiting factor in the production of melon plants worldwide. For effective control of this virus using the transgenic approach, the direct repeat of the movement protein gene of CGMMV was used for transforming melon plants by Agrobacterium tumefaciens. PCR and Southern blot analyses of T₃ confirmed that they carried the transgene. Northern blot analysis with total RNA showed that transgene transcript RNA as well as siRNA was observed in all plants tested. Separate leaves or individual plants were inoculated with CGMMV and subjected to ELISA and RNA blot analysis using the coat protein gene probe of the virus. Compared to nontransgenic control, these plants were shown to have high virus resistance. Furthermore, cytosine of the transgene DNA in the plants was methylated. Thus, these results reveal that the transgenic lines were highly resistant to the virus through RNA silencing. Key message High virus resistance was obtained in transgenic melon plants with direct repeat of movement protein gene of Cucumber green mottle mosaic tobamovirus through RNA silencing.

  14. Analysis of conservative tracer measurement results using the Frechet distribution at planted horizontal subsurface flow constructed wetlands filled with coarse gravel and showing the effect of clogging processes.

    PubMed

    Dittrich, Ernő; Klincsik, Mihály

    2015-11-01

    A mathematical process, developed in Maple environment, has been successful in decreasing the error of measurement results and in the precise calculation of the moments of corrected tracer functions. It was proved that with this process, the measured tracer results of horizontal subsurface flow constructed wetlands filled with coarse gravel (HSFCW-C) can be fitted more accurately than with the conventionally used distribution functions (Gaussian, Lognormal, Fick (Inverse Gaussian) and Gamma). This statement is true only for the planted HSFCW-Cs. The analysis of unplanted HSFCW-Cs needs more research. The result of the analysis shows that the conventional solutions (completely stirred series tank reactor (CSTR) model and convection-dispersion transport (CDT) model) cannot describe these types of transport processes with sufficient accuracy. These outcomes can help in developing better process descriptions of very difficult transport processes in HSFCW-Cs. Furthermore, a new mathematical process can be developed for the calculation of real hydraulic residence time (HRT) and dispersion coefficient values. The presented method can be generalized to other kinds of hydraulic environments.

  15. Comparison of the ability of quantitative parameters to differentiate surface texture of Atomic Force Microscope (AFM) images

    NASA Astrophysics Data System (ADS)

    Niedzielski, Bethany; Caragianis Broadbridge, Christine; DaPonte, John S.; Gherasimova, Maria

    2010-01-01

    The purpose of this study was to compare the ability of several texture analysis parameters to differentiate textured samples from a smooth control on images obtained with an Atomic Force Microscope (AFM). Surface roughness plays a major role in the realm of material science, especially in integrated electronic devices. As these devices become smaller and smaller, new materials with better electrical properties are needed. New materials with smoother surface morphology have been found to have superior electrical properties than their rougher counterparts. Therefore, in many cases surface texture is indicative of the electrical properties that material will have. Physical vapor deposition techniques such as Jet Vapor Deposition and Molecular Beam Epitaxy are being utilized to synthesize these materials as they have been found to create pure and uniform thin layers. For the current study, growth parameters were varied to produce a spectrum of textured samples. The focus of this study was the image processing techniques associated with quantifying surface texture. As a result of the limited sample size, there was no attempt to draw conclusions about specimen processing methods. The samples were imaged using an AFM in tapping mode. In the process of collecting images, it was discovered that roughness data was much better depicted in the microscope's "height" mode as opposed to "equal area" mode. The AFM quantified the surface texture of each image by returning RMS roughness and the first order histogram statistics of mean roughness, standard deviation, skewness, and kurtosis. Color images from the AFM were then processed on an off line computer running NIH ImageJ with an image texture plug in. This plug in produced another set of first order statistics computed from each images' histogram as well as second order statistics computed from each images' cooccurrence matrix. The second order statistics, which were originally proposed by Haralick, include contrast, angular

  16. AFM review study on pox viruses and living cells.

    PubMed

    Ohnesorge, F M; Hörber, J K; Häberle, W; Czerny, C P; Smith, D P; Binnig, G

    1997-10-01

    Single living cells were studied in growth medium by atomic force microscopy at a high--down to one image frame per second--imaging rate over time periods of many hours, stably producing hundreds of consecutive scans with a lateral resolution of approximately 30-40 nm. The cell was held by a micropipette mounted onto the scanner-piezo as shown in Häberle, W., J. K. H. Hörber, and G. Binnig. 1991. Force microscopy on living cells. J. Vac. Sci. Technol. B9:1210-0000. To initiate specific processes on the cell surface the cells had been infected with pox viruses as reported earlier and, most likely, the liberation of a progeny virion by the still-living cell was observed, hence confirming and supporting earlier results (Häberle, W., J. K. H. Hörber, F. Ohnesorge, D. P. E. Smith, and G. Binnig. 1992. In situ investigations of single living cells infected by viruses. Ultramicroscopy. 42-44:1161-0000; Hörber, J. K. H., W. Häberle, F. Ohnesorge, G. Binnig, H. G. Liebich, C. P. Czerny, H. Mahnel, and A. Mayr. 1992. Investigation of living cells in the nanometer regime with the atomic force microscope. Scanning Microscopy. 6:919-930). Furthermore, the pox viruses used were characterized separately by AFM in an aqueous environment down to the molecular level. Quasi-ordered structural details were resolved on a scale of a few nm where, however, image distortions and artifacts due to multiple tip effects are probably involved--just as in very high resolution (<15-20 nm) images on the cells. Although in a very preliminary manner, initial studies on the mechanical resonance properties of a single living (noninfected) cell, held by the micropipette, have been performed. In particular, frequency response spectra were recorded that indicate elastic properties and enough stiffness of these cells to make the demonstrated rapid scanning of the imaging tip plausible. Measurements of this kind, especially if they can be proven to be cell-type specific, may perhaps have a large

  17. Analysis of large new South African dataset using two host-specificity indices shows generalism in both adult and larval ticks of mammals.

    PubMed

    Espinaze, Marcela P A; Hellard, Eléonore; Horak, Ivan G; Cumming, Graeme S

    2016-03-01

    Ticks and tick-borne pathogens can have considerable impacts on the health of livestock, wildlife and people. Knowledge of tick-host preferences is necessary for both tick and pathogen control. Ticks were historically considered as specialist parasites, but the range of sampled host species has been limited, infestation intensity has not been included in prior analyses, and phylogenetic distances between hosts have not been previously considered. We used a large dataset of 35 604 individual collections and two host-specificity indices to assess the specificity of 61 South African tick species, as well as distinctions between adult and juvenile ticks, for 95 mammalian hosts. When accounting for host phylogeny, most adult and juvenile ticks behaved as generalists, with juveniles being significantly more generalist than adults. When we included the intensity of tick infestation, ticks exhibited a wider diversity of specificity in all life stages. Our results show that ticks of mammals in South Africa tend to behave largely as generalists and that adult ticks are more host-specific. More generally, our analysis shows that the incorporation of life-stage differences, infestation intensity and phylogenetic distances between hosts, as well as the use of more than one specificity index, can all contribute to a deeper understanding of host-parasite interactions.

  18. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

  19. Analysis of the mouse mutant Cloth-ears shows a role for the voltage-gated sodium channel Scn8a in peripheral neural hearing loss.

    PubMed

    Mackenzie, F E; Parker, A; Parkinson, N J; Oliver, P L; Brooker, D; Underhill, P; Lukashkina, V A; Lukashkin, A N; Holmes, C; Brown, S D M

    2009-10-01

    Deafness is the most common sensory disorder in humans and the aetiology of genetic deafness is complex. Mouse mutants have been crucial in identifying genes involved in hearing. However, many deafness genes remain unidentified. Using N-ethyl N-nitrosourea (ENU) mutagenesis to generate new mouse models of deafness, we identified a novel semi-dominant mouse mutant, Cloth-ears (Clth). Cloth-ears mice show reduced acoustic startle response and mild hearing loss from approximately 30 days old. Auditory-evoked brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) analyses indicate that the peripheral neural auditory pathway is impaired in Cloth-ears mice, but that cochlear function is normal. In addition, both Clth/Clth and Clth/+ mice display paroxysmal tremor episodes with behavioural arrest. Clth/Clth mice also show a milder continuous tremor during movement and rest. Longitudinal phenotypic analysis showed that Clth/+ and Clth/Clth mice also have complex defects in behaviour, growth, neurological and motor function. Positional cloning of Cloth-ears identified a point mutation in the neuronal voltage-gated sodium channel alpha-subunit gene, Scn8a, causing an aspartic acid to valine (D981V) change six amino acids downstream of the sixth transmembrane segment of the second domain (D2S6). Complementation testing with a known Scn8a mouse mutant confirmed that this mutation is responsible for the Cloth-ears phenotype. Our findings suggest a novel role for Scn8a in peripheral neural hearing loss and paroxysmal motor dysfunction.

  20. AFM investigation on surface evolution of amorphous carbon during ion-beam-assisted deposition

    NASA Astrophysics Data System (ADS)

    Zhu, X. D.; Ding, F.; Naramoto, H.; Narumi, K.

    2006-11-01

    Hydrogen-free amorphous carbons (a-C) have been prepared on mirror-polished Si(1 1 1) wafers through thermally evaporated C 60 with simultaneous bombardments of Ne + ions. The time evolution of film surfaces has been characterized by atomic force microscopy (AFM) at two temperatures of 400 and 700 °C, respectively. Based on the topography images and the root-mean-square (rms) roughness analysis, it is found that the a-C surfaces present roughening growth at the initial stage. With increasing growth time, the cooperative nucleation of the islands and pits appears on the surfaces, suggesting three-dimensional growth, and then they continue to evolve to irregular mounds at 400 °C, and elongated mounds at 700 °C. At the steady growth stage, these surfaces further develop to the structures of bamboo joints and ripples corresponding to these two temperatures, respectively. It is believed that besides ion sputtering effect, the chemical bonding configurations in the amorphous carbon films should be taken into considerations for elucidating the surface evolutions.

  1. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging

    NASA Astrophysics Data System (ADS)

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-01

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000–2800 cm‑1, associated with weaker bands at 1655, 1438 and 1297 cm‑1, indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons.

  2. Inhibition of cold rolled steel corrosion by Tween-20 in sulfuric acid: weight loss, electrochemical and AFM approaches.

    PubMed

    Mu, Guannan; Li, Xianghong

    2005-09-01

    The inhibiting action of a nonionic surfactant of Tween-20 on the corrosion of cold rolled steel (CRS) in 0.5-7.0 M sulfuric acid (H(2)SO(4)) was studied by weight loss and potentiodynamic polarization methods. Atomic force microscope (AFM) provided the surface conditions. The results show that inhibition efficiency increases with the inhibitor concentration, while it decreases with the sulfuric acid concentration. The adsorption of inhibitor on the cold rolled steel surface obeys the Langmuir adsorption isotherm equation. Effect of immersion time was studied and discussed. The effect of temperature on the corrosion behavior of cold rolled steel was also studied at four temperatures ranging from 30 to 60 degrees C, the thermodynamic parameters such as adsorption heat, adsorption free energy, and adsorption entropy were calculated. The results revealed that the adsorption was physisorption mechanism. A kinetic study of cold rolled steel in uninhibited and inhibited acid was also discussed. The kinetic parameters such as apparent activation energy, pre-exponential factor, rate constant, and reaction constant were calculated for the reactions of corrosion. The inhibition effect is satisfactorily explained by both thermodynamic and kinetic models. Polarization curves show that Tween-20 is a cathodic-type inhibitor in sulfuric acid. The results obtained from weight loss and potentiodynamic polarization are in good agreement, and the Tween-20 inhibition action could also be evidenced by surface AFM images.

  3. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging.

    PubMed

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-18

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000-2800 cm(-1), associated with weaker bands at 1655, 1438 and 1297 cm(-1), indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons.

  4. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging

    PubMed Central

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-01

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000–2800 cm−1, associated with weaker bands at 1655, 1438 and 1297 cm−1, indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons. PMID:28098185

  5. The morphological and biomechanical changes of keratocytes cultured on modified p (HEMA-MMA) hydrogel studied by AFM.

    PubMed

    Yan, Tuo; Sun, Rong; Deng, Hua; Tan, Baihua; Ao, Ningjian

    2009-01-01

    The poor integration with host cornea tissue and the low mechanical properties of pHEMA hydrogel for artificial cornea remains a difficult problem to solve. A modified pHEMA hydrogel, MMA copolymerized and type-I collagen and bFGF immobilized, was previously prepared in an attempt to solve the problems. In this study, the cytotoxicity of Col/bFGF-p (HEMA-MMA) and p (HEMA-MMA) was studied by cell adhesion assay and atomic force microscopy (AFM). The results of cell adhesion assay show that the attachment of keratocytes on the modified membrane is much higher than that of the unmodified membrane. This indicates that the material after modification have better cell-material interaction. The AFM images reveal that the morphology of keratocytes cultured on different substrate is obviously different. The cell cultured on modified membrane presented a completely elongated and spindle-shape morphology. The force-distance indicates that the biomechanical of keratocytes changes significantly after culturing on different substrates. The adhesion force (2328+/-523 pN) and Young's modulus (0.51+/-0.125 kPa) of the cell cultured on modified membrane are much higher, and the stiffness (0.08+/-0.022 mN/m) is lower than those of the cell cultured on unmodified membrane. These results show that the cytotoxicity of Col/bFGF-p (HEMA-MMA) for keratocytes is much improved.

  6. A rapid and automated relocation method of an AFM probe for high-resolution imaging.

    PubMed

    Zhou, Peilin; Yu, Haibo; Shi, Jialin; Jiao, Niandong; Wang, Zhidong; Wang, Yuechao; Liu, Lianqing

    2016-09-30

    The atomic force microscope (AFM) is one of the most powerful tools for high-resolution imaging and high-precision positioning for nanomanipulation. The selection of the scanning area of the AFM depends on the use of the optical microscope. However, the resolution of an optical microscope is generally no larger than 200 nm owing to wavelength limitations of visible light. Taking into consideration the two determinants of relocation-relative angular rotation and positional offset between the AFM probe and nano target-it is therefore extremely challenging to precisely relocate the AFM probe to the initial scan/manipulation area for the same nano target after the AFM probe has been replaced, or after the sample has been moved. In this paper, we investigate a rapid automated relocation method for the nano target of an AFM using a coordinate transformation. The relocation process is both simple and rapid; moreover, multiple nano targets can be relocated by only identifying a pair of reference points. It possesses a centimeter-scale location range and nano-scale precision. The main advantages of this method are that it overcomes the limitations associated with the resolution of optical microscopes, and that it is label-free on the target areas, which means that it does not require the use of special artificial markers on the target sample areas. Relocation experiments using nanospheres, DNA, SWCNTs, and nano patterns amply demonstrate the practicality and efficiency of the proposed method, which provides technical support for mass nanomanipulation and detection based on AFM for multiple nano targets that are widely distributed in a large area.

  7. The in situ characterization and structuring of electrografted polyphenylene films on silicon surfaces. An AFM and XPS study.

    PubMed

    Ghorbal, Achraf; Grisotto, Federico; Laudé, Marion; Charlier, Julienne; Palacin, Serge

    2008-12-15

    An atomic force microscope was used so as to structure by nanofriction films of polynitrophenylene electrografted on substrates of n-type silicon (100) with the native oxide on the top of the surface. AFM measurements of thin films thickness have been carried out in the electrolytic solution for different applied potentials during the electrografting. This investigation allows (i) to determine the relationship between the applied potential and the final thickness of electrografted polyphenylene films and (ii) to specify how the thin layers grow. XPS analysis confirmed the AFM observations on (i) the effective shaving of the grafted polymer chains under mechanical stress and (ii) the existence of a potential threshold for electrografting a polyphenylene film on silicon oxide surfaces. The presence of a residual film in the rubbed zone was attributed to stronger interactions between the first electrografted layer and the native oxide of silicon (through Si-C or/and Si-O-C bonds) than those insuring the cohesion of the multilayer (C-C and C-N bonds).

  8. Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance.

    PubMed

    Sun, Zhan-Min; Zhou, Mei-Liang; Xiao, Xing-Guo; Tang, Yi-Xiong; Wu, Yan-Min

    2014-09-01

    Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops.

  9. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes.

    PubMed

    Zhan, Yinxiu; Mariani, Luca; Barozzi, Iros; Schulz, Edda G; Blüthgen, Nils; Stadler, Michael; Tiana, Guido; Giorgetti, Luca

    2017-03-01

    Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here, we present a novel algorithm named CaTCH that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation, which is a single and biologically relevant parameter. By applying CaTCH to published Hi-C data sets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal boundary enrichment in CTCF and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that the likelihood that genes in a domain are coregulated during differentiation is also maximized at the scale of TADs. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the same scale. Our analysis suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the specific genomic position of regulatory sequences.

  10. Relaxation of ultralarge VWF bundles in a microfluidic-AFM hybrid reactor

    SciTech Connect

    Steppich, D.M.; Angerer, J.I.; Sritharan, K.; Schneider, S.W.; Thalhammer, S.; Wixforth, A.; Alexander-Katz, A.; Schneider, M.F.

    2008-05-02

    The crucial role of the biopolymer 'Von Willebrand factor' (VWF) in blood platelet binding is tightly regulated by the shear forces to which the protein is exposed in the blood flow. Under high-shear conditions, VWFs ability to immobilize blood platelets is strongly increased due to a change in conformation which at sufficient concentration is accompanied by the formation of ultra large VWF bundles (ULVWF). However, little is known about the dynamic and mechanical properties of such bundles. Combining a surface acoustic wave (SAW) based microfluidic reactor with an atomic force microscope (AFM) we were able to study the relaxation of stretched VWF bundles formed by hydrodynamic stress. We found that the dynamical response of the network is well characterized by stretched exponentials, indicating that the relaxation process proceeds through hopping events between a multitude of minima. This finding is in accordance with current ideas of VWF self-association. The longest relaxation time does not show a clear dependence on the length of the bundle, and is dominated by the internal conformations and effective friction within the bundle.

  11. Interaction force measurement between E. coli cells and nanoparticles immobilized surfaces by using AFM

    SciTech Connect

    Zhang, Wen; Chen, Yongsheng

    2011-01-01

    To better understand environmental behaviors of nanoparticles (NPs), we used the atomic force microscopy (AFM) to measure interaction forces between E. coli cells and NPs immobilized on surfaces in an aqueous environment. The results showed that adhesion force strength was significantly influenced by particle size for both hematite ( -Fe2 O3 ) and corundum ( -Al2 O3 ) NPs whereas the effect on the repulsive force was not observed. The adhesion force decreased from 6.3 0.7 nN to 0.8 0.4 nN as hematite NPs increased from 26 nm to 98 nm in diameter. Corundum NPs exhibited a similar dependence of adhesion force on particle size. The Johnson Kendall Roberts (JKR) model was employed to estimate the contact area between E. coli cells and NPs, and based on the JKR model a new model that considers local effective contact area was developed. The prediction of the new model matched the size dependence of adhesion force in experimental results. Size effects on adhesion forces may originate from the difference in local effective contact areas as supported by our model. These findings provide fundamental information for interpreting the environmental behaviors and biological interactions of NPs, which barely have been addressed.

  12. Optical trapping force combining an optical fiber probe and an AFM metallic probe.

    PubMed

    Liu, Binghui; Yang, Lijun; Wang, Yang

    2011-02-14

    A high-resolution optical trapping and manipulating scheme combining an optical fiber probe and an AFM metallic probe is proposed. This scheme is based on the combination of evanescent illumination and light scattering at the metallic probe apex, which shapes the optical field into a localized, three-dimensional optical trap. Detailed simulations of the electromagnetic fields in composite area and the resulting forces are described the methods of Maxwell stress tensor and three-dimensional FDTD. Calculations show that the scheme is able to overcome the disturbance of other forces to trap a polystyrene particle of up to 10 nm in radius with lower laser intensity (~1040 W/mm2) than that required by conventional optical tweezers (~10(5) W/mm2). Based on the discussion of high manipulating efficiency dependent on system parameters and the implementing procedure, the scheme allowing for effective manipulation of nano-particles opens a way for research on single nano-particle area.

  13. Combined quantitative ultrasonic and time-resolved interaction force AFM imaging

    NASA Astrophysics Data System (ADS)

    Parlak, Z.; Degertekin, F. L.

    2011-01-01

    The authors describe a method where quantitative ultrasonic atomic force microscopy (UAFM) is achieved during time-resolved interaction force (TRIF) imaging in intermittent contact mode. The method uses a calibration procedure for quantitative UAFM. It improves elasticity measurements of stiff regions of surfaces while retaining the capabilities of the TRIF mode for topography, adhesion, dissipation, and elasticity measurements on soft regions of sample surfaces. This combination is especially advantageous when measuring and imaging samples with broad stiffness range in a nondestructive manner. The experiments utilize an active AFM probe with high bandwidth and the UAFM calibration is performed by measuring the magnitude of the time-resolved UAFM signal at a judiciously chosen frequency for different contact stiffness values during individual taps. Improved sensitivity to stiff surface elasticity is demonstrated on a special sample. The results show that combining UAFM with TRIF provides 2.5 GPa (5%) standard deviation on the silicon surface reduced Young's modulus, representing 5× improvement over using only TRIF mode imaging.

  14. AFM in mode Peak Force applied to the study of un-worn contact lenses.

    PubMed

    Torrent-Burgués, J; Sanz, F

    2014-09-01

    Contact lenses (CLs) are of common use and the biocompatibility, topography and mechanical properties of the used materials are of major importance. The objective of this contribution is to apply the AFM in mode Peak Force to obtain surface topography and mechanical characteristics of un-worn CLs of different materials. One material of hydrogel, two of siloxane-hydrogel and one of rigid gas-permeable were used in the study. The results obtained with different materials have been compared, at a nanoscopic level, and the conclusions are diverse. There is no significant influence of the two environments used to measure the characteristics of the CLs, either water or saline solution. The pHEMA hydrogel CL (Polymacon of Soflens) shows the highest values of roughness, adhesion and elastic modulus. The siloxane-hydrogel CL named Asmofilcon A of PremiO presents the lowest values of mean roughness (Ra), root-mean-square roughness (RMS or Rq), adhesion (Adh) and elastic modulus (Ym), meanwhile the siloxane-hydrogel CL named Lotrafilcon B of Air Optix presents the lowest value of skewness (Rsk) and the rigid gas-permeable CL, named RXD, presents the lowest values of kurtosis (Rku) and maximum roughness (Rmax).

  15. Porous titania films fabricated via sol gel rout - Optical and AFM characterization

    NASA Astrophysics Data System (ADS)

    Karasiński, Paweł; Gondek, Ewa; Drewniak, Sabina; Kajzer, Anita; Waczyńska-Niemiec, Natalia; Basiaga, Marcin; Izydorczyk, Weronika; Kouari, Youssef E. L.

    2016-06-01

    Mesoporous titania films of low refractive index ∼1.72 and thickness within the range of 57-96 nm were fabricated via sol-gel rout and dip-coating technique on a soda-lime glass substrate. Tetrabutylorthotitanate Ti(OBu)4 was used as a titania precursor. High porosity and consequently low refractive index were achieved using the polyethylene glycol (PEG 1100) as a template. Based on transmittance, using Tauc's relations, the optical energy band gaps and the Urbach energy were determined. The research shows that in the fabricated titania films there are two types of optical energy band gaps, connected with direct and indirect electron transitions and brought about by the presence of amorphous and crystalline phase respectively. Based on the quantum size effect, the diameters of nanocrystals versus film thickness were determined. AFM studies of the titania films have demonstrated that there are changes of surface morphology taking place with the change of thickness. We have demonstrated that the surface morphology of titania films has influence on wettability.

  16. AFM investigations of the morphology features and local mechanical properties of HTS YBCO thin films

    NASA Astrophysics Data System (ADS)

    Soifer, Yakov M.; Verdyan, Armen; Lapsker, Igor; Azoulay, Jacob

    2004-08-01

    In the paper presented here the application of the atomic force microscope (AFM) is considered for evaluation of hardness and Young's modulus of high Tc superconducting YBCO thin films of different thickness (from 0.05 to 1 μm) grown on unbuffered SrTiO 3 (film I) and on sapphire with a buffer layer of CeO 2 (film II). The best film features a transition temperature Tc of 90 K, critical current density Jc ( H=0) of 3 × 10 7 A/cm 2 at 4.2 K and 2 × 10 6 A/cm 2 at 77 K. The relationship between mechanical properties and microstructure of these films was investigated. It was found that all the films comprised well-defined Cu-rich precipitates of different size and with different density on their surface. For both type of films the hardness was measured to be in the range of 12-18 GPa. The Young's modulus of the films was about 180-200 GPa. The nanoindentation and nanoscratching measurements showed that the mechanical strength of the films studied was determined mainly by mechanical failure and surface defects (secondary phases).

  17. Observation of Spin-flop Transition in Antiferromagnetic Organic Molecular Conductors using AFM Micro-cantilever

    NASA Astrophysics Data System (ADS)

    Tokumoto, Madoka; Otsuka, Takeo; Kobayashi, Akiko

    2005-03-01

    A series of (BETS)2Fe1-xGaxCl1-yBry salts is a good candidate for a systematic study of π-d interaction between the conduction electrons and local magnetic moments in organic conductors. Some of them show antiferromagnetic ground state at low temperatures. A torque magnetometry is useful for precise determination of the easy axis as well as the spin-flop field. In this work we will report on the measurements of spin-flop transitions in antiferromagnetic organic molecular conductors including λ-(BETS)2FeCl4[1], using a commercial self-sensing piezo-resistive microcantilever for Atomic Force Microscopy (AFM) developed by Seiko Instruments Inc. We have succeeded in observation of spin-flop transitions of tiny single crystals including λ-(BETS)2FeCl4 as small as less than 1μg[2]. The results are consistent with the capacitive magnetic torque study[3]. [1] M. Tokumoto et al. Synth. Metals 86, 2161 (1997). [2] M. Tokumoto et al., ICMM2004, Polyhedron in press. [3] T. Sasaki et al., Synth. Metals 120, 759 (2001).

  18. AFM characterization of spin coated carboxylated polystyrene nanospheres/xyloglucan layers on mica and silicon.

    PubMed

    Lubambo, Adriana F; Lucyszyn, Neoli; Petzhold, Cesar L; Sierakowski, Maria-R; Schreiner, Wido H; Saul, Cyro K

    2013-03-01

    Self-assembled nano-arrays have a potential application as solid-phase diagnostics in many biomedical devices. The easiness of its production is directly connected to manufacture cost reduction. In this work, we present self-assembled structures starting from spin coated thin films of carboxylated polystyrene (PSC) and xyloglucan (XG) mixtures on both mica and silicon substrates. AFM images showed PSC nanospheres on top of a homogeneous layer of XG, for both substrates. The average nanosphere diameter fluctuated for a constant speed and it was likely to be independent of the component proportions on the mixture within a range of 30-50% (v/v) PSC. It was also observed that the largest diameters were found at the center of the sample and the smallest at the border. The detected nanospheres were also more numerous at the border. This behavior presents a similarity to spin coated colloidal dispersions. We observed that the average nanosphere diameter on mica substrates was bigger than the nanosphere diameters obtained on top of silicon substrates, under the same conditions. This result seems to be possibly connected to different mixture-surface interactions.

  19. Assembly of {alpha}-synuclein fibrils in nanoscale studied by peptide truncation and AFM

    SciTech Connect

    Zhang Feng; Lin Xiaojing; Ji Lina; Du Haining; Tang Lin; He Jianhua; Hu Jun; Hu Hongyu

    2008-04-04

    {alpha}-Synuclein ({alpha}-Syn) fibrils are the major component of Lewy bodies that are closely associated with the pathogenesis of Parkinson's disease, but the mechanism for the fibril assembly remains poorly understood. Here we report using a combination of peptide truncation and atomic force microscopy (AFM) to elucidate the self-assembly and morphology of the {alpha}-Syn fibrils. The results show that protease K significantly slims the fibrils from the mean height of {approx}6.6 to {approx}4.7 nm, whereas chaotropic denaturant urea completely breaks down the fibrils into small particles. The in situ enzymatic digestion also results in thinning of the fibrils, giving rise to some nicks on the fibrils. Moreover, N- or C-terminally truncated {alpha}-Syn fragments assemble into thinner filaments with the heights depending on the peptide lengths. A nine-residue peptide corresponding to the homologous GAV-motif sequence can form very thin ({approx}2.2 nm) but long (>1 {mu}m) filaments. Thus, the central sequence of {alpha}-Syn forms a fibrillar core by cross-{beta}-structure that is flanked by two flexible termini, and the orientation of the fibril growth is perpendicular to the {beta}-sheet structures.

  20. Linking concepts in the ecology and evolution of invasive plants: network analysis shows what has been most studied and identifies knowledge gaps.

    PubMed

    Vanderhoeven, Sonia; Brown, Cynthia S; Tepolt, Carolyn K; Tsutsui, Neil D; Vanparys, Valérie; Atkinson, Sheryl; Mahy, Grégory; Monty, Arnaud

    2010-03-01

    In recent decades, a growing number of studies have addressed connections between ecological and evolutionary concepts in biologic invasions. These connections may be crucial for understanding the processes underlying invaders' success. However, the extent to which scientists have worked on the integration of the ecology and evolution of invasive plants is poorly documented, as few attempts have been made to evaluate these efforts in invasion biology research. Such analysis can facilitate recognize well-documented relationships and identify gaps in our knowledge. In this study, we used a network-based method for visualizing the connections between major aspects of ecology and evolution in the primary research literature. Using the family Poaceae as an example, we show that ecological concepts were more studied and better interconnected than were evolutionary concepts. Several possible connections were not documented at all, representing knowledge gaps between ecology and evolution of invaders. Among knowledge gaps, the concepts of plasticity, gene flow, epigenetics and human influence were particularly under-connected. We discuss five possible research avenues to better understand the relationships between ecology and evolution in the success of Poaceae, and of alien plants in general.

  1. AFM1 in Milk: Physical, Biological, and Prophylactic Methods to Mitigate Contamination

    PubMed Central

    Giovati, Laura; Magliani, Walter; Ciociola, Tecla; Santinoli, Claudia; Conti, Stefania; Polonelli, Luciano

    2015-01-01

    Aflatoxins (AFs) are toxic, carcinogenic, immunosuppressive secondary metabolites produced by some Aspergillus species which colonize crops, including many dietary staple foods and feed components. AFB1 is the prevalent and most toxic among AFs. In the liver, it is biotransformed into AFM1, which is then excreted into the milk of lactating mammals, including dairy animals. AFM1 has been shown to be cause of both acute and chronic toxicoses. The presence of AFM1 in milk and dairy products represents a worldwide concern since even small amounts of this metabolite may be of importance as long-term exposure is concerned. Contamination of milk may be mitigated either directly, decreasing the AFM1 content in contaminated milk, or indirectly, decreasing AFB1 contamination in the feed of dairy animals. Current strategies for AFM1 mitigation include good agricultural practices in pre-harvest and post-harvest management of feed crops (including storage) and physical or chemical decontamination of feed and milk. However, no single strategy offers a complete solution to the issue. PMID:26512694

  2. Combined force spectroscopy, AFM and calorimetric studies to reveal the nanostructural organization of biomimetic membranes.

    PubMed

    Suárez-Germà, C; Morros, A; Montero, M T; Hernández-Borrell, J; Domènech, Ò

    2014-10-01

    In this work we studied a binary lipid matrix of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), a composition that mimics the inner membrane of Escherichia coli. More specifically, liposomes with varying fractions of POPG were analysed by differential scanning calorimetry (DSC) and a binary phase diagram of the system was created. Additionally, we performed atomic force microscopy (AFM) imaging of supported lipid bilayers (SLBs) of similar compositions at different temperatures, in order to create a pseudo-binary phase diagram specific to this membrane model. AFM study of SLBs is of particular interest, as it is conceived as the most adequate technique not only for studying lipid bilayer systems but also for imaging and even nanomanipulating inserted membrane proteins. The construction of the above-mentioned phase diagram enabled us to grasp better the thermodynamics of the thermal lipid transition from a gel-like POPE:POPG phase system to a more fluid phase system. Finally, AFM force spectroscopy (FS) was used to determine the nanomechanics of these two lipid phases at 27°C and at different POPG fractions. The resulting data correlated with the specific composition of each phase was calculated from the AFM phase diagram obtained. All the experiments were done in the presence of 10 mM of Ca(2+), as this ion is commonly used when performing AFM with negatively charged phospholipids.

  3. Noise in NC-AFM measurements with significant tip–sample interaction

    PubMed Central

    Lübbe, Jannis; Temmen, Matthias

    2016-01-01

    The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip–sample interactions. The total noise power spectral density D Δ f(f m) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip–sample interaction, by the coupling between the amplitude and tip–sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure D Δ f(f m) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip–sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops. PMID:28144538

  4. Effect of AFM probe geometry on visco-hyperelastic characterization of soft materials

    NASA Astrophysics Data System (ADS)

    Boccaccio, Antonio; Lamberti, Luciano; Papi, Massimiliano; De Spirito, Marco; Pappalettere, Carmine

    2015-08-01

    Atomic force microscopy (AFM) nanoindentation is very suited for nano- and microscale mechanical characterization of soft materials. Although the structural response of polymeric networks that form soft matter depends on viscous effects caused by the relative slippage of polymeric chains, the usual assumption made in the AFM-based characterization is that the specimen behaves as a purely elastic material and viscous forces are negligible. However, for each geometric configuration of the AFM tip, there will be a limit indentation rate above which viscous effects must be taken into account to correctly determine mechanical properties. A parametric finite element study conducted on 12 geometric configurations of a blunt cone AFM tip (overall, the study included about 200 finite element analyses) allowed us to determine the limit indentation rate for each configuration. The selected tip dimensions cover commercially available products and account for changes in tip geometry caused by serial measurements. Nanoindentation rates cover typical experimental conditions set in AFM bio-measurements on soft matter. Viscous effects appear to be more significant in the case of sharper tips. This implies that, if quantitative data on sample viscosity are not available, using a rounded indenter and carrying out experiments below the limit indentation rate will allow errors in the determination of mechanical properties to be minimized.

  5. Evaluating interaction forces between BSA and rabbit anti-BSA in sulphathiazole sodium, tylosin and levofloxacin solution by AFM

    NASA Astrophysics Data System (ADS)

    Wang, Congzhou; Wang, Jianhua; Deng, Linhong

    2011-11-01

    Protein-protein interactions play crucial roles in numerous biological processes. However, it is still challenging to evaluate the protein-protein interactions, such as antigen and antibody, in the presence of drug molecules in physiological liquid. In this study, the interaction between bovine serum albumin (BSA) and rabbit anti-BSA was investigated using atomic force microscopy (AFM) in the presence of various antimicrobial drugs (sulphathiazole sodium, tylosin and levofloxacin) under physiological condition. The results show that increasing the concentration of tylosin decreased the single-molecule-specific force between BSA and rabbit anti-BSA. As for sulphathiazole sodium, it dramatically decreased the specific force at a certain critical concentration, but increased the nonspecific force as its concentration increasing. In addition, the presence of levofloxacin did not greatly influence either the specific or nonspecific force. Collectively, these results suggest that these three drugs may adopt different mechanisms to affect the interaction force between BSA and rabbit anti-BSA. These findings may enhance our understanding of antigen/antibody binding processes in the presence of drug molecules, and hence indicate that AFM could be helpful in the design and screening of drugs-modulating protein-protein interaction processes.

  6. Study of the influence of the acrylic acid plasma parameters on silicon and polyurethane substrates using XPS and AFM

    NASA Astrophysics Data System (ADS)

    Vilani, C.; Weibel, D. E.; Zamora, R. R. M.; Habert, A. C.; Achete, C. A.

    2007-10-01

    XPS and AFM have been used to investigate surface modifications produced by acrylic acid (AA) vapor plasma treatment of silicon (Si)(1 0 0) substrates and polyurethanes (PUs) membranes. XPS analyses of Si and PUs treated substrates at low plasma power (5-20 W) revealed the formation of a thin film on the surfaces, which chemically resembles the poly(acrylic acid) film conventionally synthesised. No signal of the Si substrate could be seen under these low plasma power applications on silicon. However, when the plasma power is higher than 30 W one can clearly see XPS silicon signatures. AFM measurements of silicon substrates treated with AA plasma at low power (5-20 W) showed the formation of a thin polymer film of about 220-55 nm thickness. Further, applications of high plasma power (30-100 W) displayed a marked difference from low plasma modifications and it was found sputtering of the silicon substrate. Pervaporation results of AA plasma treated PUs membranes revealed that the selectivity for the separation of methanol from methyl- t-butyl ether is higher at 100 W and 1 min treatment time, than the other conditions studied. This last finding is discussed concerning the surface modifications produced on plasma treated silicon substrates and PU membranes.

  7. Bi-stability of amplitude modulation AFM in air: deterministic and stochastic outcomes for imaging biomolecular systems.

    PubMed

    Santos, Sergio; Barcons, Victor; Font, Josep; Thomson, Neil H

    2010-06-04

    The dynamics of the oscillating microcantilever for amplitude modulation atomic force microscopy (AM AFM) operating in air is well understood theoretically but the experimental outcomes are still emerging. We use double-stranded DNA on mica as a model biomolecular system for investigating the connection between theory and experiment. A demonstration that the switching between the two cantilever oscillation states is stochastic in nature is achieved, and it can be induced by means of topographical anomalies on the surface. Whether one or the other attractor basin is accessed depends on the tip-sample separation history used to achieve the imaging conditions, and we show that the behaviour is reproducible when the tip is stable and well characterized. Emergence of background noise occurs in certain regions of parameter space regardless of whether two cantilever oscillation states coexist. The low state has been explored in detail and we note that at low to intermediate values of the free amplitude, noise-free imaging is achieved. The outcomes shown here are general and demonstrate that a thorough and systematic experimental approach in conjunction with standard modelling gives insight into the mechanisms behind image contrast formation in AM AFM in air.

  8. Characterization of microscale wear in a ploysilicon-based MEMS device using AFM and PEEM-NEXAFS spectromicroscopy.

    SciTech Connect

    Grierson, D. S.; Konicek, A. R.; Wabiszewski, G. E.; Sumant, A. V.; de Boer, M. P.; Corwin, A. D.; Carpick, R. W.

    2009-12-01

    Mechanisms of microscale wear in silicon-based microelectromechanical systems (MEMS) are elucidated by studying a polysilicon nanotractor, a device specifically designed to conduct friction and wear tests under controlled conditions. Photoelectron emission microscopy (PEEM) was combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and atomic force microscopy (AFM) to quantitatively probe chemical changes and structural modification, respectively, in the wear track of the nanotractor. The ability of PEEM-NEXAFS to spatially map chemical variations in the near-surface region of samples at high lateral spatial resolution is unparalleled and therefore ideally suited for this study. The results show that it is possible to detect microscopic chemical changes using PEEM-NEXAFS, specifically, oxidation at the sliding interface of a MEMS device. We observe that wear induces oxidation of the polysilicon at the immediate contact interface, and the spectra are consistent with those from amorphous SiO{sub 2}. The oxidation is correlated with gouging and debris build-up in the wear track, as measured by AFM and scanning electron microscopy (SEM).

  9. Showing What They Know

    ERIC Educational Resources Information Center

    Cech, Scott J.

    2008-01-01

    Having students show their skills in three dimensions, known as performance-based assessment, dates back at least to Socrates. Individual schools such as Barrington High School--located just outside of Providence--have been requiring students to actively demonstrate their knowledge for years. The Rhode Island's high school graduating class became…

  10. The Ozone Show.

    ERIC Educational Resources Information Center

    Mathieu, Aaron

    2000-01-01

    Uses a talk show activity for a final assessment tool for students to debate about the ozone hole. Students are assessed on five areas: (1) cooperative learning; (2) the written component; (3) content; (4) self-evaluation; and (5) peer evaluation. (SAH)

  11. What Do Maps Show?

    ERIC Educational Resources Information Center

    Geological Survey (Dept. of Interior), Reston, VA.

    This curriculum packet, appropriate for grades 4-8, features a teaching poster which shows different types of maps (different views of Salt Lake City, Utah), as well as three reproducible maps and reproducible activity sheets which complement the maps. The poster provides teacher background, including step-by-step lesson plans for four geography…

  12. Show Me the Way

    ERIC Educational Resources Information Center

    Dicks, Matthew J.

    2005-01-01

    Because today's students have grown up steeped in video games and the Internet, most of them expect feedback, and usually gratification, very soon after they expend effort on a task. Teachers can get quick feedback to students by showing them videotapes of their learning performances. The author, a 3rd grade teacher describes how the seemingly…

  13. Chemistry Game Shows

    NASA Astrophysics Data System (ADS)

    Campbell, Susan; Muzyka, Jennifer

    2002-04-01

    We present a technological improvement to the use of game shows to help students review for tests. Our approach uses HTML files interpreted with a browser on a computer attached to an LCD projector. The HTML files can be easily modified for use of the game in a variety of courses.

  14. Honored Teacher Shows Commitment.

    ERIC Educational Resources Information Center

    Ratte, Kathy

    1987-01-01

    Part of the acceptance speech of the 1985 National Council for the Social Studies Teacher of the Year, this article describes the censorship experience of this honored social studies teacher. The incident involved the showing of a videotape version of the feature film entitled "The Seduction of Joe Tynan." (JDH)

  15. Talk Show Science.

    ERIC Educational Resources Information Center

    Moore, Mitzi Ruth

    1992-01-01

    Proposes having students perform skits in which they play the roles of the science concepts they are trying to understand. Provides the dialog for a skit in which hot and cold gas molecules are interviewed on a talk show to study how these properties affect wind, rain, and other weather phenomena. (MDH)

  16. Stage a Water Show

    ERIC Educational Resources Information Center

    Frasier, Debra

    2008-01-01

    In the author's book titled "The Incredible Water Show," the characters from "Miss Alaineus: A Vocabulary Disaster" used an ocean of information to stage an inventive performance about the water cycle. In this article, the author relates how she turned the story into hands-on science teaching for real-life fifth-grade students. The author also…

  17. Structural analysis of the alcohol acyltransferase protein family from Cucumis melo shows that enzyme activity depends on an essential solvent channel.

    PubMed

    Galaz, Sebastián; Morales-Quintana, Luis; Moya-León, María Alejandra; Herrera, Raúl

    2013-03-01

    Alcohol acyltransferases (AAT) play a key role in ester biosynthesis. In Cucumis melo var. cantalupensis, AATs are encoded by a gene family of four members (CmAAT1-4). CmAAT1, CmAAT3 and CmAAT4 are capable of synthesizing esters, with CmAAT1 the most active. CmAAT2 is inactive and has an Ala268 residue instead of a threonine which is present in all other active AATs, although the role of this residue is still unclear. The present work aims to understand the molecular mechanism involved in ester biosynthesis in melon fruit and to clarify the importance of the Ala268 residue. First, structural models for each protein were built by comparative modelling methodology. Afterwards, conformational interaction between the protein and several ligands, alcohols and acyl-CoAs was explored by molecular docking and molecular dynamics simulation. Structural analysis showed that CmAATs share a similar structure. Also, well-defined solvent channels were described in the CmAATs except for CmAAT2 which does not have a proper channel and instead has a small pocket around Ala268. Residues of the catalytic HxxxD motif interact with substrates within the solvent channel, with Ser363 also important. Strong binding interaction energies were described for the best substrate couple of each CmAAT (hexyl-, benzyl- and cinnamyl-acetate for CmAAT1, 3 and 4 respectively). CmAAT1 and CmAAT2 protein surfaces share similar electrostatic potentials; nevertheless the entrance channels for the substrates differ in location and electrostatic character, suggesting that Ala268 might be responsible for that. This could partly explain the major differences in activity reported for these two enzymes.

  18. Fine Resolution Analysis of Lake Malawi Sediment Record Shows No Significant Climatic Impacts from the Mount Toba Super-Eruption of ~75ky

    NASA Astrophysics Data System (ADS)

    Jackson, L. J.; Stone, J.; Cohen, A. S.

    2014-12-01

    Debate over long, and short-term climatic impacts of the Mt. Toba super-eruption circa 75ky is often focused on East Africa. A severe drop in anatomically modern human populations has been hypothesized to be synchronous with a volcanic winter caused by the Toba super-eruption. If the Toba eruption caused a volcanic winter in East Africa, climatologically-sensitive ecosystems, such as Lake Malawi and its immediate watershed should show a direct and observable response in the sediment record. Cooler temperatures would cause a reduction of density contrast between epilimnion and hypolimnion waters, allowing for increased mixing and oxygenation of normally anoxic bottom waters. Enhanced mixing would cause noticeable changes in lake fly and algal communities. Cooler temperatures might also affect precipitation and the fire regime in the surrounding watershed. We analyzed two Lake Malawi cores at the finest practical resolution. Core 2A-10H-2 was analyzed in less than 6-year intervals and core 1C-8H-1 in 7-year intervals surrounding the Youngest Toba Tephra (YTT) for microfaunal abundance and variability, sediment composition, and evidence of changes in the occurrence of fires or watershed precipitation. Our analysis included point counts of diatoms and other algae, lake flies, charcoal, and siliciclastics. Changes in microfossil assemblage, variability, and abundance, as well as sediment composition around the YTT in Core 2A and 1C do not indicate that increased mixing or cooler temperatures occurred in either the central or northern basins of Lake Malawi. Similarly, charcoal counts do not suggest a change in fire regime. Our results indicate that at a subdecadal scale there was no substantial response in Lake Malawi or its immediate watershed to the Mt. Toba super-eruption, in contrast to predictions from the volcanic winter hypothesis.

  19. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

    PubMed Central

    Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

    2002-01-01

    Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

  20. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

    PubMed

    Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

    2002-06-01

    Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops.

  1. DNA-duplex linker for AFM-SELEX of DNA aptamer against human serum albumin.

    PubMed

    Takenaka, Musashi; Okumura, Yuzo; Amino, Tomokazu; Miyachi, Yusuke; Ogino, Chiaki; Kondo, Akihiko

    2017-02-15

    DNA-duplex interactions in thymines and adenins are used as a linker for the novel methodology of Atomic Force Microscope-Systematic Evolution of Ligands by EXpotential enrichment (AFM-SELEX). This study used the hydrogen bonds in 10 mer of both thymines (T10) and adenines (A10). Initially, the interactive force in T10-A10 was measured by AFM, which returned an average interactive force of approximately 350pN. Based on this result, DNA aptamers against human serum albumin could be selected in the 4th round, and 15 different clones could be sequenced. The lowest dissociation constant of the selected aptamer was identified via surface plasmon resonance, and it proved to be identical to that of the commercial aptamer. Therefore, specific hydrogen bonds in DNA can be useful linkers for AFM-SELEX.

  2. In situ nanomanipulators as a tool to separate individual tobermorite crystals for AFM studies.

    PubMed

    Yang, Tianhe; Holzer, Lorenz; Kägi, Ralf; Winnefeld, Frank; Keller, Bruno

    2007-10-01

    Atomic force microscopy (AFM) studies of cementitious materials are limited, mainly due to the lack of appropriate sample preparation techniques. In porous autoclaved aerated concrete (AAC), calcium silicate hydrate (C-S-H) is produced in its crystalline form, tobermorite. The crystals are lath-like with a length of several micrometers. In this work, we demonstrate the application of nanomanipulators to separate an individual tobermorite crystal from the bulk AAC for subsequent AFM investigations. The nanomanipulators are operated directly in an environmental scanning electron microscope (ESEM). We studied the interaction between moisture and the tobermorite surface under controlled relative humidity (RH). The results of topography and adhesion force measurements with AFM suggest that the surface of tobermorite is hydrophobic, which contrasts the macroscopic material properties (e.g. moisture transport in capillary pores).

  3. Imaging and force measurement of LDL and HDL by AFM in air and liquid

    PubMed Central

    Gan, Chaoye; Ao, Meiying; Liu, Zhanghua; Chen, Yong

    2015-01-01

    The size and biomechanical properties of lipoproteins are tightly correlated with their structures/functions. While atomic force microscopy (AFM) has been used to image lipoproteins the force measurement of these nano-sized particles is missing. We detected that the sizes of LDL and HDL in liquid are close to the commonly known values. The Young’s modulus of LDL or HDL is ∼0.4 GPa which is similar to that of some viral capsids or nanovesicles but greatly larger than that of various liposomes. The adhesive force of LDL or HDL is small (∼200 pN). The comparison of AFM detection in air and liquid was also performed which is currently lacking. Our data may provide useful information for better understanding and AFM detection of lipoproteins. PMID:25893163

  4. AFM characterization of nonwoven material functionalized by ZnO sputter coating

    SciTech Connect

    Deng Bingyao; Yan Xiong; Wei Qufu Gao Weidong

    2007-10-15

    Sputter coatings provide new approaches to the surface functionalization of textile materials. In this study, polyethylene terephthalate (PET) nonwoven material was used as a substrate for creating functional nanostructures on the fiber surfaces. A magnetron sputter coating was used to deposit functional zinc oxide (ZnO) nanostructures onto the nonwoven substrate. The evolution of the surface morphology of the fibers in the nonwoven web was examined using atomic force microscopy (AFM). The AFM observations revealed a significant difference in the morphology of the fibers before and after the sputter coating. The AFM images also indicated the effect of the sputtering conditions on the surface morphology of the fibers. The increase in the sputtering time led to the growth of the ZnO grains on the fiber surfaces. The higher pressure in the sputtering chamber could cause the formation of larger grains on the fiber surfaces. The higher power used also generated larger grains on the fiber surfaces.

  5. Imaging and force measurement of LDL and HDL by AFM in air and liquid.

    PubMed

    Gan, Chaoye; Ao, Meiying; Liu, Zhanghua; Chen, Yong

    2015-01-01

    The size and biomechanical properties of lipoproteins are tightly correlated with their structures/functions. While atomic force microscopy (AFM) has been used to image lipoproteins the force measurement of these nano-sized particles is missing. We detected that the sizes of LDL and HDL in liquid are close to the commonly known values. The Young's modulus of LDL or HDL is ∼0.4 GPa which is similar to that of some viral capsids or nanovesicles but greatly larger than that of various liposomes. The adhesive force of LDL or HDL is small (∼200 pN). The comparison of AFM detection in air and liquid was also performed which is currently lacking. Our data may provide useful information for better understanding and AFM detection of lipoproteins.

  6. The AFM Observation of Single Polyethylene Molecules in Coiled State on Mica

    NASA Astrophysics Data System (ADS)

    Prokhorov, V. V.; Yaminsky, I. V.

    2003-12-01

    Single polyethylene molecules and their small aggregates have been deposited on mica from diluted solutions at elevated temperatures and visualized by AFM in coiled and crystalline states. Coils have two-dimensional conformations with both highly tangled sites and locally extended segments with a length much exceeding the persistent length in a solution. The length measurements of coils reveal a wide distribution with the length of a maximum much smaller than the length of fully stretched molecules, moreover the long coils have been observed indicating the existence of linear multimolecular aggregates. Two models have been considered for the explanation of the observed deficit in the coils length, correspondingly the model implying the substantial smoothing of a winding chain trajectory due to the lack of the AFM resolution and the model of locally extended surface conformations with the long intramolecular folds. The roots of the apparent negative AFM height contrast of coils have been discussed.

  7. Custom AFM for X-ray beamlines: in situ biological investigations under physiological conditions

    PubMed Central

    Gumí-Audenis, B.; Carlà, F.; Vitorino, M. V.; Panzarella, A.; Porcar, L.; Boilot, M.; Guerber, S.; Bernard, P.; Rodrigues, M. S.; Sanz, F.; Giannotti, M. I.; Costa, L.

    2015-01-01

    A fast atomic force microscope (AFM) has been developed that can be installed as a sample holder for grazing-incidence X-ray experiments at solid/gas or solid/liquid interfaces. It allows a wide range of possible investigations, including soft and biological samples under physiological conditions (hydrated specimens). The structural information obtained using the X-rays is combined with the data gathered with the AFM (morphology and mechanical properties), providing a unique characterization of the specimen and its dynamics in situ during an experiment. In this work, lipid monolayers and bilayers in air or liquid environment have been investigated by means of AFM, both with imaging and force spectroscopy, and X-ray reflectivity. In addition, this combination allows the radiation damage induced by the beam on the sample to be studied, as has been observed on DOPC and DPPC supported lipid bilayers under physiological conditions. PMID:26524300

  8. Effects of fluoride treatment on phosphoric acid-etching in primary teeth: an AFM observation.

    PubMed

    Choi, Samjin; Rhee, Yeri; Park, Jeong-Hoon; Lee, Gi-Ja; Kim, Kyung-Sook; Park, Jae-Hong; Park, Young-Guk; Park, Hun-Kuk

    2010-07-01

    The aim of this study was to examine the effect of fluoride application on 37% phosphoric acid-etching by atomic force microscopy (AFM) in primary tooth samples based on a clinical protocol used in a pediatric dental hospital. Enamel samples were prepared from 36 exfoliated and non-carious primary teeth. Primary tooth samples were randomly assigned to one of the four groups based on the timing of acid-etching with 37% phosphoric acid after an acidulated phosphate fluoride (APF) pre-treatment. Group 1 received no fluoride application, Group 2 was pre-treated with fluoride and then received acid-etching 2 weeks later. One week separated the fluoride treatment and the acid-etching in Group 3, while Group 4 received acid-etching immediately after the fluoride treatment. The vestibular enamel surfaces of each primary tooth sample were scanned in air at a resolution of 512 x 512 pixels and a scan speed of 0.8 line/s. On the enamel surfaces of the primary teeth after APF pre-treatment, debris were observed although the teeth were smoother than they were prior to APF. As a result, it was concluded that APF treatment is responsible for decreased primary tooth surface roughness. The enamel surfaces etched for 20s showed that acid-etching was effective not only in removing scratches and debris, but also for evaluating enamel rod characteristics. Primary tooth enamel surfaces after etching showed minute structures caused by the decreased hydroxyapatite nanoparticle space, compared to those before etching. Also, acid-etching showed significantly increased roughness effects (p<0.0001, n=9). Finally, as more time elapsed after APF pre-treatment, the roughness was decreased to a lesser degree (p=0.005, n=9). We suggest that primary teeth etching 2 weeks after APF pre-treatment used clinically in pediatric hospitals may be effective to obtain properly etched enamel surfaces.

  9. An AFM Study of the Effects of Silanization Temperature, Hydration, and Annealing on the Nucleation and Aggregation of Condensed OTS Domains on Mica.

    PubMed

    Britt, David W; Hlady, Vladimir

    1996-03-25

    Partial monolayers of octadecyltrichlorosilane (OTS) were formed on mica under different reaction conditions in which the silanization temperature, time, and amount of water adsorbed on the mica substrates were varied. OTS surface coverage increased with silanization time for all samples; however, the amount and distribution of adsorbed OTS varied greatly under these different reaction conditions. AFM analysis showed that OTS formed two phases on mica silanized at 25°C: condensed "island-like" domains and expanded "liquid-like" domains. Partially dehydrated mica silanized at 9°C, however, displayed only condensed domains which were of smaller size compared to those on the 25°C samples. The lateral diffusion and aggregation of small condensed OTS domains to form larger aggregates was evident on all surfaces except the 25°C partially dehydrated mica. A uniform distribution of many small condensed domains surrounded by expanded OTS phases was seen instead. Extended annealing resulted in surface diffusion and aggregation of these domains and nucleation of new condensed domains from the surrounding expanded OTS phases. These observations are consistent with a deposition, diffusion, and aggregation model (DDA) which allows for activated diffusion; however, rigorous modeling is not presented here.

  10. Studying post-etching silicon crystal defects on 300mm wafer by automatic defect review AFM

    NASA Astrophysics Data System (ADS)

    Zandiatashbar, Ardavan; Taylor, Patrick A.; Kim, Byong; Yoo, Young-kook; Lee, Keibock; Jo, Ahjin; Lee, Ju Suk; Cho, Sang-Joon; Park, Sang-il

    2016-03-01

    Single crystal silicon wafers are the fundamental elements of semiconductor manufacturing industry. The wafers produced by Czochralski (CZ) process are very high quality single crystalline materials with known defects that are formed during the crystal growth or modified by further processing. While defects can be unfavorable for yield for some manufactured electrical devices, a group of defects like oxide precipitates can have both positive and negative impacts on the final device. The spatial distribution of these defects may be found by scattering techniques. However, due to limitations of scattering (i.e. light wavelength), many crystal defects are either poorly classified or not detected. Therefore a high throughput and accurate characterization of their shape and dimension is essential for reviewing the defects and proper classification. While scanning electron microscopy (SEM) can provide high resolution twodimensional images, atomic force microscopy (AFM) is essential for obtaining three-dimensional information of the defects of interest (DOI) as it is known to provide the highest vertical resolution among all techniques [1]. However AFM's low throughput, limited tip life, and laborious efforts for locating the DOI have been the limitations of this technique for defect review for 300 mm wafers. To address these limitations of AFM, automatic defect review AFM has been introduced recently [2], and is utilized in this work for studying DOI on 300 mm silicon wafer. In this work, we carefully etched a 300 mm silicon wafer with a gaseous acid in a reducing atmosphere at a temperature and for a sufficient duration to decorate and grow the crystal defects to a size capable of being detected as light scattering defects [3]. The etched defects form a shallow structure and their distribution and relative size are inspected by laser light scattering (LLS). However, several groups of defects couldn't be properly sized by the LLS due to the very shallow depth and low

  11. FRAME (Force Review Automation Environment): MATLAB-based AFM data processor.

    PubMed

    Partola, Kostyantyn R; Lykotrafitis, George

    2016-05-03

    Data processing of force-displacement curves generated by atomic force microscopes (AFMs) for elastic moduli and unbinding event measurements is very time consuming and susceptible to user error or bias. There is an evident need for consistent, dependable, and easy-to-use AFM data processing software. We have developed an open-source software application, the force review automation environment (or FRAME), that provides users with an intuitive graphical user interface, automating data processing, and tools for expediting manual processing. We did not observe a significant difference between manually processed and automatically processed results from the same data sets.

  12. Measuring the biomechanical properties of the actin in MCF-7 breast cancer cell with a combined system of AFM and SIM

    NASA Astrophysics Data System (ADS)

    You, Minghai; Chen, Jianling; Wang, Yuhua; Jiang, Ningcheng; Xie, Shusen; Yang, Hongqin

    2016-10-01

    Biomechanics of cell plays an important role in the behavior and development of diseases, which has a profound influence on the health, structural integrity, and function of cells. In this study, we proposed a method to assess the biomechanical properties in single breast cancer cell line MCF-7 by combining structured illumination microscopy (SIM) with atomic force microscopy (AFM). High resolution optical image of actin in MCF-7 cell and its elastography were obtained. The result shows that the quantitative resolution was improved by SIM, with 490 nm of conventional fluorescence image and 285 nm of reconstructed SIM image, which could give a precise location for AFM measurement. The elasticity of actin is about in the range of 10 1000 kPa. The proposed methods will be helpful in the understanding and clinical diagnosis of diseases at single cell level.

  13. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain

    PubMed Central

    2014-01-01

    Background The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum. Results In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell

  14. Not a "reality" show.

    PubMed

    Wrong, Terence; Baumgart, Erica

    2013-01-01

    The authors of the preceding articles raise legitimate questions about patient and staff rights and the unintended consequences of allowing ABC News to film inside teaching hospitals. We explain why we regard their fears as baseless and not supported by what we heard from individuals portrayed in the filming, our decade-long experience making medical documentaries, and the full un-aired context of the scenes shown in the broadcast. The authors don't and can't know what conversations we had, what documents we reviewed, and what protections we put in place in each televised scene. Finally, we hope to correct several misleading examples cited by the authors as well as their offhand mischaracterization of our program as a "reality" show.

  15. Public medical shows.

    PubMed

    Walusinski, Olivier

    2014-01-01

    In the second half of the 19th century, Jean-Martin Charcot (1825-1893) became famous for the quality of his teaching and his innovative neurological discoveries, bringing many French and foreign students to Paris. A hunger for recognition, together with progressive and anticlerical ideals, led Charcot to invite writers, journalists, and politicians to his lessons, during which he presented the results of his work on hysteria. These events became public performances, for which physicians and patients were transformed into actors. Major newspapers ran accounts of these consultations, more like theatrical shows in some respects. The resultant enthusiasm prompted other physicians in Paris and throughout France to try and imitate them. We will compare the form and substance of Charcot's lessons with those given by Jules-Bernard Luys (1828-1897), Victor Dumontpallier (1826-1899), Ambroise-Auguste Liébault (1823-1904), Hippolyte Bernheim (1840-1919), Joseph Grasset (1849-1918), and Albert Pitres (1848-1928). We will also note their impact on contemporary cinema and theatre.

  16. Charge injection in thin dielectric layers by atomic force microscopy: influence of geometry and material work function of the AFM tip on the injection process

    NASA Astrophysics Data System (ADS)

    Villeneuve-Faure, C.; Makasheva, K.; Boudou, L.; Teyssedre, G.

    2016-06-01

    Charge injection and retention in thin dielectric layers remain critical issues for the reliability of many electronic devices because of their association with a large number of failure mechanisms. To overcome this drawback, a deep understanding of the mechanisms leading to charge injection close to the injection area is needed. Even though the charge injection is extensively studied and reported in the literature to characterize the charge storage capability of dielectric materials, questions about charge injection mechanisms when using atomic force microscopy (AFM) remain open. In this paper, a thorough study of charge injection by using AFM in thin plasma-processed amorphous silicon oxynitride layers with properties close to that of thermal silica layers is presented. The study considers the impact of applied voltage polarity, work function of the AFM tip coating and tip curvature radius. A simple theoretical model was developed and used to analyze the obtained experimental results. The electric field distribution is computed as a function of tip geometry. The obtained experimental results highlight that after injection in the dielectric layer the charge lateral spreading is mainly controlled by the radial electric field component independently of the carrier polarity. The injected charge density is influenced by the nature of electrode metal coating (work function) and its geometry (tip curvature radius). The electron injection is mainly ruled by the Schottky injection barrier through the field electron emission mechanism enhanced by thermionic electron emission. The hole injection mechanism seems to differ from the electron one depending on the work function of the metal coating. Based on the performed analysis, it is suggested that for hole injection by AFM, pinning of the metal Fermi level with the metal-induced gap states in the studied silicon oxynitride layers starts playing a role in the injection mechanisms.

  17. The Great Cometary Show

    NASA Astrophysics Data System (ADS)

    2007-01-01

    its high spatial and spectral resolution, it was possible to zoom into the very heart of this very massive star. In this innermost region, the observations are dominated by the extremely dense stellar wind that totally obscures the underlying central star. The AMBER observations show that this dense stellar wind is not spherically symmetric, but exhibits a clearly elongated structure. Overall, the AMBER observations confirm that the extremely high mass loss of Eta Carinae's massive central star is non-spherical and much stronger along the poles than in the equatorial plane. This is in agreement with theoretical models that predict such an enhanced polar mass-loss in the case of rapidly rotating stars. ESO PR Photo 06c/07 ESO PR Photo 06c/07 RS Ophiuchi in Outburst Several papers from this special feature focus on the later stages in a star's life. One looks at the binary system Gamma 2 Velorum, which contains the closest example of a star known as a Wolf-Rayet. A single AMBER observation allowed the astronomers to separate the spectra of the two components, offering new insights in the modeling of Wolf-Rayet stars, but made it also possible to measure the separation between the two stars. This led to a new determination of the distance of the system, showing that previous estimates were incorrect. The observations also revealed information on the region where the winds from the two stars collide. The famous binary system RS Ophiuchi, an example of a recurrent nova, was observed just 5 days after it was discovered to be in outburst on 12 February 2006, an event that has been expected for 21 years. AMBER was able to detect the extension of the expanding nova emission. These observations show a complex geometry and kinematics, far from the simple interpretation of a spherical fireball in extension. AMBER has detected a high velocity jet probably perpendicular to the orbital plane of the binary system, and allowed a precise and careful study of the wind and the shockwave

  18. Biomechanical analysis of a new carbon fiber/flax/epoxy bone fracture plate shows less stress shielding compared to a standard clinical metal plate.

    PubMed

    Bagheri, Zahra S; Tavakkoli Avval, Pouria; Bougherara, Habiba; Aziz, Mina S R; Schemitsch, Emil H; Zdero, Radovan

    2014-09-01

    Femur fracture at the tip of a total hip replacement (THR), commonly known as Vancouver B1 fracture, is mainly treated using rigid metallic bone plates which may result in "stress shielding" leading to bone resorption and implant loosening. To minimize stress shielding, a new carbon fiber (CF)/Flax/Epoxy composite plate has been developed and biomechanically compared to a standard clinical metal plate. For fatigue tests, experiments were done using six artificial femurs cyclically loaded through the femoral head in axial compression for four stages: Stage 1 (intact), stage 2 (after THR insertion), stage 3 (after plate fixation of a simulated Vancouver B1 femoral midshaft fracture gap), and stage 4 (after fracture gap healing). For fracture fixation, one group was fitted with the new CF/Flax/Epoxy plate (n = 3), whereas another group was repaired with a standard clinical metal plate (Zimmer, Warsaw, IN) (n = 3). In addition to axial stiffness measurements, infrared thermography technique was used to capture the femur and plate surface stresses during the testing. Moreover, finite element analysis (FEA) was performed to evaluate the composite plate's axial stiffness and surface stress field. Experimental results showed that the CF/Flax/Epoxy plated femur had comparable axial stiffness (fractured = 645 ± 67 N/mm; healed = 1731 ± 109 N/mm) to the metal-plated femur (fractured = 658 ± 69 N/mm; healed = 1751 ± 39 N/mm) (p = 1.00). However, the bone beneath the CF/Flax/Epoxy plate was the only area that had a significantly higher average surface stress (fractured = 2.10 ± 0.66 MPa; healed = 1.89 ± 0.39 MPa) compared to bone beneath the metal plate (fractured = 1.18 ± 0.93 MPa; healed = 0.71 ± 0.24 MPa) (p < 0.05). FEA bone surface stresses yielded peak of 13 MPa at distal epiphysis (stage 1), 16 MPa at distal epiphysis (stage 2), 85 MPa for composite and 129

  19. Stretched View Showing 'Victoria'

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Stretched View Showing 'Victoria'

    This pair of images from the panoramic camera on NASA's Mars Exploration Rover Opportunity served as initial confirmation that the two-year-old rover is within sight of 'Victoria Crater,' which it has been approaching for more than a year. Engineers on the rover team were unsure whether Opportunity would make it as far as Victoria, but scientists hoped for the chance to study such a large crater with their roving geologist. Victoria Crater is 800 meters (nearly half a mile) in diameter, about six times wider than 'Endurance Crater,' where Opportunity spent several months in 2004 examining rock layers affected by ancient water.

    When scientists using orbital data calculated that they should be able to detect Victoria's rim in rover images, they scrutinized frames taken in the direction of the crater by the panoramic camera. To positively characterize the subtle horizon profile of the crater and some of the features leading up to it, researchers created a vertically-stretched image (top) from a mosaic of regular frames from the panoramic camera (bottom), taken on Opportunity's 804th Martian day (April 29, 2006).

    The stretched image makes mild nearby dunes look like more threatening peaks, but that is only a result of the exaggerated vertical dimension. This vertical stretch technique was first applied to Viking Lander 2 panoramas by Philip Stooke, of the University of Western Ontario, Canada, to help locate the lander with respect to orbiter images. Vertically stretching the image allows features to be more readily identified by the Mars Exploration Rover science team.

    The bright white dot near the horizon to the right of center (barely visible without labeling or zoom-in) is thought to be a light-toned outcrop on the far wall of the crater, suggesting that the rover can see over the low rim of Victoria. In figure 1, the northeast and southeast rims are labeled

  20. Investigation of Molecular Interactions between AFM-Tip and Thiol Films

    NASA Astrophysics Data System (ADS)

    Touhami, Ahmed; Moore, Justin; Lee, T. Randall

    Among various self-assembly processes, the formation of a self-assembled monolayer (SAM) is one of the most elegant ways for making an organic film with specific surface properties. Recently, much effort has been devoted in using AFM-based single-molecule force spectroscopy (SMFS) to understanding the formation of alkanethiol SAMs on gold surfaces. Investigating the factors that affect the AFM tip-SAMs interactions is necessary to clarify the controversial results of these studies. Here, we investigated the interactions between bare AFM-tips and several SAMs thiols-gold surfaces under controlled humidity conditions. Our results demonstrate that the Tip-SAM interactions can be used to precisely determine the length of the thiol chains, the adhesion force between thiols head groups and the AFM tip, and the strength of the thiol-gold contact. Our findings on the dynamics and the structure of the SAMs of alkanethiols on gold are useful for detail understanding of the thermodynamics, kinetics and mechanisms of SAM technology assembly. NSF.

  1. AFM tip characterization by using FFT filtered images of step structures.

    PubMed

    Yan, Yongda; Xue, Bo; Hu, Zhenjiang; Zhao, Xuesen

    2016-01-01

    The measurement resolution of an atomic force microscope (AFM) is largely dependent on the radius of the tip. Meanwhile, when using AFM to study nanoscale surface properties, the value of the tip radius is needed in calculations. As such, estimation of the tip radius is important for analyzing results taken using an AFM. In this study, a geometrical model created by scanning a step structure with an AFM tip was developed. The tip was assumed to have a hemispherical cone shape. Profiles simulated by tips with different scanning radii were calculated by fast Fourier transform (FFT). By analyzing the influence of tip radius variation on the spectra of simulated profiles, it was found that low-frequency harmonics were more susceptible, and that the relationship between the tip radius and the low-frequency harmonic amplitude of the step structure varied monotonically. Based on this regularity, we developed a new method to characterize the radius of the hemispherical tip. The tip radii estimated with this approach were comparable to the results obtained using scanning electron microscope imaging and blind reconstruction methods.

  2. Formation of hierarchical molecular assemblies from poly(oxypropylene)-segmented amido acids under AFM tapping.

    PubMed

    Lin, Jiang-Jen; Tsai, Wei-Cheng; Wang, Chi-He

    2007-04-10

    Molecular self-aligning of amphiphilic molecules into bundles with a constant width of 7-13 nm was observed under tapping-mode atomic force microscopy (TM-AFM). The requisite amphiphile, a poly(oxypropylene)-trimellitic amido acid sodium salt, is constituted of a symmetric amido acid structure with potential noncovalent forces of ionic charges, hydrogen bonds, pi-pi aromatic stacking, and hydrophobic interactions for intermolecular interaction. The amphiphiles are able to self-align into orderly hierarchical assemblies after simply being dissolved in water and dried under spin-coated evaporation. Under the TM-AFM tapping process, the bundles increased their length from an initial 20 to 600 nm. A sequential TM-AFM scanning and interval heating process was designed to probe the morphological transformations from the molecular bundles to lengthy strips (nearly micrometer scale) and to columns (with 5-7 nm spacing between the parallel strips). The formation of hierarchical arrays via molecular stretching, aligning, and connecting to each other was simultaneously observed and accelerated under the TM-AFM vibration energy. The molecular self-alignment caused by vibrations is envisioned to be a potential methodology for manipulating molecules into assembled templates, sensors, and optoelectronic devices.

  3. Single-Molecule Studies of Integrins by AFM-Based Force Spectroscopy on Living Cells

    NASA Astrophysics Data System (ADS)

    Eibl, Robert H.

    The characterization of cell adhesion between two living cells at the single-molecule level, i.e., between one adhesion receptor and its counter-receptor, appears to be an experimental challenge. Atomic force microscopy (AFM) can be used in its force spectroscopy mode to determine unbinding forces of a single pair of adhesion receptors, even with a living cell as a probe. This chapter provides an overview of AFM force measurements of the integrin family of cell adhesion receptors and their ligands. A focus is given to major integrins expressed on leukocytes, such as lymphocyte function-associated antigen 1 (LFA-1) and very late antigen 4 (VLA-4). These receptors are crucial for leukocyte trafficking in health and disease. LFA-1 and VLA-1 can be activated within the bloodstream from a low-affinity to a high-affinity receptor by chemokines in order to adhere strongly to the vessel wall before the receptor-bearing leukocytes extravasate. The experimental considerations needed to provide near-physiological conditions for a living cell and to be able to measure adequate forces at the single-molecule level are discussed in detail. AFM technology has been developed into a modern and extremely sensitive tool in biomedical research. It appears now that AFM force spectroscopy could enter, within a few years, medical applications in diagnosis and therapy of cancer and autoimmune diseases.

  4. [AFM-based technologies as the way towards the reverse Avogadro number].

    PubMed

    Pleshakova, T O; Shumov, I D; Ivanov, Yu D; Malsagova, K A; Kaysheva, A L; Archakov, A I

    2015-01-01

    Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.

  5. First-principles AFM image simulation with frozen density embedding theory

    NASA Astrophysics Data System (ADS)

    Sakai, Yuki; Lee, Alex J.; Chelikowsky, James R.

    We present efficient first-principles method of non-contact atomic force microscopy (nc-AFM). Ordinary nc-AFM simulations based on density functional theory (DFT) require exhaustive computational cost because it involves thousands of total energy calculations. Regarding the sample as a fixed external potential can reduce the computational cost, and we adopt frozen density embedding theory (FDET) for this purpose. Simulated nc-AFM images with FDET using a carbon monoxide tip well reproduces the full DFT images of benzene, pentacene, and graphene, although optimized tip-sample distances and interaction energies in FDET are underestimated and overestimated, respectively. The FDET-based simulation method is promising for AFM image simulation of surfaces and two-dimensional materials. This work was supported by U.S. DOE under Grant No. DE-FG02-06ER46286 and Award No. DE-SC0008877, and by Welch Foundation under Grant F-1837. Computational resources are provided by NERSC and TACC.

  6. Investigation of mussel adhesive protein adsorption on polystyrene and poly(octadecyl methacrylate) using angle dependent XPS, ATR-FTIR, and AFM

    SciTech Connect

    Baty, A.M.; Suci, P.A.; Tyler, B.J.; Geesey, G.G.

    1996-02-10

    Despite many years of research effort, the molecular interactions that are responsible for microbial adhesion and fouling of surfaces remain obscure. An understanding of these interactions would contribute to the development of surfaces that resist colonization of microorganisms. The irreversible adsorption of mussel adhesive proteins (MAP) from the marine mussel Mytilus edulis has been investigated on polystyrene (PS) and poly(octadecyl methacrylate) (POMA) surfaces using angle resolved X-ray photoelectron spectroscopy (XPS), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectrometry, and atomic force microscopy (AFM). Angle resolved XPS was used to quantify the elemental composition with depth of the upper 90 {angstrom} of the surface, and AFM was used to obtain the surface topography. The adsorption pattern of MAP, revealed by AFM images, is distinctly different on the two polymer surfaces and suggests that the substratum influences protein adhesion. The depth profiles of MAP, obtained from angle resolved XPS, show differences in nitrogen composition with depth for MAP adsorbed to PS and POMA. Infrared spectra of hydrated adsorbed MAP revealed significant differences in the amide III region and in two bands which may originate from residues in the tandemly repeated sequences of MAP. This data demonstrates that the chemistry of the polymer film that is present at the protein-polymer interface can influence protein-protein and protein-surface interactions.

  7. Restriction enzyme analysis of ribosomal DNA shows that Candida inconspicua clinical isolates can be misidentified as Candida norvegensis with traditional diagnostic procedures.

    PubMed

    Majoros, L; Kardos, G; Belák, A; Maráz, A; Asztalos, L; Csánky, E; Barta, Z; Szabó, B

    2003-11-01

    We identified 29 yeast isolates from 22 patients using the API ID32C panel. Twenty-eight of these isolates were Candida norvegensis and one was C. inconspicua. Although C. norvegensis is considered a pseudohypha-producing species, only one isolate produced pseudohyphae. Restriction enzyme analysis of PCR-amplified ribosomal DNA with four different enzymes proved that all isolates were C. inconspicua.

  8. Effect of enamel morphology on nanoscale adhesion forces of streptococcal bacteria : An AFM study.

    PubMed

    Wang, Chuanyong; Zhao, Yongqi; Zheng, Sainan; Xue, Jing; Zhou, Jinglin; Tang, Yi; Jiang, Li; Li, Wei

    2015-01-01

    We explore the influence of enamel surface morphology on nanoscale bacterial adhesion forces. Three dimensional morphology characteristics of enamel slices, which were treated with phosphoric acid (for 0 s, 5 s, 10 s, 20 s, and 30 s), were acquired. Adhesion forces of three initial colonizers (Streptococcus oralis, Streptococcus sanguinis, and Streptococcus mitis) and two cariogenic bacterial strains (Streptococcus mutans and Streptococcus sobrinus) with etched enamel surfaces were determined. Comparison of the forces was made by using bacterial probe method under atomic force microscope (AFM) in adhesion buffer. The results showed that enamel morphology was significantly altered by etching treatment. The roughness, peak-to-valley height, and valley-to-valley width of the depth profile, surface area, and volume increased linearly with acid exposure time, and reached the maximum at 30s, respectively. The adhesion forces of different strains increased accordingly with etching time. Adhesion forces of S. oralis, S. mitis, S. mutans, and S. sobrinus reached the maximum values of 0.81 nN, 0.84 nN, 0.73 nN, and 0.64 nN with enamel treated for 20s, respectively, whereas that of S. sanguinis at 10s (1.28nN), and dropped on coarser enamel surfaces. In conclusion, enamel micro-scale morphology may significantly alter the direct adhesion forces of bacteria. And there may be a threshold roughness for bacterial adhesion on enamel surface.

  9. Triaxial AFM probes for noncontact trapping and manipulation.

    PubMed

    Brown, Keith A; Westervelt, Robert M

    2011-08-10

    We show that a triaxial atomic force microscopy probe creates a noncontact trap for a single particle in a fluid via negative dielectrophoresis. A zero in the electric field profile traps the particle above the probe surface, avoiding adhesion, and the repulsive region surrounding the zero pushes other particles away, preventing clustering. Triaxial probes are promising for three-dimensional assembly and for selective imaging of a particular property of a sample using interchangeable functionalized particles.

  10. Versatile method for AFM-tip functionalization with biomolecules: fishing a ligand by means of an in situ click reaction.

    PubMed

    Kumar, Rakesh; Ramakrishna, Shivaprakash N; Naik, Vikrant V; Chu, Zonglin; Drew, Michael E; Spencer, Nicholas D; Yamakoshi, Yoko

    2015-04-21

    A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions.

  11. Interaction of Nano-Sized Materials With Polymer Chains in Polymer-Nanocomposite Thin Films-An AFM Perspective

    NASA Astrophysics Data System (ADS)

    Verma, Gaurav; Kaushik, Anupama; Ghosh, Anup K.

    2011-12-01

    Nanocomposite thin films were prepared with polyurethane as a matrix and organically modified clay as a filler. The interfacial interaction between the exfoliated clay nanoplatelets and the polymeric chains has been investigated by using Atomic Force Microscopy (AFM). The nanoclay platelets show a preferential association with the hard domains of polyurethane matrix on the surface of the thin films. The pendant hydroxyl group on the nanoplatelets attract the isocyanate of the polyisocyanate and a urethane group is formed. This leads to the `clouding' and `entwining' of the nanoplatelets by the hard segmental chains. This is the first visual evidence of nanomaterial filler and polymer matrix interaction and it could open up a spectrum of novel property achievements in nanocomposite thin films. Also the understanding of this interaction can lead to more controlled architecture of nanocomposites.

  12. Mechano-chemical manipulation of Sn chains on Si(1 0 0) by NC-AFM.

    PubMed

    Sweetman, A; Lekkas, I; Moriarty, P

    2017-02-22

    We investigate the atomic structure of Sn dimer chains grown on the Si(1 0 0) surface using non-contact atomic force microscopy (NC-AFM) at cryogenic temperatures. We find that similar to the native Si(1 0 0) dimer structure, the ground state of the Sn dimer structure is buckled at low temperature. At 5 K we show that the buckling state of the Sn dimers may be controllably, and reversibly, manipulated with atomic precision by close approach of the tip, without modification of the underlying substrate buckling structure. At intermediate cryogenic temperatures we observe changes in the configuration of the dimer chains in the region where the tip-sample interaction is very weak, suggesting that the energy barrier to transit between configurations is sufficiently small to be surmounted at 78 K.

  13. Mechano-chemical manipulation of Sn chains on Si(1 0 0) by NC-AFM

    NASA Astrophysics Data System (ADS)

    Sweetman, A.; Lekkas, I.; Moriarty, P.

    2017-02-01

    We investigate the atomic structure of Sn dimer chains grown on the Si(1 0 0) surface using non-contact atomic force microscopy (NC-AFM) at cryogenic temperatures. We find that similar to the native Si(1 0 0) dimer structure, the ground state of the Sn dimer structure is buckled at low temperature. At 5 K we show that the buckling state of the Sn dimers may be controllably, and reversibly, manipulated with atomic precision by close approach of the tip, without modification of the underlying substrate buckling structure. At intermediate cryogenic temperatures we observe changes in the configuration of the dimer chains in the region where the tip-sample interaction is very weak, suggesting that the energy barrier to transit between configurations is sufficiently small to be surmounted at 78 K.

  14. Nano-palpation AFM and its quantitative mechanical property mapping.

    PubMed

    Nakajima, Ken; Ito, Makiko; Wang, Dong; Liu, Hao; Nguyen, Hung Kim; Liang, Xiaobin; Kumagai, Akemi; Fujinami, So

    2014-06-01

    We review nano-palpation atomic force microscopy, which offers quantitative mechanical property mapping especially for soft materials. The method measures force-deformation curves on the surfaces of soft materials. The emphasis is placed on how both Hertzian and Derjaguin-Muller-Toporov contact mechanics fail to reproduce the experimental curves and, alternatively, how the Johnson-Kendall-Roberts model does. We also describe the force-volume technique for obtaining a two-dimensional map of mechanical properties, such as the elastic modulus and adhesive energy, based on the above-mentioned analysis. Finally, we conclude with several counterpart measurements, which describe the viscoelastic nature of soft materials, and give examples, including vulcanized isoprene rubber and the current status of ISO standardization.

  15. Single-Cell Analysis and Next-Generation Immuno-Sequencing Show That Multiple Clones Persist in Patients with Chronic Lymphocytic Leukemia.

    PubMed

    Kriangkum, Jitra; Motz, Sarah N; Mack, Tanner; Beiggi, Sara; Baigorri, Eva; Kuppusamy, Hemalatha; Belch, Andrew R; Johnston, James B; Pilarski, Linda M

    2015-01-01

    The immunoglobulin heavy chain (IGH) gene rearrangement in chronic lymphocytic leukemia (CLL) provides a unique molecular signature; however, we demonstrate that 26/198 CLL patients (13%) had more than one IGH rearrangement, indicating the power of molecular technology over phenotypic analysis. Single-cell PCR analysis and next-generation immuno-sequencing identified IGH-defined clones. In 23% (18/79) of cases whose clones carried unmutated immunoglobulin heavy chain variable (IGHV) genes (U-CLL), IGH rearrangements were bialleic with one productive (P) and one non-productive (NP) allele. Two U-CLL were biclonal, each clone being monoallelic (P). In 119 IGHV-mutated (M-CLL) cases, one had biallelic rearrangements in their CLL (P/NP) and five had 2-4 distinct clones. Allelic exclusion was maintained in all B-clones analyzed. Based on single-cell PCR analysis, 5/11 partner clones (45%) reached levels of >5x10(9) cells/L, suggesting second CLL clones. Partner clones persisted over years. Conventional IGH characterization and next-generation sequencing of 13 CLL, 3 multiple myeloma, 2 Waldenstrom's macroglobulinemia and 3 age-matched healthy donors consistently identified the same rearranged IGH sequences. Most multiple clones occurred in M-CLL, perhaps indicative of weak clonal dominance, thereby associating with a good prognosis. In contrast, biallelic CLL occurred primarily in U-CLL thus being associated with poor prognosis. Extending beyond intra-clonal diversity, molecular analysis of clonal evolution and apparent subclones in CLL may also reflect inter-clonal diversity.

  16. Restriction Enzyme Analysis of Ribosomal DNA Shows that Candida inconspicua Clinical Isolates Can Be Misidentified as Candida norvegensis with Traditional Diagnostic Procedures

    PubMed Central

    Majoros, L.; Kardos, G.; Belák, Á.; Maráz, A.; Asztalos, L.; Csánky, E.; Barta, Z.; Szabó, B.

    2003-01-01

    We identified 29 yeast isolates from 22 patients using the API ID32C panel. Twenty-eight of these isolates were Candida norvegensis and one was C. inconspicua. Although C. norvegensis is considered a pseudohypha-producing species, only one isolate produced pseudohyphae. Restriction enzyme analysis of PCR-amplified ribosomal DNA with four different enzymes proved that all isolates were C. inconspicua. PMID:14605175

  17. Waardenburg syndrome (WS): the analysis of a single family with a WS1 mutation showing linkage to RFLP markers on human chromosome 2q.

    PubMed Central

    Asher, J H; Morell, R; Friedman, T B

    1991-01-01

    Waardenburg syndrome type I (WS1; MIM 19350) is caused by a pleiotropic, autosomal dominant mutation with variable penetrance and expressivity. Of individuals with this mutation, 20%-25% are hearing impaired. A multilocus linkage analysis of RFLP data from a single WS1 family with 11 affected individuals indicates that the WS1 mutation in this family is linked to the following four marker loci located on the long arm of chromosome 2: ALPP (alkaline phosphatase, placental), FN1 (fibronectin 1), D2S3 (a unique-copy DNA segment), and COL6A3 (collagen VI, alpha 3). For the RFLP marker loci, a multilocus linkage analysis using MLINK produced a peak lod (Z) of 3.23 for the following linkage relationships and recombination fractions (theta i): (ALPP----.000----FN1)----.122----D2S3----.267----CO L6A3. A similar analysis produced a Z of 6.67 for the following linkage relationships and theta i values among the markers and WS1: (FN1----.000----WS1----.000----ALPP)----.123----D2S 3----.246----COL6A3. The data confirm the conclusion of Foy et al. that at least some WS1 mutations map to chromosome 2q. Images Figure 2 PMID:1670751

  18. High throughput nanofabrication of silicon nanowire and carbon nanotube tips on AFM probes by stencil-deposited catalysts.

    PubMed

    Engstrom, Daniel S; Savu, Veronica; Zhu, Xueni; Bu, Ian Y Y; Milne, William I; Brugger, Juergen; Boggild, Peter

    2011-04-13

    A new and versatile technique for the wafer scale nanofabrication of silicon nanowire (SiNW) and multiwalled carbon nanotube (MWNT) tips on atomic force microscope (AFM) probes is presented. Catalyst material for the SiNW and MWNT growth was deposited on prefabricated AFM probes using aligned wafer scale nanostencil lithography. Individual vertical SiNWs were grown epitaxially by a catalytic vapor-liquid-solid (VLS) process and MWNTs were grown by a plasma-enhanced chemical vapor (PECVD) process on the AFM probes. The AFM probes were tested for imaging micrometers-deep trenches, where they demonstrated a significantly better performance than commercial high aspect ratio tips. Our method demonstrates a reliable and cost-efficient route toward wafer scale manufacturing of SiNW and MWNT AFM probes.

  19. Measuring the energy landscape of complex bonds using AFM

    NASA Astrophysics Data System (ADS)

    Mayyas, Essa; Hoffmann, Peter; Runyan, Lindsay

    2009-03-01

    We measured rupture force of a complex bond of two interacting proteins with atomic force microscopy. Proteins of interest were active and latent Matrix metalloproteinases (MMPs), type 2 and 9, and their tissue inhibitors TIMP1 and TIMP2. Measurements show that the rupture force depends on the pulling speed; it ranges from 30 pN to 150 pN at pulling speeds 30nm/s to 48000nm/s. Analyzing data using an extended theory enabled us to understand the mechanism of MMP-TIMP interaction; we determined all physical parameters that form the landscape energy of the interaction, in addition to the life time of the bond and its length. Moreover, we used the pulling experiment to study the interaction of TIMP2 with the receptor MT1-MMP on the surface of living cells.

  20. Effect of chain lengths of PEO-PPO-PEO on small unilamellar liposome morphology and stability: an AFM investigation.

    PubMed

    Liang, Xuemei; Mao, Guangzhao; Ng, K Y Simon

    2005-05-01

    The morphology and stability of small unilamellar egg yolk phosphatidylcholine (EggPC) liposomes modified with the Pluronic copolymer (poly (oxyethylene)-poly (oxypropylene)-poly (oxyethylene) (PEO-PPO-PEO)) with different compositions on mica surface have been investigated using atomic force microscopy. Morphology studies reveal significant morphological changes of liposomes upon incorporating the Pluronic copolymer. Bilayers are observed for Pluronic with small hydrophilic (PEO) chain lengths such as L81 [(PEO)2(PPO)40(PEO)2] and L121 [(PEO)4(PPO)60(PEO)4]; bilayer and vesicle coexistence is observed for P85 [(PEO)26(PPO)39.5(PEO)26] and F87 [(PEO)61.1(PPO)39.7(PEO)61.1]; and stable vesicles are observed for F88 [(PEO)103.5(PPO)39.2(PEO)103.5], F127 [(PEO)100(PPO)65(PEO)100], and F108 [(PEO)132.6(PPO)50.3(PEO)132.6]. The micromechanical properties of Pluronic-modified EggPC vesicles were studied by analyzing AFM approaching force curve. The bending modulus (k(c)) of the Pluronic-modified EggPC vesicles increased several-fold compared with that of the pure EggPC vesicles. The significant difference is due to the enhanced rigidity of the EggPC vesicles as a result of the incorporation of PPO molecules and PEO chains. Based on the analysis of onset point by AFM and diameters of vesicles by light scattering, it was concluded that the favorable model to describe the polymer-bilayer interaction is the membrane-spanning model.

  1. Comparative proteome analysis of Penicillium verrucosum grown under light of short wavelength shows an induction of stress-related proteins associated with modified mycotoxin biosynthesis.

    PubMed

    Stoll, Dominic A; Link, Sebastian; Kulling, Sabine; Geisen, Rolf; Schmidt-Heydt, Markus

    2014-04-03

    In this study the differentially expressed protein population of Penicillium verrucosum grown either in the dark or under light with a wavelength of 450nm has been analyzed. Light of short wavelength led to oxidative stress in the fungal cell; under this condition the mycotoxin biosynthesis revealed a mutual shift from ochratoxin A to citrinin. Using a proteomic approach combining an optimized protein extraction method with 2-dimensional SDS-PAGE followed by HPLC-ESI-TOF-MS/MS mass spectrometric analysis, initially 56 significantly differential proteins (light vs. dark) were detected comprising proteins of a broad range of isoelectric points and molecular masses. In total, 46 proteins could be identified further by database query, most of these proteins are assumed to be involved in response to stress (e.g. antioxidative proteins, heat shock proteins) and general metabolic processes (e.g. glycolysis, ATP supply). Proteome analyses are necessary to unravel the regulation of secondary metabolite biosynthesis at a translational level. This may enable identification of proteins which are involved in mycotoxin biosynthesis, adaption processes or even stress compensation mechanisms. This study depicts the first proteome analysis of P. verrucosum.

  2. Chitosan dressing promotes healing in third degree burns in mice: gene expression analysis shows biphasic effects for rapid tissue regeneration and decreased fibrotic signaling.

    PubMed

    Baxter, Ruth M; Dai, Tianhong; Kimball, Jess; Wang, Eugenia; Hamblin, Michael R; Wiesmann, William P; McCarthy, Simon J; Baker, Shenda M

    2013-02-01

    Burns are a significant health challenge and healing can result in scar formation. Chitosan, a derivative of chitin, has been used to promote wound healing. In this study we used gene expression profiling in a mouse model of full thickness cutaneous burn to assess the benefits of treating with a chitosan lactate dressing. Three days after wounding mice treated with chitosan showed increased expression of genes associated with formation of granulation tissue. At a later time point, seven days after wounding, genes that initially showed increased expression were now down-regulated, and there was increased expression of genes involved in remodeling suggesting that the chitosan treatment results in accelerated healing. Quantitative RT-PCR showed modulated mRNA levels for TGFβ1 by the chitosan dressing. TGFβ1 initially promotes healing but extended activity can result in scarring. Importantly we found that expression was elevated at day three, but decreased at day seven suggesting that chitosan treatment will not result in scar formation, and may even be beneficial in preventing scar formation. Additionally, the biphasic regulation of expression of TGFβ1 could be a powerful biomarker for future studies of the wound-healing potential of chitosan based and other treatments for burn wounds.

  3. Maps showing interpretation, using R-mode factor analysis, of trace-element abundances in heavy-mineral concentrate samples, Delta 1° x 2° Quadrangle, Utah

    USGS Publications Warehouse

    Zimbelman, David R.

    1994-01-01

    A set of heavy-mineral concentrate data for the Delta 1° x 2° quadrangle, Utah Conterminous U.S. Mineral Assessment Program (CUSMAP) project was compiled from results of analyses of samples collected during the National Uranium Resource Evaluation Program (SURE), as well as results obtained from samples collected more recently by the USGS. Data results, sampling methods, and analytical methods are provided in Abrogast and others, 1993; 1990; 1988a; 1988b). A similar report, discussing results obtained from stream-sediment samples, is presented in Zimbelman (1993a). The Delta 1° x 2° quadrangle, Utah (figure 1) contains a variety of hydrothermal mineral deposit types, including porphyry-, vein-, replacement-, and Carlin-type deposits. These deposit types have been worked for commodities including gold, silver, beryllium, uranium, lead, zinc, copper, manganese, and cadmium (Lindsey, 1977; Morris and Mogensen, 1978; Zimbelman and others, 1990; Zimbelman and others, 1988). Heavy-mineral concentrate and stream-sediment samples derived from these hydrothermally altered rocks typically contain many geochemical anomalies (for example, see Zimbelman 1993b, c, d). Element associations characterizing lithology and hydrothermal mineral deposits can be distinguished using R-mode factor analysis. This tool often is useful in reconnaissance-scale surveys where sample anomalies are often weak. and single-element distributions may not help to delineate targets. R-mode factors analysis can help identify geologic trends and areas most likely to contain the mineral deposits. R-mode factor analysis was performed on a data set of results of analyses for 19 elements in 643 samples and produced a six-factor model. These six factors represent the geochemical contributions to the data set provided by lithologic and mineralization processes, The distribution of samples that contain high scores for mineralization-related factors is widespread in the Delta quadrangle. These sample sites

  4. Diffusion tensor MRI shows progressive changes in the hippocampus and dentate gyrus after status epilepticus in rat - histological validation with Fourier-based analysis.

    PubMed

    Salo, Raimo A; Miettinen, Tuukka; Laitinen, Teemu; Gröhn, Olli; Sierra, Alejandra

    2017-03-04

    Imaging markers for monitoring disease progression, recovery, and treatment efficacy are a major unmet need for many neurological diseases, including epilepsy. Recent evidence suggests that diffusion tensor imaging (DTI) provides high microstructural contrast even outside major white matter tracts. We hypothesized that in vivo DTI could detect progressive microstructural changes in the dentate gyrus and the hippocampal CA3bc in the rat brain after status epilepticus (SE). To test this hypothesis, we induced SE with systemic kainic acid or pilocarpine in adult male Wistar rats and subsequently scanned them using in vivo DTI at five time-points: prior to SE, and 10, 20, 34, and 79 days post SE. In order to tie the DTI findings to changes in the tissue microstructure, myelin- and glial fibrillary acidic protein (GFAP)-stained sections from the same animals underwent Fourier analysis. We compared the Fourier analysis parameters, anisotropy index and angle of myelinated axons or astrocyte processes, to corresponding DTI parameters, fractional anisotropy (FA) and the orientation angle of the principal eigenvector. We found progressive detectable changes in DTI parameters in both the dentate gyrus (FA, axial diffusivity [D||], linear anisotropy [CL] and spherical anisotropy [CS], p<0.001, linear mixed-effects model [LMEM]) and the CA3bc (FA, D||, CS, and angle, p<0.001, LMEM; CL and planar anisotropy [CP], p<0.01, LMEM) post SE. The Fourier analysis revealed that both myelinated axons and astrocyte processes played a role in the water diffusion anisotropy changes detected by DTI in individual portions of the dentate gyrus (suprapyramidal blade, mid-portion, and infrapyramidal blade). In the whole dentate gyrus, myelinated axons markedly contributed to the water diffusion changes. In CA3bc as well as in CA3b and CA3c, both myelinated axons and astrocyte processes contributed to water diffusion anisotropy and orientation. Our study revealed that DTI is a promising method

  5. Open channel current noise analysis of S6 peptides from KvAP channel on bilayer lipid membrane shows bimodal power law scaling

    NASA Astrophysics Data System (ADS)

    Shrivastava, Rajan; Malik, Chetan; Ghosh, Subhendu

    2016-06-01

    Open channel current noise in synthetic peptide S6 of KvAP channel was investigated in a voltage clamp experiment on bilayer lipid membrane (BLM). It was observed that the power spectral density (PSD) of the component frequencies follows power law with different slopes in different frequency ranges. In order to know the origin of the slopes PSD analysis was done with signal filtering. It was found that the first slope in the noise profile follows 1 / f pattern which exists at lower frequencies and has high amplitude current noise, while the second slope corresponds to 1 /f 2 - 3 pattern which exists at higher frequencies with low amplitude current noise. In addition, white noise was observed at very large frequencies. It was concluded that the plausible reason for the multiple power-law scaling is the existence of different modes of non-equilibrium ion transport through the S6 channel.

  6. Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process

    PubMed Central

    Karlsson, Stefan L.; Thomson, Nicholas; Mutreja, Ankur; Connor, Thomas; Sur, Dipika; Ali, Mohammad; Clemens, John; Dougan, Gordon; Holmgren, Jan; Lebens, Michael

    2016-01-01

    Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata, India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa. The change from Ogawa to Inaba resulted from mutational disruption of the methyltransferase encoded by the wbeT gene. Re-emergence of the Ogawa serotype was found to result either from expansion of an already existing Ogawa clade or reversion of the mutation in an Inaba clade. Our data suggests that such transitions are not random events but rather driven by as yet unidentified selection mechanisms based on differences in the structure of the O1 antigen or in the serotype-determining wbeT gene. PMID:27706170

  7. Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process.

    PubMed

    Karlsson, Stefan L; Thomson, Nicholas; Mutreja, Ankur; Connor, Thomas; Sur, Dipika; Ali, Mohammad; Clemens, John; Dougan, Gordon; Holmgren, Jan; Lebens, Michael

    2016-10-01

    Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata, India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa. The change from Ogawa to Inaba resulted from mutational disruption of the methyltransferase encoded by the wbeT gene. Re-emergence of the Ogawa serotype was found to result either from expansion of an already existing Ogawa clade or reversion of the mutation in an Inaba clade. Our data suggests that such transitions are not random events but rather driven by as yet unidentified selection mechanisms based on differences in the structure of the O1 antigen or in the serotype-determining wbeT gene.

  8. Analysis of the Fgfr2C342Y mouse model shows condensation defects due to misregulation of Sox9 expression in prechondrocytic mesenchyme

    PubMed Central

    Peskett, Emma; Kumar, Samin; Baird, William; Jaiswal, Janhvi; Li, Ming; Patel, Priyanca; Britto, Jonathan A.

    2017-01-01

    ABSTRACT Syndromic craniosynostosis caused by mutations in FGFR2 is characterised by developmental pathology in both endochondral and membranous skeletogenesis. Detailed phenotypic characterisation of features in the membranous calvarium, the endochondral cranial base and other structures in the axial and appendicular skeleton has not been performed at embryonic stages. We investigated bone development in the Crouzon mouse model (Fgfr2C342Y) at pre- and post-ossification stages to improve understanding of the underlying pathogenesis. Phenotypic analysis was performed by whole-mount skeletal staining (Alcian Blue/Alizarin Red) and histological staining of sections of CD1 wild-type (WT), Fgfr2C342Y/+ heterozygous (HET) and Fgfr2C342Y/C342Y homozygous (HOM) mouse embryos from embryonic day (E)12.5-E17.5 stages. Gene expression (Sox9, Shh, Fgf10 and Runx2) was studied by in situ hybridisation and protein expression (COL2A1) by immunohistochemistry. Our analysis has identified severely decreased osteogenesis in parts of the craniofacial skeleton together with increased chondrogenesis in parts of the endochondral and cartilaginous skeleton in HOM embryos. The Sox9 expression domain in tracheal and basi-cranial chondrocytic precursors at E13.5 in HOM embryos is increased and expanded, correlating with the phenotypic observations which suggest FGFR2 signalling regulates Sox9 expression. Combined with abnormal staining of type II collagen in pre-chondrocytic mesenchyme, this is indicative of a mesenchymal condensation defect. An expanded spectrum of phenotypic features observed in the Fgfr2C342Y/C342Y mouse embryo paves the way towards better understanding the clinical attributes of human Crouzon–Pfeiffer syndrome. FGFR2 mutation results in impaired skeletogenesis; however, our findings suggest that many phenotypic aberrations stem from a primary failure of pre-chondrogenic/osteogenic mesenchymal condensation and link FGFR2 to SOX9, a principal regulator of skeletogenesis

  9. Sequence analysis of the non-recurring C-terminal domains shows that insect lipoprotein receptors constitute a distinct group of LDL receptor family members.

    PubMed

    Rodenburg, Kees W; Smolenaars, Marcel M W; Van Hoof, Dennis; Van der Horst, Dick J

    2006-04-01

    Lipoprotein-mediated delivery of lipids in mammals involves endocytic receptors of the low density lipoprotein (LDL) receptor (LDLR) family. In contrast, in insects, the lipoprotein, lipophorin (Lp), functions as a reusable lipid shuttle in lipid delivery, and these animals, therefore, were not supposed to use endocytic receptors. However, recent data indicate additional endocytic uptake of Lp, mediated by a Lp receptor (LpR) of the LDLR family. The two N-terminal domains of LDLR family members are involved in ligand binding and dissociation, respectively, and are composed of a mosaic of multiple repeats. The three C-terminal domains, viz., the optional O-linked glycosylation domain, the transmembrane domain, and the intracellular domain, are of a non-repetitive sequence. The present classification of newly discovered LDLR family members, including the LpRs, bears no relevance to physiological function. Therefore, as a novel approach, the C-terminal domains of LDLR family members across the entire animal kingdom were used to perform a sequence comparison analysis in combination with a phylogenetic tree analysis. The LpRs appeared to segregate into a specific group distinct from the groups encompassing the other family members, and each of the three C-terminal domains of the insect receptors is composed of unique set of sequence motifs. Based on conservation of sequence motifs and organization of these motifs in the domains, LpR resembles most the groups of the LDLRs, very low density lipoprotein (VLDL) receptors, and vitellogenin receptors. However, in sequence aspects in which LpR deviates from these three receptor groups, it most notably resembles LDLR-related protein-2, or megalin. These features might explain the functional differences disclosed between insect and mammalian lipoprotein receptors.

  10. Genome analysis shows Bacillus axarquiensis is not a later heterotypic synonym of Bacillus mojavensis; reclassification of Bacillus malacitensis and Brevibacterium halotolerans as heterotypic synonyms of Bacillus axarquiensis.

    PubMed

    Dunlap, Christopher A; Bowman, Michael J; Schisler, David A; Rooney, Alejandro P

    2016-06-01

    Bacillus axarquiensis and Bacillus malacitensis were previously reported to be later heterotypic synonyms of Bacillus mojavensis, based primarily on DNA-DNA relatedness values. We have sequenced draft genomes of Bacillus axarquiensis NRRL B-41617T and Bacillus malacitensis NRRL B-41618T. Comparative genomics and DNA-DNA relatedness calculations showed that while Bacillus axarquiensis and Bacillus malacitensis are synonymous with each other, they are not synonymous with Bacillus mojavensis. In addition, a draft genome was completed for Brevibacterium halotolerans, a strain long suspected of being a Bacillus subtilis group member based on 16S rRNA similarities (99.8 % with Bacillus mojavensis). Comparative genomics and DNA-DNA relatedness calculations showed that Brevibacterium halotolerans is synonymous with Bacillus axarquiensis and Bacillus malacitensis. The pairwise in silico DNA-DNA hybridization values calculated in comparisons between the three conspecific strains were all greater than 92 %, which is well above the standard species threshold of 70 %. While the pairwise in silico DNA-DNA hybridization values calculated in comparisons of the three conspecific strains with Bacillus mojavensis were all less than 65 %. The combined results of our genotype and phenotype studies showed that Bacillus axarquiensis, Bacillus malacitensis and Brevibacterium halotolerans are conspecific and distinct from Bacillus mojavensis. Because the valid publication of the name Bacillus axarquiensis predates the publication of the name Bacillus malacitensis, we propose that Bacillus malacitensis be reclassified as a synonym of Bacillus axarquiensis. In addition, we propose to reclassify Brevibacterium halotolerans as a synonym of Bacillus axarquiensis. An amended description of Bacillus axarquiensis is provided.

  11. Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation.

    PubMed

    Andrushchenko, V; Leonenko, Z; Cramb, D; van de Sande, H; Wieser, H

    The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.

  12. AFM study of the thermotropic behaviour of supported DPPC bilayers with and without the model peptide WALP23.

    PubMed

    Yarrow, F; Kuipers, B W M

    2011-01-01

    Temperature-controlled Atomic Force Microscopy (TC-AFM) in Contact Mode is used here to directly image the mechanisms by which melting and crystallization of supported, hydrated DPPC bilayers proceed in the presence and absence of the model peptide WALP23. Melting from the gel L(β)' to the liquid-crystalline L(α) phase starts at pre-existing line-type packing defects (grain boundaries) in absence of the peptide. The exact transition temperature is shown to be influenced by the magnitude of the force exerted by the AFM probe on the bilayer, but is higher than the main transition temperature of non-supported DPPC vesicles in all cases due to bilayer-substrate interactions. Cooling of the fluid L(α) bilayer shows the formation of the line-type defects at the borders between different gel-phase regions that originate from different nuclei. The number of these defects depends directly on the rate of cooling through the transition, as predicted by classical nucleation theory. The presence of the transmembrane, synthetic model peptide WALP23 is known to give rise to heterogeneity in the bilayer as microdomains with a striped appearance are formed in the DPPC bilayer. This striated phase consists of alternating lines of lipids and peptide. It is shown here that melting starts with the peptide-associated lipids in the domains, whose melting temperature is lowered by 0.8-2.0°C compared to the remaining, peptide-free parts of the bilayer. The stabilization of the fluid phase is ascribed to adaptations of the lipids to the shorter peptide. The lipids not associated with the peptide melt at the same temperature as those in the pure DPPC supported bilayer.

  13. Vaccination against hepatitis B in liver transplant recipients: pilot analysis of cellular immune response shows evidence of HBsAg-specific regulatory T cells.

    PubMed

    Bauer, Tanja; Günther, Matthias; Bienzle, Ulrich; Neuhaus, Ruth; Jilg, Wolfgang

    2007-03-01

    After liver transplantation for hepatitis-B-related diseases, patients currently receive lifelong treatment with hepatitis B immunoglobulin to prevent endogenous reinfection with hepatitis B virus (HBV). Active immunization with hepatitis B vaccine would be a preferable alternative; however, most attempts to immunize these patients with standard vaccine have failed. A recent study with a new adjuvanted hepatitis B vaccine was exceptionally successful, leading to a high-titered long-lasting antibody response in 80% of all vaccinees. To identify the immunological mechanisms behind these unexpected results, the successfully vaccinated participants were tested for hepatitis B surface antigen (HBsAg)-specific T and B cells, and their cellular responses to revaccination with conventional vaccine were studied. HBsAg-specific CD4(+) T lymphocytes could be detected in 13 of 16 patients after immunization with the new vaccine. Unexpectedly, these T cells produced almost exclusively interleukin (IL)-10 and had a CD4(+)/CD25(+) phenotype. They were functionally active, suppressing cytokine secretion in HBsAg-specific (Th1) cells, thus representing antigen-specific regulatory T cells (T(Reg)). Following a booster dose with conventional vaccine 22-31 months after completion of the initial vaccination series, the T-cell pattern in the revaccinated individuals changed substantially: 7 days after revaccination 9 of 11 individuals showed a switch to a Th1-type immune response with HBsAg-specific T cells secreting IL-2, interferon gamma and tumor necrosis factor alpha as observed in healthy controls. Four weeks after the booster, 4 patients still showed a Th1-type cytokine pattern, whereas in 5 patients only IL-10-secreting cells were detectable. After 1 year, in 3 of 4 revaccinated individuals only IL-10-secreting cells could be found, whereas the specific T cells of the fourth patient still showed a Th1-type of response. HBsAg-specific T(Reg) cells could be demonstrated in HBV

  14. Structure analysis of the membrane-bound PhoD signal peptide of the Tat translocase shows an N-terminal amphiphilic helix.

    PubMed

    Klein, Marco J; Grage, Stephan L; Muhle-Goll, Claudia; Bürck, Jochen; Afonin, Sergii; Ulrich, Anne S

    2012-12-01

    Tat signal peptides provide the key signature for proteins that get exported by the bacterial twin arginine translocase. We have characterized the structure of the PhoD signal peptide from Bacillus subtilis in suitable membrane-mimicking environments. High-resolution ¹³C/¹⁵N NMR analysis in detergent micelles revealed a helical stretch in the signal peptide between positions 5 and 15, in good agreement with secondary structure prediction and circular dichroism results. This helix was found to be aligned parallel to the membrane surface according to oriented circular dichroism experiments carried out with planar lipid bilayers. The N-terminal α-helix exhibits a pronounced amphiphilic character, in contrast to the general view in the literature. So far, signal sequences had been supposed to consist of a positively charged N-terminal domain, followed by an α-helical hydrophobic segment, plus a C-terminal domain carrying the peptidase cleavage site. Based on our new structural insights, we propose a model for the folding and membrane interactions of the Tat signal sequence from PhoD.

  15. Global meta-analysis shows that relationships of leaf mass per area with species shade tolerance depend on leaf habit and ontogeny.

    PubMed

    Lusk, Christopher H; Warton, David I

    2007-01-01

    It was predicted that relationships of leaf mass per area (LMA) with juvenile shade tolerance will depend on leaf habit, and on whether species are compared at a common age as young seedlings, or at a common size as saplings. A meta-analysis of 47 comparative studies (372 species) was used to test predictions, and the effect of light environment on this relationship. The LMA of evergreens was positively correlated with shade tolerance, irrespective of ontogeny or light environment. The LMA of young seedlings (

  16. Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms.

    PubMed

    Galli, Andrea; Lai, Alessia; Corvasce, Stefano; Saladini, Francesco; Riva, Chiara; Dehò, Lorenzo; Caramma, Ilaria; Franzetti, Marco; Romano, Laura; Galli, Massimo; Zazzi, Maurizio; Balotta, Claudia

    2008-12-01

    Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.

  17. Phylogenetic analysis of 626 hepatitis E virus (HEV) isolates from humans and animals in China (1986-2011) showing genotype diversity and zoonotic transmission.

    PubMed

    Liu, Peng; Li, Lingjun; Wang, Ling; Bu, Qiuning; Fu, Hongwei; Han, Jian; Zhu, Yonghong; Lu, Fengmin; Zhuang, Hui

    2012-03-01

    Hepatitis E is considered as a public health problem in China. To determine the overall molecular epidemiology of hepatitis E virus (HEV) and analyze the situation of cross-species transmission between humans and swine in China over the last 25 years (1986-2011), 626 HEV complete and partial sequences (89 isolates identified by our group) isolated from humans and animals in China were retrieved from GenBank and subjected to phylogenetic analysis. There were three genotypes and 11 sub-genotypes of HEV prevailing in China. Furthermore, rabbit HEVs, of which the genotype is controversial, are also widespread in China. Genotype 1 was the most isolated genotype prior to 2000 and mainly detected in Xinjiang, Beijing and East China. However, genotype 4, which was identified in most regions of China during the last 10 years, has overtaken genotype 1 in frequency of isolation nationwide. Genotype 3 HEV strains have been found only in eastern China and were thought to be imported from Japan. Both genotypes 3 and 4 were found in humans and swine and cross-species transmission from pigs to humans of the two genotypes may have occurred in Northeast, Northwest, North, East and South China. These results indicate that HEV strains with considerable genetic diversity are widespread and the zoonotic transmission between swine and humans appears ubiquitous in China.

  18. Analysis of gene-disruption mutants of a sucrose phosphate synthase gene in rice, OsSPS1, shows the importance of sucrose synthesis in pollen germination.

    PubMed

    Hirose, Tatsuro; Hashida, Yoichi; Aoki, Naohiro; Okamura, Masaki; Yonekura, Madoka; Ohto, Chikara; Terao, Tomio; Ohsugi, Ryu

    2014-08-01

    The molecular function of an isoform of sucrose phosphate synthase (SPS) in rice, OsSPS1, was investigated using gene-disruption mutant lines generated by retrotransposon insertion. The progeny of the heterozygote of disrupted OsSPS1 (SPS1(+/-)) segregated into SPS1(+/+), SPS1(+/-), and SPS1(-/-) at a ratio of 1:1:0. This distorted segregation ratio, together with the expression of OsSPS1 in the developing pollen revealed by quantitative RT-PCR analysis and promoter-beta-glucuronidase (GUS) fusion assay, suggested that the disruption of OsSPS1 results in sterile pollen. This hypothesis was reinforced by reciprocal crosses of SPS1(+/-) plants with wild-type plants in which the disrupted OsSPS1 was not paternally transmitted to the progeny. While the pollen grains of SPS(+/-) plants normally accumulated starch during their development, pollen germination on the artificial media was reduced to half of that observed in the wild-type control. Overall, our data suggests that sucrose synthesis via OsSPS1 is essential in pollen germination in rice.

  19. Program impact pathway analysis of a social franchise model shows potential to improve infant and young child feeding practices in Vietnam.

    PubMed

    Nguyen, Phuong H; Menon, Purnima; Keithly, Sarah C; Kim, Sunny S; Hajeebhoy, Nemat; Tran, Lan M; Ruel, Marie T; Rawat, Rahul

    2014-10-01

    By mapping the mechanisms through which interventions are expected to achieve impact, program impact pathway (PIP) analysis lays out the theoretical causal links between program activities, outcomes, and impacts. This study examines the pathways through which the Alive & Thrive (A&T) social franchise model is intended to improve infant and young child feeding (IYCF) practices in Vietnam. Mixed methods were used, including qualitative interviews with franchise management board members (n = 12), surveys with health providers (n = 120), counseling observations (n = 160), and household surveys (n = 2045). Six PIP components were assessed: 1) franchise management, 2) training and IYCF knowledge of health providers, 3) service delivery, 4) program exposure and utilization, 5) maternal behavioral determinants (knowledge, beliefs, and intentions) toward optimal IYCF practices, and 6) IYCF practices. Data were collected from A&T-intensive areas (A&T-I; mass media + social franchise) and A&T-nonintensive areas (A&T-NI; mass media only) by using a cluster-randomized controlled trial design. Data from 2013 were compared with baseline where similar measures were available. Results indicate that mechanisms are in place for effective management of the franchise system, despite challenges to routine monitoring. A&T training was associated with increased capacity of providers, resulting in higher-quality IYCF counseling (greater technical knowledge and communication skills during counseling) in A&T-I areas. Franchise utilization increased from 10% in 2012 to 45% in 2013 but fell below the expected frequency of 9-15 contacts per mother-child dyad. Improvements in breastfeeding knowledge, beliefs, intentions, and practices were greater among mothers in A&T-I areas than among those in A&T-NI areas. In conclusion, there are many positive changes along the impact pathway of the franchise services, but challenges in utilization and demand creation should be addressed to achieve the full

  20. Comprehensive Behavioral Analysis of Male Ox1r (-/-) Mice Showed Implication of Orexin Receptor-1 in Mood, Anxiety, and Social Behavior.

    PubMed

    Abbas, Md G; Shoji, Hirotaka; Soya, Shingo; Hondo, Mari; Miyakawa, Tsuyoshi; Sakurai, Takeshi

    2015-01-01

    Neuropeptides orexin A and orexin B, which are exclusively produced by neurons in the lateral hypothalamic area, play an important role in the regulation of a wide range of behaviors and homeostatic processes, including regulation of sleep/wakefulness states and energy homeostasis. The orexin system has close anatomical and functional relationships with systems that regulate the autonomic nervous system, emotion, mood, the reward system, and sleep/wakefulness states. Recent pharmacological studies using selective antagonists have suggested that orexin receptor-1 (OX1R) is involved in physiological processes that regulate emotion, the reward system, and autonomic nervous system. Here, we examined Ox1r (-/-) mice with a comprehensive behavioral test battery to screen additional OX1R functions. Ox1r (-/-) mice showed increased anxiety-like behavior, altered depression-like behavior, slightly decreased spontaneous locomotor activity, reduced social interaction, increased startle response, and decreased prepulse inhibition. These results suggest that OX1R plays roles in social behavior and sensory motor gating in addition to roles in mood and anxiety.

  1. Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation

    PubMed Central

    Corley, Susan M.; Wilkins, Marc R.; Shannon Weickert, Cynthia

    2016-01-01

    Many genes are differentially expressed in the cortex of people with schizophrenia, implicating factors that control transcription more generally. Hormone nuclear receptors dimerize to coordinate context-dependent changes in gene expression. We hypothesized that members of two families of nuclear receptors (NR4As), and retinoid receptors (RARs and RXRs), are altered in the dorsal lateral prefrontal cortex (DLPFC) of people with schizophrenia. We used next generation sequencing and then qPCR analysis to test for changes in mRNA levels for transcripts encoding nuclear receptors: orphan nuclear receptors (3 in the NR4A, 3 in the RAR, 3 in the RXR families and KLF4) in total RNA extracted from the DLPFC from people with schizophrenia compared to controls (n = 74). We also correlated mRNA levels with demographic factors and with estimates of antipsychotic drug exposure (schizophrenia group only). We tested for correlations between levels of transcription factor family members and levels of genes putatively regulated by these transcription factors. We found significantly down regulated expression of NR4A1 (Nurr 77) and KLF4 mRNAs in people with schizophrenia compared to controls, by both NGS and qPCR (p = or <0.01). We also detected decreases in NR4A2 (Nurr1) and RXRB mRNAs by using qPCR in the larger cohort (p<0.05 and p<0.01, respectively). We detected decreased expression of RARG and NR4A2 mRNAs in females with schizophrenia (p<0.05). The mRNA levels of NR4A1, NR4A2 and NR4A3 were all negative correlated with lifetime estimates of antipsychotic exposure. These novel findings, which may be influenced by antipsychotic drug exposure, implicate the orphan and retinoid nuclear receptors in the cortical pathology found in schizophrenia. Genes down stream of these receptors can be dysregulated as well, but the direction of change is not immediately predictable based on the putative transcription factor changes. PMID:27992436

  2. AFM stiffness nanotomography of normal, metaplastic and dysplastic human esophageal cells

    NASA Astrophysics Data System (ADS)

    Fuhrmann, A.; Staunton, J. R.; Nandakumar, V.; Banyai, N.; Davies, P. C. W.; Ros, R.

    2011-02-01

    The mechanical stiffness of individual cells is important in tissue homeostasis, cell growth, division and motility, and the epithelial-mesenchymal transition in the initiation of cancer. In this work, a normal squamous cell line (EPC2) and metaplastic (CP-A) as well as dysplastic (CP-D) Barrett's Esophagus columnar cell lines are studied as a model of pre-neoplastic progression in the human esophagus. We used the combination of an atomic force microscope (AFM) with a scanning confocal fluorescence lifetime imaging microscope to study the mechanical properties of single adherent cells. Sixty four force indentation curves were taken over the nucleus of each cell in an 8 × 8 grid pattern. Analyzing the force indentation curves, indentation depth-dependent Young's moduli were found for all cell lines. Stiffness tomograms demonstrate distinct differences between the mechanical properties of the studied cell lines. Comparing the stiffness for indentation forces of 1 nN, most probable Young's moduli were calculated to 4.7 kPa for EPC2 (n = 18 cells), 3.1 kPa for CP-A (n = 10) and 2.6 kPa for CP-D (n = 19). We also tested the influence of nuclei and nucleoli staining organic dyes on the mechanical properties of the cells. For stained EPC2 cells (n = 5), significant stiffening was found (9.9 kPa), while CP-A cells (n = 5) showed no clear trend (2.9 kPa) and a slight softening was observed (2.1 kPa) in the case of CP-D cells (n = 16). Some force-indentation curves show non-monotonic discontinuities with segments of negative slope, resembling a sawtooth pattern. We found the incidence of these 'breakthrough events' to be highest in the dysplastic CP-D cells, intermediate in the metaplastic CP-A cells and lowest in the normal EPC2 cells. This observation suggests that the microscopic explanation for the increased compliance of cancerous and pre-cancerous cells may lie in their susceptibility to 'crumble and yield' rather than their ability to 'bend and flex'.

  3. Probing ternary solvent effect in high Voc polymer solar cells using advanced AFM techniques

    SciTech Connect

    Li, Chao; Soleman, Mikhael; Lorenzo, Josie; Dhasmana, Nitesh; Chantharasupawong, Panit; Ievlev, Anton; Gesquiere, Andre; Tetard, Laurene; Thomas, Jayan

    2016-01-25

    This work describes a simple method to develop a high Voc low band gap PSCs. In addition, two new atomic force microscopy (AFM)-based nanoscale characterization techniques to study the surface morphology and physical properties of the structured active layer are introduced. With the help of ternary solvent processing of the active layer and C60 buffer layer, a bulk heterojunction PSC with Voc more than 0.9 V and conversion efficiency 7.5% is developed. In order to understand the fundamental properties of the materials ruling the performance of the PSCs tested, AFM-based nanoscale characterization techniques including Pulsed-Force-Mode AFM (PFM-AFM) and Mode-Synthesizing AFM (MSAFM) are introduced. Interestingly, MSAFM exhibits high sensitivity for direct visualization of the donor–acceptor phases in the active layer of the PSCs. Lastly, conductive-AFM (cAFM) studies reveal local variations in conductivity in the donor and acceptor phases as well as a significant increase in photocurrent in the PTB7:ICBA sample obtained with the ternary solvent processing.

  4. Study of relaxation and transport processes by means of AFM based dielectric spectroscopy

    SciTech Connect

    Miccio, Luis A.

    2014-05-15

    Since its birth a few years ago, dielectric spectroscopy studies based on atomic force microscopy (AFM) have gained a growing interest. Not only the frequency and temperature ranges have become broader since then but also the kind of processes that can be studied by means of this approach. In this work we analyze the most adequate experimental setup for the study of several dielectric processes with a spatial resolution of a few nanometers by using force mode AFM based dielectric spectroscopy. Proof of concept experiments were performed on PS/PVAc blends and PMMA homopolymer films, for temperatures ranging from 300 to 400 K. Charge transport processes were also studied by this approach. The obtained results were analyzed in terms of cantilever stray contribution, film thickness and relaxation strength. We found that the method sensitivity is strongly coupled with the film thickness and the relaxation strength, and that it is possible to control it by using an adequate experimental setup.

  5. Confocal Raman spectroscopy and AFM for evaluation of sidewalls in type II superlattice FPAs

    NASA Astrophysics Data System (ADS)

    Rotter, T. J.; Busani, T.; Rathi, P.; Jaeckel, F.; Reyes, P. A.; Malloy, K. J.; Ukhanov, A. A.; Plis, E.; Krishna, S.; Jaime-Vasquez, M.; Baril, N. F.; Benson, J. D.; Tenne, D. A.

    2015-06-01

    We propose to utilize confocal Raman spectroscopy combined with high resolution atomic force microscopy (AFM) for nondestructive characterisation of the sidewalls of etched and passivated small pixel (24 μm×24 μm) focal plane arrays (FPA) fabricated using LW/LWIR InAs/GaSb type-II strained layer superlattice (T2SL) detector material. Special high aspect ratio Si and GaAs AFM probes, with tip length of 13 μm and tip aperture less than 7°, allow characterisation of the sidewall morphology. Confocal microscopy enables imaging of the sidewall profile through optical sectioning. Raman spectra measured on etched T2SL FPA single pixels enable us to quantify the non-uniformity of the mesa delineation process.

  6. AFM investigation and optical band gap study of chemically deposited PbS thin films

    NASA Astrophysics Data System (ADS)

    Zaman, S.; Mansoor, M.; Abubakar; Asim, M. M.

    2016-08-01

    The interest into deposition of nanocrystalline PbS thin films, the potential of designing and tailoring both the topographical features and the band gap energy (Eg) by controlling growth parameters, has significant technological importance. Nanocrystalline thin films of lead sulfide were grown onto glass substrates by chemical bath deposition (CBD) method. The experiments were carried out by varying deposition temperature. We report on the modification of structural and optical properties as a function of deposition temperature. The morphological changes of the films were analyzed by using SEM and AFM. AFM was also used to calculate average roughness of the films. XRD spectra indicated preferred growth of cubic phase of PbS films in (200) direction with increasing deposition time. Optical properties have been studied by UV-Spectrophotometer. From the diffused reflectance spectra we have calculated the optical Eg shift from 0.649-0.636 eV with increasing deposition time.

  7. Nano-Electrochemistry and Nano-Electrografting with an Original Combined AFM-SECM

    PubMed Central

    Ghorbal, Achraf; Grisotto, Federico; Charlier, Julienne; Palacin, Serge; Goyer, Cédric; Demaille, Christophe; Ben Brahim, Ammar

    2013-01-01

    This study demonstrates the advantages of the combination between atomic force microscopy and scanning electrochemical microscopy. The combined technique can perform nano-electrochemical measurements onto agarose surface and nano-electrografting of non-conducting polymers onto conducting surfaces. This work was achieved by manufacturing an original Atomic Force Microscopy-Scanning ElectroChemical Microscopy (AFM-SECM) electrode. The capabilities of the AFM-SECM-electrode were tested with the nano-electrografting of vinylic monomers initiated by aryl diazonium salts. Nano-electrochemical and technical processes were thoroughly described, so as to allow experiments reproducing. A plausible explanation of chemical and electrochemical mechanisms, leading to the nano-grafting process, was reported. This combined technique represents the first step towards improved nano-processes for the nano-electrografting.

  8. Exploring electron transport through organic monolayers using conductive tip AFM techniques

    NASA Astrophysics Data System (ADS)

    Scaini, Denis; Castronovo, Matteo; Dell'Angela, Martina; Hudej, Robert; Casalis, Loredana; Scoles, Giacinto

    2006-03-01

    We follow an alternative approach to the study of Metal-molecule-Metal junctions that uses a combination of two atomic force microscopy (AFM) techniques. We use Nanografting to build a nanopatch of the molecules of interest and a second made of a reference molecule into a hosting self assembled monolayer (SAM) typically made of alkanethiols. After the tip is changed to a conductive one CT-AFM is used to characterized the whole system recording, at the same time, the system topography. Some of the advantages of this approach are the possibility to build and study a wide range of different M-m-M junctions and the in-situ control of the quality of the monolayers and patches. Results will be presented on saturated and unsaturated thiols self-assembled and nanografted on Au(111) surfaces. The results will be compared with those obtained by Liang and Scoles at Princeton using similar techniques.

  9. BOREAS AFM-5 Level-2 Upper Air Network Standard Pressure Level Data

    NASA Technical Reports Server (NTRS)

    Barr, Alan; Hrynkiw, Charmaine; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS AFM-5 team collected and processed data from the numerous radiosonde flights during the project. The goals of the AFM-05 team were to provide large-scale definition of the atmosphere by supplementing the existing AES aerological network, both temporally and spatially. This data set includes basic upper-air parameters interpolated at 0.5 kiloPascal increments of atmospheric pressure from data collected from the network of upper-air stations during the 1993, 1994, and 1996 field campaigns over the entire study region. The data are contained in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  10. Characterization of the polycaprolactone melt crystallization: complementary optical microscopy, DSC, and AFM studies.

    PubMed

    Speranza, V; Sorrentino, A; De Santis, F; Pantani, R

    2014-01-01

    The first stages of the crystallization of polycaprolactone (PCL) were studied using several techniques. The crystallization exotherms measured by differential scanning calorimetry (DSC) were analyzed and compared with results obtained by polarized optical microscopy (POM), rheology, and atomic force microscope (AFM). The experimental results suggest a strong influence of the observation scale. In particular, the AFM, even if limited on time scale, appears to be the most sensitive technique to detect the first stages of crystallization. On the contrary, at least in the case analysed in this work, rheology appears to be the least sensitive technique. DSC and POM provide closer results. This suggests that the definition of induction time in the polymer crystallization is a vague concept that, in any case, requires the definition of the technique used for its characterization.

  11. Dynamics of a disturbed sessile drop measured by atomic force microscopy (AFM).

    PubMed

    McGuiggan, Patricia M; Grave, Daniel A; Wallace, Jay S; Cheng, Shengfeng; Prosperetti, Andrea; Robbins, Mark O

    2011-10-04

    A new method for studying the dynamics of a sessile drop by atomic force microscopy (AFM) is demonstrated. A hydrophobic microsphere (radius, r ∼ 20-30 μm) is brought into contact with a small sessile water drop resting on a polytetrafluoroethylene (PTFE) surface. When the microsphere touches the liquid surface, the meniscus rises onto it because of capillary forces. Although the microsphere volume is 6 orders of magnitude smaller than the drop, it excites the normal resonance modes of the liquid interface. The sphere is pinned at the interface, whose small (<100 nm) oscillations are readily measured with AFM. Resonance oscillation frequencies were measured for drop volumes between 5 and 200 μL. The results for the two lowest normal modes are quantitatively consistent with continuum calculations for the natural frequency of hemispherical drops with no adjustable parameters. The method may enable sensitive measurements of volume, surface tension, and viscosity of small drops.

  12. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  13. Accurate and precise calibration of AFM cantilever spring constants using laser Doppler vibrometry.

    PubMed

    Gates, Richard S; Pratt, Jon R

    2012-09-21

    Accurate cantilever spring constants are important in atomic force microscopy both in control of sensitive imaging and to provide correct nanomechanical property measurements. Conventional atomic force microscope (AFM) spring constant calibration techniques are usually performed in an AFM. They rely on significant handling and often require touching the cantilever probe tip to a surface to calibrate the optical lever sensitivity of the configuration. This can damage the tip. The thermal calibration technique developed for laser Doppler vibrometry (LDV) can be used to calibrate cantilevers without handling or touching the tip to a surface. Both flexural and torsional spring constants can be measured. Using both Euler-Bernoulli modeling and an SI traceable electrostatic force balance technique as a comparison we demonstrate that the LDV thermal technique is capable of providing rapid calibrations with a combination of ease, accuracy and precision beyond anything previously available.

  14. AFM fishing nanotechnology is the way to reverse the Avogadro number in proteomics.

    PubMed

    Archakov, Alexander Ivanovich; Ivanov, Yurii Dmitrievich; Lisitsa, Andrey Valerevich; Zgoda, Victor Gavrilovich

    2007-01-01

    Future development of proteomics may be hindered by limitations in the concentration sensitivity of widespread technological approaches. The concentration sensitivity limit (CSL) of currently used approaches, like 2-DE/LC separation coupled with MS detection, etc., varies from 10(-9) to 10(-12) M. Therefore, proteomic technologies enable detection of up to 20% of the protein species present in the plasma. New technologies, like atomic force microscopy (AFM molecular detector), enable the counting of single molecules, whereas biospecific fishing can be used to capture these molecules from the biomaterial. At the same time, fishing also has thermodynamic limitations due to the reversibility of the binding. In cases where the fishing becomes irreversible, its combination with an AFM detector enables the registration of single protein molecules, and that opens up a way to lower the CSL down to the reverse Avogadro number.

  15. Influence of Fluid Cell Design on the Frequency Response of AFM Microcantilevers in Liquid Media

    PubMed Central

    Motamedi, Ramin; Wood-Adams, Paula M.

    2008-01-01

    A study of the frequency response of AFM microcantilevers in liquid media contained in a commercial fluid cell is presented. Such systems exhibit complicated dynamics which are often not well described by available theories. Their dynamic behavior has a direct effect on the use of the AFM in dynamic mode while imaging in liquid or while extracting the rheological properties of the fluid. We explore the issues related to the design of the cantilever holder/fluid cell and propose an approach for evaluating, minimizing and recognizing the ultimate limitations of commercial cantilever holders. A technique for estimating the frequency response spectrum of the fluid cell itself from experimental data is presented. This spectrum can then be used to evaluate whether or not the fluid cell is suited for the desired purpose. PMID:27873849

  16. Mechanism of high-resolution STM, AFM and IETS-STM imaging with functionalized tips

    NASA Astrophysics Data System (ADS)

    Temirov, R.; Hapala, P.; Tautz, F. S.; Jelinek, P.

    2015-03-01

    High-resolution AFM and STM with functionalized tips is well established, but a detailed understanding of the image mechanism is still missing. Moreover, recently this family of imaging techniques has been complemented by a method based on inelastic electron tunneling spectroscopy. Here we present a comprehensive mechanical and transport simulation model that explains essentially all image features in functionalized tip STM, AFM and IETS-STM. Important aspects of the mechanism are: (i) Images are dominantly determined by Pauli repulsion, (ii) in STM and IETS STM this force signal is transduced into an elastic or inelastic conductance signal, (iii) probe particle relaxation leads to image sharpening, (iv) the apparent imaging of hydrogen bonds can be explained by a relaxation effect, and (v) electrostatic forces may also influence the image contrast.

  17. Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa.

    PubMed

    Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

    2015-01-01

    Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas

  18. Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa

    PubMed Central

    Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

    2015-01-01

    Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas

  19. U.S. Army Training and Testing Area Carrying Capacity (ATTACC) for Munitions (AFM)

    DTIC Science & Technology

    2006-11-01

    days. The RUSLE dataset delivered with the AFM model is defined below and in Appendix E. The Adapted RUSLE is defined as A=R*K* LS *C*P where: A...hr [hundreds of ft-tons]-1 in.-1) LS = slope length and steepness factor (dimensionless) C = cover and management factor (dimensionless) P...erosion index unit under standardized conditions. Higher K factor values indicate more easily erodible soils. • LS Factor. The rate of soil

  20. Single-cycle-PLL detection for real-time FM-AFM applications.

    PubMed

    Schlecker, Benedikt; Dukic, Maja; Erickson, Blake; Ortmanns, Maurits; Fantner, Georg; Anders, Jens

    2014-04-01

    In this paper we present a novel architecture for phase-locked loop (PLL) based high-speed demodulation of frequency-modulated (FM) atomic force microscopy (AFM) signals. In our approach, we use single-sideband (SSB) frequency upconversion to translate the AFM signal from the position sensitive detector to a fixed intermediate frequency (IF) of 10 MHz. In this way, we fully benefit from the excellent noise performance of PLL-based FM demodulators still avoiding the intrinsic bandwidth limitation of such systems. In addition, the upconversion to a fixed IF renders the PLL demodulator independent of the cantilever's resonance frequency, allowing the system to work with a large range of cantilever frequencies. To investigate if the additional noise introduced by the SSB upconverter degrades the system noise figure we present a model of the AM-to-FM noise conversion in PLLs incorporating a phase-frequency detector. Using this model, we can predict an upper corner frequency for the demodulation bandwidth above which the converted noise from the single-sideband upconverter becomes the dominant noise source and therefore begins to deteriorate the overall system performance. The approach is validated by both electrical and AFM measurements obtained with a PCB-based prototype implementing the proposed demodulator architecture.

  1. Topographical and electrical study of contact and intermittent contact mode InP AFM lithography

    NASA Astrophysics Data System (ADS)

    Tranvouez, E.; Budau, P.; Bremond, G.

    2006-01-01

    In order to fabricate nanoscale oxide patterns on an InP(001) surface, local anodization by atomic force microscopy (AFM) contact and intermittent contact modes has been performed. Contact mode results are similar to those obtained with the local anodization of silicon, and mainly limited by the effect of space charge that occurs during the oxide growth. The existence of this space charge associated with the poor dielectric quality of the obtained oxide has been verified by performing scanning capacitance microscopy (SCM) measurements. Results for oxidation using intermittent AFM contact mode associated with a modulated voltage are more specific. For a more than two decade variation of probe velocity (0.01-5 µm s-1), the AFM oxidation introduces no significant changes in the oxide pattern. Experiments on the influence of oxidation time give rise to two regimes. First, for times shorter than 100 ms, a high growth rate is found. Second, for oxidation times longer than 100 ms, we observe an oxide height saturation and a significant decrease of lateral growth rate. These results provide a way to easily control the oxide shape. The space charge neutralization in this mode has also been investigated by SCM. The interesting results for intermittent contact oxidation confirm the capability of this technique to modify a nanoscale InP surface.

  2. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies

    NASA Astrophysics Data System (ADS)

    Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.

    2015-10-01

    APOBEC3G (A3G) protein has antiviral activity against HIV and other pathogenic retroviruses. A3G has two domains: a catalytic C-terminal domain (CTD) that deaminates cytidine, and a N-terminal domain (NTD) that binds to ssDNA. Although abundant information exists about the biological activities of A3G protein, the interplay between sequence specific deaminase activity and A3G binding to ssDNA remains controversial. We used the topographic imaging and force spectroscopy modalities of Atomic Force Spectroscopy (AFM) to characterize the interaction of A3G protein with deaminase specific and nonspecific ssDNA substrates. AFM imaging demonstrated that A3G has elevated affinity for deaminase specific ssDNA than for nonspecific ssDNA. AFM force spectroscopy revealed two distinct binding modes by which A3G interacts with ssDNA. One mode requires sequence specificity, as demonstrated by stronger and more stable complexes with deaminase specific ssDNA than with nonspecific ssDNA. Overall these observations enforce prior studies suggesting that both domains of A3G contribute to the sequence specific binding of ssDNA.

  3. A novel dog-bone oscillating AFM probe with thermal actuation and piezoresistive detection.

    PubMed

    Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

    2014-10-31

    In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments.

  4. A Novel Dog-Bone Oscillating AFM Probe with Thermal Actuation and Piezoresistive Detection †

    PubMed Central

    Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

    2014-01-01

    In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments. PMID:25365463

  5. Graphene Nanopore Support System for Simultaneous High-Resolution AFM Imaging and Conductance Measurements

    PubMed Central

    2015-01-01

    Accurately defining the nanoporous structure and sensing the ionic flow across nanoscale pores in thin films and membranes has a wide range of applications, including characterization of biological ion channels and receptors, DNA sequencing, molecule separation by nanoparticle films, sensing by block co-polymers films, and catalysis through metal–organic frameworks. Ionic conductance through nanopores is often regulated by their 3D structures, a relationship that can be accurately determined only by their simultaneous measurements. However, defining their structure–function relationships directly by any existing techniques is still not possible. Atomic force microscopy (AFM) can image the structures of these pores at high resolution in an aqueous environment, and electrophysiological techniques can measure ion flow through individual nanoscale pores. Combining these techniques is limited by the lack of nanoscale interfaces. We have designed a graphene-based single-nanopore support (∼5 nm thick with ∼20 nm pore diameter) and have integrated AFM imaging and ionic conductance recording using our newly designed double-chamber recording system to study an overlaid thin film. The functionality of this integrated system is demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore and simultaneous AFM imaging of the bilayer. PMID:24581087

  6. Non--Cubic Symmetry of the Electronic Response in AFM Late Transition--Metal Oxides.

    NASA Astrophysics Data System (ADS)

    Posternak, M.; Baldereschi, A.; Massidda, S.; Resta, R.

    1998-03-01

    The late transition--metal monoxides (MnO, FeO, CoO, NiO) have the rocksalt structure in their paramagnetic phase, while below the Neel temperature a weak structural distortion accompanies an AFM ordering of type II. Therefore, it is generally assumed that most nonmagnetic (i.e. spin--integrated) crystalline properties are essentially cubic: we give here convincing evidence of the contrary. We focus on the half--filled d shell oxide MnO as the most suitable case study, on which we perform accurate ab--initio, all--electron calculations, within different one--particle schemes. In order to study the symmetry lowering due to AFM ordering, we assume an ideal cubic geometry throughout. The calculated TO frequencies and Born effective charge tensor do not have cubic symmetry. The standard LSD severely exaggerates the deviations from cubic symmetry, confirming its unreliability for calculating properties of insulating AFM oxides, while a model self--energy correction scheme(S. Massidda et al.), Phys. Rev. B 55, 13494 (1997). reduces considerably the anisotropy. We also explain the origin and the magnitude of this effect in terms of the mixed charge--transfer/Mott--Hubbard character of MnO.

  7. Modelling of the X,Y,Z positioning errors and uncertainty evaluation for the LNE’s mAFM using the Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Ceria, Paul; Ducourtieux, Sebastien; Boukellal, Younes; Allard, Alexandre; Fischer, Nicolas; Feltin, Nicolas

    2017-03-01

    In order to evaluate the uncertainty budget of the LNE’s mAFM, a reference instrument dedicated to the calibration of nanoscale dimensional standards, a numerical model has been developed to evaluate the measurement uncertainty of the metrology loop involved in the XYZ positioning of the tip relative to the sample. The objective of this model is to overcome difficulties experienced when trying to evaluate some uncertainty components which cannot be experimentally determined and more specifically, the one linked to the geometry of the metrology loop. The model is based on object-oriented programming and developed under Matlab. It integrates one hundred parameters that allow the control of the geometry of the metrology loop without using analytical formulae. The created objects, mainly the reference and the mobile prism and their mirrors, the interferometers and their laser beams, can be moved and deformed freely to take into account several error sources. The Monte Carlo method is then used to determine the positioning uncertainty of the instrument by randomly drawing the parameters according to their associated tolerances and their probability density functions (PDFs). The whole process follows Supplement 2 to ‘The Guide to the Expression of the Uncertainty in Measurement’ (GUM). Some advanced statistical tools like Morris design and Sobol indices are also used to provide a sensitivity analysis by identifying the most influential parameters and quantifying their contribution to the XYZ positioning uncertainty. The approach validated in the paper shows that the actual positioning uncertainty is about 6 nm. As the final objective is to reach 1 nm, we engage in a discussion to estimate the most effective way to reduce the uncertainty.

  8. Showing "F = BIL" Using Video Analysis

    ERIC Educational Resources Information Center

    Smith, Leon; Parker, David; Brown, Carl; Ireson, Gren

    2011-01-01

    The force on a current-carrying conductor in a magnetic field is a common aspect of post-16 physics courses. Many textbooks approach this topic via a current balance, e.g. Hutchins (1990) through to Duncan (2000), with websites such as "Practical Physics" giving a qualitative version. This article takes the approach of equating "F = BIL"sin[theta]…

  9. High aspect ratio AFM Probe processing by helium-ion-beam induced deposition.

    PubMed

    Onishi, Keiko; Guo, Hongxuan; Nagano, Syoko; Fujita, Daisuke

    2014-11-01

    A Scanning Helium Ion Microscope (SHIM) is a high resolution surface observation instrument similar to a Scanning Electron Microscope (SEM) since both instruments employ finely focused particle beams of ions or electrons [1]. The apparent difference is that SHIMs can be used not only for a sub-nanometer scale resolution microscopic research, but also for the applications of very fine fabrication and direct lithography of surfaces at the nanoscale dimensions. On the other hand, atomic force microscope (AFM) is another type of high resolution microscopy which can measure a three-dimensional surface morphology by tracing a fine probe with a sharp tip apex on a specimen's surface.In order to measure highly uneven and concavo-convex surfaces by AFM, the probe of a high aspect ratio with a sharp tip is much more necessary than the probe of a general quadrangular pyramid shape. In this paper we report the manufacture of the probe tip of the high aspect ratio by ion-beam induced gas deposition using a nanoscale helium ion beam of SHIM.Gas of platinum organic compound was injected into the sample surface neighborhood in the vacuum chamber of SHIM. The decomposition of the gas and the precipitation of the involved metal brought up a platinum nano-object in a pillar shape on the normal commercial AFM probe tip. A SHIM system (Carl Zeiss, Orion Plus) equipped with the gas injection system (OmniProbe, OmniGIS) was used for the research. While the vacuum being kept to work, we injected platinum organic compound ((CH3)3(CH3C5H4)Pt) into the sample neighborhood and irradiated the helium ion beam with the shape of a point on the apex of the AFM probe tip. It is found that we can control the length of the Pt nano-pillar by irradiation time of the helium ion beam. The AFM probe which brought up a Pt nano-pillar is shown in Figure 1. It is revealed that a high-aspect-ratio Pt nano-pillar of ∼40nm diameter and up to ∼2000 nm length can be grown. In addition, for possible heating

  10. AFM/MFM hybrid nanocharacterization of martensitic transformation and degradation for Fe-Pd shape memory alloy

    NASA Astrophysics Data System (ADS)

    Suzuki, Takayuki; Nagatani, Kohei; Hirano, Kazumi; Teramoto, Tokuo; Taya, Minoru

    2003-07-01

    Martensitic transformation and degradation characteristics for Fe-Pd ferromagnetic shape memory alloy were investigated by the developed AFM (Atomic Force Microscope)/MFM (Magnetic Force Microscope) hybrid nano-characterization technique. In AFM martensitic transformation was detected by the changes of surface topography of martensite plates. In MFM martensitic transformation was detected by the changes of magnetic domain structures. This technique has an advantage that martensitic transformation characteristics such as martensitic transformation temperature and reverse transformation temperature can be measured at microscopic and nanoscopic small area. Degradation characteristics of martensitic transformation under cyclic loading were also detected by the changes of AFM and MFM images. In AFM images surface topography of martensite plates became flat and in MFM images the morphology of magnetic domain structures became unfocused under cyclic loading. Then it was found that the hybrid nano-characterization was very high sensitive technique to evaluate degradation for Fe-Pd ferromagnetic shape memory alloy.

  11. Characterization of the specific interaction between the DNA aptamer sgc8c and protein tyrosine kinase-7 receptors at the surface of T-cells by biosensing AFM.

    PubMed

    Leitner, Michael; Poturnayova, Alexandra; Lamprecht, Constanze; Weich, Sabine; Snejdarkova, Maja; Karpisova, Ivana; Hianik, Tibor; Ebner, Andreas

    2017-04-01

    We studied the interaction of the specific DNA aptamer sgc8c immobilized at the AFM tip with its corresponding receptor, the protein tyrosine kinase-7 (PTK7) embedded in the membrane of acute lymphoblastic leukemia (ALL) cells (Jurkat T-cells). Performing single molecule force spectroscopy (SMFS) experiments, we showed that the aptamer sgc8c bound with high probability (38.3 ± 7.48%) and high specificity to PTK7, as demonstrated by receptor blocking experiments and through comparison with the binding behavior of a nonspecific aptamer. The determined kinetic off-rate (koff = 5.16 s(-1)) indicates low dissociation of the sgc8c-PTK7 complex. In addition to the pulling force experiments, simultaneous topography and recognition imaging (TREC) experiments using AFM tips functionalized with sgc8c aptamers were realized on the outer regions surface of surface-immobilized Jurkat cells for the first time. This allowed determination of the distribution of PTK7 without any labeling and at near physiological conditions. As a result, we could show a homogeneous distribution of PTK7 molecules on the outer regions of ALL cells with a surface density of 325 ± 12 PTK7 receptors (or small receptor clusters) per μm(2). Graphical Abstract The specific interaction of the DNA aptamer sgc8c and protein tyrosine kinase-7 (PTK7) on acute lymphoblastic leukemia (ALL) cells was characterized. AFM based single molecule force spectroscopy (SMFS) yielded a kinetic off-rate of 5.16 s(-1) of the complex. Simultaneous topography and recognition imaging (TREC) revealed a PTK7 density of 325 ± 12 molecules or clusters per μm(2) in the cell membrane.

  12. An AFM-based pit-measuring method for indirect measurements of cell-surface membrane vesicles

    SciTech Connect

    Zhang, Xiaojun; Chen, Yuan; Chen, Yong

    2014-03-28

    Highlights: • Air drying induced the transformation of cell-surface membrane vesicles into pits. • An AFM-based pit-measuring method was developed to measure cell-surface vesicles. • Our method detected at least two populations of cell-surface membrane vesicles. - Abstract: Circulating membrane vesicles, which are shed from many cell types, have multiple functions and have been correlated with many diseases. Although circulating membrane vesicles have been extensively characterized, the status of cell-surface membrane vesicles prior to their release is less understood due to the lack of effective measurement methods. Recently, as a powerful, micro- or nano-scale imaging tool, atomic force microscopy (AFM) has been applied in measuring circulating membrane vesicles. However, it seems very difficult for AFM to directly image/identify and measure cell-bound membrane vesicles due to the similarity of surface morphology between membrane vesicles and cell surfaces. Therefore, until now no AFM studies on cell-surface membrane vesicles have been reported. In this study, we found that air drying can induce the transformation of most cell-surface membrane vesicles into pits that are more readily detectable by AFM. Based on this, we developed an AFM-based pit-measuring method and, for the first time, used AFM to indirectly measure cell-surface membrane vesicles on cultured endothelial cells. Using this approach, we observed and quantitatively measured at least two populations of cell-surface membrane vesicles, a nanoscale population (<500 nm in diameter peaking at ∼250 nm) and a microscale population (from 500 nm to ∼2 μm peaking at ∼0.8 μm), whereas confocal microscopy only detected the microscale population. The AFM-based pit-measuring method is potentially useful for studying cell-surface membrane vesicles and for investigating the mechanisms of membrane vesicle formation/release.

  13. Automated hollow-fiber liquid-phase microextraction coupled with liquid chromatography/tandem mass spectrometry for the analysis of aflatoxin M₁ in milk.

    PubMed

    Huang, Siming; Hu, Du; Wang, Ying; Zhu, Fang; Jiang, Ruifen; Ouyang, Gangfeng

    2015-10-16

    An automated hollow fiber liquid-phase microextraction (HF-LPME) coupled with liquid chromatography/tandem mass spectrometry (LC-MS/MS) method was developed for the extraction and determination of aflatoxin M1 (AFM1) in milk samples. Parameters affecting the extraction efficiency, such as the extraction phase, matrix conditions, extraction time and temperature, were investigated. Under the optimal conditions (ratio of water to milk, 4:1; extraction time, 50 min; extraction temperature, 50°C; extraction phase, 50 mg L(-1) anti-AFM1 antibody in PBS buffer solution; volume of HCl solution, 250 μL; agitation speed, 250 rpm), the matrix-matched calibration curve for AFM1 determination showed good linearity in the range of 0.25-5 μg kg(-1). The enrichment factor (EF) reached 48, and the limits of detection and quantification were 0.06 and 0.21 μg kg(-1), respectively. The developed method was successfully applied for the extraction of AFM1 from spiked milk samples, with recoveries from 61.0% to 106.7%. The method was highly specific to AFM1 analysis, and the results demonstrated that the method can be automated, inexpensive, and free from interference.

  14. AFM study shows prominent physical changes in elasticity and pericellular layer in human acute leukemic cells due to inadequate cell-cell communication

    NASA Astrophysics Data System (ADS)

    Guz, Nataliia V.; Patel, Sapan J.; Dokukin, Maxim E.; Clarkson, Bayard; Sokolov, Igor

    2016-12-01

    Biomechanical properties of single cells in vitro or ex vivo and their pericellular interfaces have recently attracted a lot of attention as a potential biophysical (and possibly prognostic) marker of various diseases and cell abnormalities. At the same time, the influence of the cell environment on the biomechanical properties of cells is not well studied. Here we use atomic force microscopy to demonstrate that cell-cell communication can have a profound effect on both cell elasticity and its pericellular coat. A human pre-B p190BCR/ABL acute lymphoblastic leukemia cell line (ALL3) was used in this study. Assuming that cell-cell communication is inversely proportional to the distance between cells, we study ALL3 cells in vitro growing at different cell densities. ALL3 cells demonstrate a clear density dependent behavior. These cells grow very well if started at a relatively high cell density (HD, >2 × 105 cells ml-1) and are poised to grow at low cell density (LD, <1 × 104 cells ml-1). Here we observe ˜6× increase in the elastic (Young’s) modulus of the cell body and ˜3.6× decrease in the pericellular brush length of LD cells compared to HD ALL3 cells. The difference observed in the elastic modulus is much larger than typically reported for pathologically transformed cells. Thus, cell-cell communication must be taken into account when studying biomechanics of cells, in particular, correlating cell phenotype and its biophysical properties.

  15. Applications of AFM in semiconductor R&D and manufacturing at 45 nm technology node and beyond

    NASA Astrophysics Data System (ADS)

    Lee, Moon-Keun; Shin, Minjung; Bao, Tianming; Song, Chul-Gi; Dawson, Dean; Ihm, Dong-Chul; Ukraintsev, Vladimir

    2009-03-01

    Continuing demand for high performance microelectronic products propelled integrated circuit technology into 45 nm node and beyond. The shrinking device feature geometry created unprecedented challenges for dimension metrology in semiconductor manufacturing and research and development. Automated atomic force microscope (AFM) has been used to meet the challenge and characterize narrower lines, trenches and holes at 45nm technology node and beyond. AFM is indispensable metrology techniques capable of non-destructive full three-dimensional imaging, surface morphology characterization and accurate critical dimension (CD) measurements. While all available dimensional metrology techniques approach their limits, AFM continues to provide reliable information for development and control of processes in memory, logic, photomask, image sensor and data storage manufacturing. In this paper we review up-todate applications of automated AFM in every mentioned above semiconductor industry sector. To demonstrate benefits of AFM at 45 nm node and beyond we compare capability of automated AFM with established in-line and off-line metrologies like critical dimension scanning electron microscopy (CDSEM), optical scatterometry (OCD) and transmission electronic microscopy (TEM).

  16. Characterization of Pebax angioplasty balloon surfaces with AFM, SEM, TEM, and SAXS.

    PubMed

    Warner, Jacob A; Forsyth, Bruce; Zhou, Fang; Myers, Jason; Frethem, Chris; Haugstad, Greg

    2016-04-01

    In the medical device industry, angioplasty balloons have been widely used in the less invasive treatment of heart disease by expanding and relieving clogged structures in various arterial segments. However, new applications using thin coatings on the balloon surface have been explored to enhance therapeutic value in the delivery of pharmaceuticals (drug-elution) or control thermal energy output (RF ablation). In this study, angioplasty balloon materials comprised of poly(ether-block-amide) (Pebax) were investigated via atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and small-angle X-ray scattering (SAXS) to characterize physical properties at the balloon surface that may affect coating adhesion. The soft segment of this Pebax 1074 material is polyethylene oxide (PEO) and the hard segment is nylon-12. The morphology of the hard segments of this block co-polymer are found via AFM stiffness measurements to be (40 ± 20) nm by (300 ± 150) nm and are oriented parallel to the surface of the balloon. SAXS measurements found the lamellar spacing to be (18.5 ± 0.5) nm, and demonstrate a preferential orientation in agreement with TEM and AFM measurements. Fixation of this balloon in resin, followed by cryo-sectioning is shown to provide a novel manner in which to investigate surface characteristics on the balloon such as material or coating thickness as well as uniformity in comparison to the bulk structure. These outputs were deemed critical to improve overall balloon processing such as molding and surface treatment options for robust designs toward better procedural outcomes targeting new therapeutic areas.

  17. Measurement of Cationic and Intracellular Modulation of Integrin Binding Affinity by AFM-Based Nanorobot

    PubMed Central

    Patterson, Kevin C.; Yang, Ruiguo; Zeng, Bixi; Song, Bo; Wang, Shouye; Xi, Ning; Basson, Marc D.

    2013-01-01

    Integrins are dynamic transmembrane cation-dependent heterodimers that both anchor cells in position and transduce signals into and out of cells. We used an atomic force microscope (AFM)-based nanorobotic system to measure integrin-binding forces in intact human intestinal epithelial Caco-2 cells. The AFM-based nanorobot enables human-directed, high-accuracy probe positioning and site-specific investigations. Functionalizing the AFM probe with an arginine-glycine-aspartate (RGD)-containing sequence (consensus binding sequence for integrins) allowed us to detect a series of peptide-cell membrane interactions with a median binding force of 115.1 ± 4.9 pN that were not detected in control interactions. Chelating divalent cations from the culture medium abolished these interactions, as did inhibiting intracellular focal adhesion kinase (FAK) using Y15. Adding 1 mM Mg2+ to the medium caused a rightward shift in the force-binding curve. Adding 1 mM Ca2+ virtually abolished the RGD-membrane specific interactions and blocked the Mg2+ effects. Cell adhesion assays demonstrated parallel effects of divalent cations and the FAK inhibitor on cell adhesion. These results demonstrate direct modulation of integrin-binding affinity by both divalent cations and intracellular signal inhibition. Additionally, three binding states (nonspecific, specific inactivated, and specific activated) were delineated from affinity measurements. Although other research has assumed that this process of integrin conformational change causes altered ligand binding, in this work we directly measured these three states in individual integrins in a physiologically based study. PMID:23823222

  18. Measurement of cationic and intracellular modulation of integrin binding affinity by AFM-based nanorobot.

    PubMed

    Patterson, Kevin C; Yang, Ruiguo; Zeng, Bixi; Song, Bo; Wang, Shouye; Xi, Ning; Basson, Marc D

    2013-07-02

    Integrins are dynamic transmembrane cation-dependent heterodimers that both anchor cells in position and transduce signals into and out of cells. We used an atomic force microscope (AFM)-based nanorobotic system to measure integrin-binding forces in intact human intestinal epithelial Caco-2 cells. The AFM-based nanorobot enables human-directed, high-accuracy probe positioning and site-specific investigations. Functionalizing the AFM probe with an arginine-glycine-aspartate (RGD)-containing sequence (consensus binding sequence for integrins) allowed us to detect a series of peptide-cell membrane interactions with a median binding force of 115.1 ± 4.9 pN that were not detected in control interactions. Chelating divalent cations from the culture medium abolished these interactions, as did inhibiting intracellular focal adhesion kinase (FAK) using Y15. Adding 1 mM Mg(2+) to the medium caused a rightward shift in the force-binding curve. Adding 1 mM Ca(2+) virtually abolished the RGD-membrane specific interactions and blocked the Mg(2+) effects. Cell adhesion assays demonstrated parallel effects of divalent cations and the FAK inhibitor on cell adhesion. These results demonstrate direct modulation of integrin-binding affinity by both divalent cations and intracellular signal inhibition. Additionally, three binding states (nonspecific, specific inactivated, and specific activated) were delineated from affinity measurements. Although other research has assumed that this process of integrin conformational change causes altered ligand binding, in this work we directly measured these three states in individual integrins in a physiologically based study.

  19. Fabrication and characterization of mesoscale protein patterns using atomic force microscopy (AFM)

    NASA Astrophysics Data System (ADS)

    Gao, Pei

    2011-07-01

    A versatile AFM local oxidation lithography was developed for fabricating clean protein patterns ranging from nanometer to sub-millimeter scale on octadecyltrichlorosilane (OTS) layer of Si (100) wafer. This protein patterning method can generate bio-active protein pattern with a clean background without the need of the anti-fouling the surface or repetitive rinsing. As a model system, lysozyme protein patterns were investigated through their binding reactions with antibodies and aptamers by AFM. Polyclonal anti-lysozyme antibodies and anti-lysozyme aptamer are found to preferentially bind to the lysozyme molecules on the edge of a protein pattern before their binding to the interior ones. It was also demonstrated that the topography of the immobilized protein pattern affects the antibody binding direction. We found that the anti-lysozyme antibodies binding to the edge lysozyme molecules on the half-buried pattern started from the top but the binding on the extruded pattern started from the side because of their different spatial accessibility. In addition, after incubating lysozyme pattern with anti-lysozyme aptamer in buffer solution for enough long time, some fractal-shaped aptamer fibers with 1-6nm high and up to tens of micrometers long were formed by the self-assembling of aptamer molecules on the surface. The aptamer fibers anchor specifically on the edge of protein patterns, which originates from the biospecific recognition between the aptamer and its target protein. Once these edge-bound fibers have formed, they can serve as scaffolds for further assembly processes. We used these aptamer fibers as templates to fabricate palladium and streptavidin nanowires, which anchored on the pattern edges and never cross over or collapse over each other. The aptamer fiber scaffold potentially can lead to an effective means to fabricate and interface nanowires to existing surface patterns. KEYWORDS: Atomic Force Microscopy (AFM), Protein Patterns, Lysozyme, Aptamer

  20. BOREAS AFM-3 NCAR Electra 1994 Aircraft Flux and Moving Window Data

    NASA Technical Reports Server (NTRS)

    Lenschow, Donald H.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Shanot, Al; Oncley, Steven P.; Cooper, Al; Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS AFM-3 team used the NCAR Electra aircraft data to make measurements of the fluxes of momentum, sensible and latent heat, carbon dioxide, and ozone over the entire BOREAS region to tie together measurements made in both the SSA and the NSA in 1994. These data were also used to study the planetary boundary layer using both in situ and remote sensing measurements. This data set contains both the aircraft flux and the moving window data. These data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  1. High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties.

    PubMed

    Preiner, Johannes; Horner, Andreas; Karner, Andreas; Ollinger, Nicole; Siligan, Christine; Pohl, Peter; Hinterdorfer, Peter

    2015-01-14

    The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.

  2. High-Speed AFM Images of Thermal Motion Provide Stiffness Map of Interfacial Membrane Protein Moieties

    PubMed Central

    2014-01-01

    The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges. PMID:25516527

  3. Lateral Tip Control Effects in CD-AFM Metrology: The Large Tip Limit.

    PubMed

    Dixson, Ronald G; Orji, Ndubuisi G; Goldband, Ryan S

    2016-01-25

    Sidewall sensing in critical dimension atomic force microscopes (CD-AFMs) usually involves continuous lateral dithering of the tip or the use of a control algorithm and fast response piezo actuator to position the tip in a manner that resembles touch-triggering of coordinate measuring machine (CMM) probes. All methods of tip position control, however, induce an effective tip width that may deviate from the actual geometrical tip width. Understanding the influence and dependence of the effective tip width on the dither settings and lateral stiffness of the tip can improve the measurement accuracy and uncertainty estimation for CD-AFM measurements. Since CD-AFM typically uses tips that range from 15 nm to 850 nm in geometrical width, the behavior of effective tip width throughout this range should be understood. The National Institute of Standards and Technology (NIST) has been investigating the dependence of effective tip width on the dither settings and lateral stiffness of the tip, as well as the possibility of material effects due to sample composition. For tip widths of 130 nm and lower, which also have lower lateral stiffness, the response of the effective tip width to lateral dither is greater than for larger tips. However, we have concluded that these effects will not generally result in a residual bias, provided that the tip calibration and sample measurement are performed under the same conditions. To validate that our prior conclusions about the dependence of effective tip width on lateral stiffness are valid for large CD-tips, we recently performed experiments using a very large non-CD tip with an etched plateau of approximately 2 μm width. The effective lateral stiffness of these tips is at least 20 times greater than typical CD-AFM tips, and these results supported our prior conclusions about the expected behavior for larger tips. The bottom-line importance of these latest observations is that we can now reasonably conclude that a dither slope of 3 nm

  4. Investigation of the resistive switching in AgxAsS2 layer by conductive AFM

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Kutalek, Petr; Knotek, Petr; Hromadko, Ludek; Macak, Jan M.; Wagner, Tomas

    2016-09-01

    In this paper, a study of resistive switching in AgxAsS2 layer, based on a utilization of conductive atomic force microscope (AFM), is reported. As the result of biasing, two distinct regions were created on the surface (the conductive region and non-conductive region). Both were analysed from the spread current maps. The volume change, corresponding to the growth of Ag particles, was derived from the topological maps, recorded simultaneously with the current maps. Based on the results, a model explaining the mechanism of the Ag particle and Ag filament formation was proposed from the distribution of charge carriers and Ag ions.

  5. AFM imaging reveals the tetrameric structure of the TRPC1 channel

    SciTech Connect

    Barrera, Nelson P.; Shaifta, Yasin; McFadzean, Ian; Ward, Jeremy P.T.; Henderson, Robert M.; Edwardson, J. Michael . E-mail: jme1000@cam.ac.uk

    2007-07-13

    We have determined the subunit stoichiometry of the transient receptor potential C1 (TRPC1) channel by imaging isolated channels using atomic force microscopy (AFM). A frequency distribution of the molecular volumes of individual channel particles had two peaks, at 170 and 720 nm{sup 3}, corresponding with the expected sizes of TRPC1 monomers and tetramers, respectively. Complexes were formed between TRPC1 channels and antibodies against a V5 epitope tag present on each subunit. The frequency distribution of angles between pairs of bound antibodies had two peaks, at 88{sup o} and 178{sup o}. This result again indicates that the channel assembles as a tetramer.

  6. Proceedings of the 2011 AFMS Medical Research Symposium. Volume 4. Healthcare Informatics Track

    DTIC Science & Technology

    2011-08-02

    University, Applied Physics Laboratory Major Heather Halvorson, MD, MPH Major Cecili Sessions, MD, MPH AFMS Medical Innovations Division August 2011...incorporating all available patient information • Targeted prevention, diagnostics and therapy • Two parallel efforts • PC2-Ciinical (Air Force Clinical...Current, board-approved conditions and drug/variant pairs Rosk~tol’!! {ot~erthanqent!l<c wm:;nt) ’tm’ttmte’ Lupus CYP2C191 Cbpido~l Famit,’h6k:l l

  7. Force and function: probing proteins with AFM-based force spectroscopy.

    PubMed

    Puchner, Elias M; Gaub, Hermann E

    2009-10-01

    Forces play a pivotal role in life, and the response of live systems to forces requires molecules and molecular interactions with adequate properties to counteract both in a passive and also, if needed, in an active, dynamic manner. However, at the level of individual molecules these forces are so minute, that the development of sophisticated experiments to measure and control them was required. With the maturation of these techniques, particularly the AFM-based single-molecule force spectroscopy into commercial instruments, the scope has widened considerably and more and more studies shed light onto the different aspects of biomolecular mechanics. Many surprises turned up and more are waiting for us.

  8. Crystal structures of Boro-AFm and sBoro-AFt phases

    SciTech Connect

    Champenois, Jean-Baptiste; Cau Dit Coumes, Celine; Leroux, Fabrice; Mercier, Cyrille; Revel, Bertrand; Damidot, Denis

    2012-10-15

    Crystal structures of boron-containing AFm (B-AFm) and AFt (B-AFt) phases have been solved ab-initio and refined from X-ray powder diffraction. {sup 11}B NMR and Raman spectroscopies confirm the boron local environment in both compounds: three-fold coordinated in B-AFm corresponding to HBO{sub 3}{sup 2-} species, and four-fold coordinated in B-AFt corresponding to B (OH){sub 4}{sup -} species. B-AFm crystallizes in the rhombohedral R3{sup Macron }c space group and has the 3CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}CaHBO{sub 3}{center_dot}12H{sub 2}O (4CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}1/2B{sub 2}O{sub 3}{center_dot}12.5H{sub 2}O, C{sub 4}AB{sub 1/2}H{sub 12.5}) general formulae with planar trigonal HBO{sub 3}{sup 2-} anions weakly bonded at the centre of the interlayer region. One HBO{sub 3}{sup 2-} anion is statistically distributed with two weakly bonded water molecules on the same crystallographic site. B-AFt crystallizes in the trigonal P3cl space group and has the 3CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}Ca(OH){sub 2}{center_dot}2Ca(B (OH){sub 4}){sub 2}{center_dot}24H{sub 2}O (6CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}2B{sub 2}O{sub 3}{center_dot}33H{sub 2}O, C{sub 6}AB{sub 2}H{sub 33}) general formulae with tetrahedral B (OH){sub 4}{sup -} anions located in the channel region of the structure. All tetrahedral anions are oriented in a unique direction, leading to a hexagonal c lattice parameter about half that of ettringite.

  9. Analytical solutions of the first three frequency shifts of AFM non-uniform probe subjected to the Lennard-Jones force.

    PubMed

    Lin, Shueei-Muh; Liauh, Chihng-Tsung; Wang, Wen-Rong; Ho, Shing-Huei

    2006-04-01

    The role of higher cantilever modes is important to obtain some material contrast. The analysis of AFM subjected to a short-range force can improve greatly the studies of surface topography and interaction energies and interaction forces, especially for chemical and biological materials. When the tip-sample distance is in the order of inter-atomic spacing, the short-range tip-sample force is usually simulated by the Lennard-Jones model. In this study, the analytical method to determine the frequency shift of AFM subjected to the Lennard-Jones force is proposed. The closed-form solution of the partial differential equation with a nonlinear boundary condition is derived and then the corresponding frequency shifts of higher modes can be determined easily. Moreover, the conventional perturbation method is usually used to determine the frequency shift, but only for the first mode. This is because the original continuous beam system is transformed into a discrete lumped-masses model. Although the above disadvantages exist, the lumped-masses model is simple and intuitive. Using the principle of dynamic strain energy, the conventional perturbation method is revised successfully to determine the frequency shifts of higher modes. The assessment of the generalized perturbation method and the proposed method is made. Finally, the effects of several parameters on the first three frequency shifts are investigated.

  10. In vivo characterization of protein uptake by yeast cell envelope: single cell AFM imaging and μ-tip-enhanced Raman scattering study.

    PubMed

    Naumenko, Denys; Snitka, Valentinas; Serviene, Elena; Bruzaite, Ingrida; Snopok, Boris

    2013-09-21

    Direct detection of biological transformations of single living cells in vivo has been performed by the advanced combination of local topographic imaging by Atomic Force Microscopy (AFM) and label-free sub-surface chemical characterization using new μ-Tip-Enhanced Raman Spectroscopy (μ-TERS). The enhancing mechanism for μ-TERS tips with micrometre range radius differs significantly to that of the conventional tapered structures terminated by a sharp apex and conditioned by the effects of propagating instead of localizing surface plasmon resonance phenomena. Sub-wavelength light confinement in the form of a nonradiative evanescent wave near the tip surface with penetration depth in the sub-micrometre range opens the way for monitoring of subsurface processes near or within the cell wall, inaccessible by other methods. The efficiency of the approach has been demonstrated by the analysis of the cell envelope of genetically modified (by glucose dehydrogenase (GDH) gene bearing Kluyveromyces lactis toxin signal sequence) yeast cells enriched by GDH protein. The presence of trans-membrane fragments in GDH together with the tendency to form active dimers and tetramers causes the accumulation of the proteins within the periplasmic space. These results demonstrate that the advanced combination of AFM imaging and subsurface chemical characterization by the novel μ-TERS technique provides a new analytical tool for the investigation of single living cells in vivo.

  11. An innovative method and experiment for fabricating bulgy shape nanochannel using AFM

    NASA Astrophysics Data System (ADS)

    Lin, Zone-Ching; Jheng, Hao-Yuan; Ding, Hao-Yang

    2015-08-01

    The paper proposes using atomic force microscopy (AFM) and the concept of specific down force energy (SDFE) to establish an innovative offset cycle cutting method for fabricating a bulgy shape nanochannel on a single-crystal silicon substrate. In the offset cycle cutting method, cutting is performed at a constant down force in all cutting passes. After the first cutting pass, the AFM probe is offset rightward for the second pass and subsequently offset leftward to the middle (i.e., between the positions of the first two cutting passes) for the third cutting pass. Applying a step-by-step method to modify the offset distance and approach the defined SDFE value, this study determined the depth of the middle cutting pass and smaller values of upward bulginess and downward indentation at the bottom of the nanochannel. The nanochannel width can be increased by increasing the number of offset cycle cutting passes. In addition, by applying the proposed method, this study involved a simulation and experiment concerning the cutting path plan of bulgy shape nanochannels. Furthermore, using a small down force along the burr path is proposed for reducing burr height. The results of the simulation and experiment were compared to verify the feasibility of the method.

  12. Low and high cycle fatigue -- A continuum supported by AFM observations

    SciTech Connect

    Gerberich, W.W.; Harvey, S.E.; Kramer, D.E.; Hoehn, J.W.

    1998-09-01

    It is proposed that fatigue damage evolution is controlled by surface displacements and these can be accurately measured by atomic force microscopy (AFM). As these displacements can be followed throughout the history of a fatigued component, the fatigue process in general represents a continuum of behavior. In 10 and 200 {micro}m grain size titanium, AFM measurements demonstrate that the fraction of plasticity contributing to surface damage can be expressed as a single function over nearly five decades of cycles. Regarding this function, the effect of grain size appears to be small. In terms of damage accumulation rates, cyclic hardening parameters, and the threshold stress intensity, the proposed model represents a microstructurally-sensitive Manson-Coffin law for fatigue initiation. Coupling this with a more standard fracture mechanics approach for the latter stage of life allows a simple expression for life prediction. Over the range of 10{sup 3}--10{sup 6} cycles, this expression predicts fatigue life of titanium exposed to air and saline environments to first order.

  13. Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM

    PubMed Central

    Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger

    2015-01-01

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455

  14. Comparative AFM nanoscratching tests in air of bulk copper and electrogenerated cuprous oxide films

    NASA Astrophysics Data System (ADS)

    Chaal, Lila; Debiemme-Chouvy, Catherine; Deslouis, Claude; Maurin, Georges; Pailleret, Alain; Saidani, Boualem

    2011-01-01

    The normal and lateral spring constants of rectangular silicon AFM cantilevers bearing pyramidal silicon tips were a