Sample records for afm analysis revealed

  1. Measuring bacterial cells size with AFM

    PubMed Central

    Osiro, Denise; Filho, Rubens Bernardes; Assis, Odilio Benedito Garrido; Jorge, Lúcio André de Castro; Colnago, Luiz Alberto

    2012-01-01

    Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described. PMID:24031837

  2. Amyloid and membrane complexity: The toxic interplay revealed by AFM.

    PubMed

    Canale, Claudio; Oropesa-Nuñez, Reinier; Diaspro, Alberto; Dante, Silvia

    2018-01-01

    Lipid membranes play a fundamental role in the pathological development of protein misfolding diseases. Several pieces of evidence suggest that the lipid membrane could act as a catalytic surface for protein aggregation. Furthermore, a leading theory indicates the interaction between the cell membrane and misfolded oligomer species as the responsible for cytotoxicity, hence, for neurodegeneration in disorders such as Alzheimer's and Parkinson's disease. The definition of the mechanisms that drive the interaction between pathological protein aggregates and plasma membrane is fundamental for the development of effective therapies for a large class of diseases. Atomic force microscopy (AFM) has been employed to study how amyloid aggregates affect the cell physiological properties. Considerable efforts were spent to characterize the interaction with model systems, i.e., planar supported lipid bilayers, but some works also addressed the problem directly on living cells. Here, an overview of the main works involving the use of the AFM on both model system and living cells will be provided. Different kind of approaches will be presented, as well as the main results derived from the AFM analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. 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.

  4. Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

    PubMed

    Mikulska-Ruminska, Karolina; Kulik, Andrej J; Benadiba, Carine; Bahar, Ivet; Dietler, Giovanni; Nowak, Wieslaw

    2017-08-18

    Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.

  5. Using 2D correlation analysis to enhance spectral information available from highly spatially resolved AFM-IR spectra

    NASA Astrophysics Data System (ADS)

    Marcott, Curtis; Lo, Michael; Hu, Qichi; Kjoller, Kevin; Boskey, Adele; Noda, Isao

    2014-07-01

    The recent combination of atomic force microscopy and infrared spectroscopy (AFM-IR) has led to the ability to obtain IR spectra with nanoscale spatial resolution, nearly two orders-of-magnitude better than conventional Fourier transform infrared (FT-IR) microspectroscopy. This advanced methodology can lead to significantly sharper spectral features than are typically seen in conventional IR spectra of inhomogeneous materials, where a wider range of molecular environments are coaveraged by the larger sample cross section being probed. In this work, two-dimensional (2D) correlation analysis is used to examine position sensitive spectral variations in datasets of closely spaced AFM-IR spectra. This analysis can reveal new key insights, providing a better understanding of the new spectral information that was previously hidden under broader overlapped spectral features. Two examples of the utility of this new approach are presented. Two-dimensional correlation analysis of a set of AFM-IR spectra were collected at 200-nm increments along a line through a nucleation site generated by remelting a small spot on a thin film of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). There are two different crystalline carbonyl band components near 1720 cm-1 that sequentially disappear before a band at 1740 cm-1 due to more disordered material appears. In the second example, 2D correlation analysis of a series of AFM-IR spectra spaced every 1 μm of a thin cross section of a bone sample measured outward from an osteon center of bone growth. There are many changes in the amide I and phosphate band contours, suggesting changes in the bone structure are occurring as the bone matures.

  6. A fully-automated neural network analysis of AFM force-distance curves for cancer tissue diagnosis

    NASA Astrophysics Data System (ADS)

    Minelli, Eleonora; Ciasca, Gabriele; Sassun, Tanya Enny; Antonelli, Manila; Palmieri, Valentina; Papi, Massimiliano; Maulucci, Giuseppe; Santoro, Antonio; Giangaspero, Felice; Delfini, Roberto; Campi, Gaetano; De Spirito, Marco

    2017-10-01

    Atomic Force Microscopy (AFM) has the unique capability of probing the nanoscale mechanical properties of biological systems that affect and are affected by the occurrence of many pathologies, including cancer. This capability has triggered growing interest in the translational process of AFM from physics laboratories to clinical practice. A factor still hindering the current use of AFM in diagnostics is related to the complexity of AFM data analysis, which is time-consuming and needs highly specialized personnel with a strong physical and mathematical background. In this work, we demonstrate an operator-independent neural-network approach for the analysis of surgically removed brain cancer tissues. This approach allowed us to distinguish—in a fully automated fashion—cancer from healthy tissues with high accuracy, also highlighting the presence and the location of infiltrating tumor cells.

  7. AFM 4.0: a toolbox for DNA microarray analysis

    PubMed Central

    Breitkreutz, Bobby-Joe; Jorgensen, Paul; Breitkreutz, Ashton; Tyers, Mike

    2001-01-01

    We have developed a series of programs, collectively packaged as Array File Maker 4.0 (AFM), that manipulate and manage DNA microarray data. AFM 4.0 is simple to use, applicable to any organism or microarray, and operates within the familiar confines of Microsoft Excel. Given a database of expression ratios, AFM 4.0 generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data. AFM 4.0 should be especially useful to laboratories that do not have access to specialized commercial or in-house software. PMID:11532221

  8. Multi-frequency data analysis in AFM by wavelet transform

    NASA Astrophysics Data System (ADS)

    Pukhova, V.; Ferrini, G.

    2017-10-01

    Interacting cantilevers in AFM experiments generate non-stationary, multi-frequency signals consisting of numerous excited flexural and torsional modes and their harmonics. The analysis of such signals is challenging, requiring special methodological approaches and a powerful mathematical apparatus. The most common approach to the signal analysis is to apply Fourier transform analysis. However, FT gives accurate spectra for stationary signals, and for signals changing their spectral content over time, FT provides only an averaged spectrum. Hence, for non-stationary and rapidly varying signals, such as those from interacting cantilevers, a method that shows the spectral evolution in time is needed. One of the most powerful techniques, allowing detailed time-frequency representation of signals, is the wavelet transform. It is a method of analysis that allows representation of energy associated to the signal at a particular frequency and time, providing correlation between the spectral and temporal features of the signal, unlike FT. This is particularly important in AFM experiments because signals nonlinearities contains valuable information about tip-sample interactions and consequently surfaces properties. The present work is aimed to show the advantages of wavelet transform in comparison with FT using as an example the force curve analysis in dynamic force spectroscopy.

  9. Simulation of CNT-AFM tip based on finite element analysis for targeted probe of the biological cell

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yousefi, Amin Termeh, E-mail: at.tyousefi@gmail.com; Miyake, Mikio, E-mail: miyakejaist@gmail.com; Ikeda, Shoichiro, E-mail: sho16.ikeda@gmail.com

    Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nano scale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cell’s. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cellmore » analysis.« less

  10. 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.

  11. 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

  12. [AFM fishing of proteins under impulse electric field].

    PubMed

    Ivanov, Yu D; Pleshakova, T O; Malsagova, K A; Kaysheva, A L; Kopylov, A T; Izotov, A A; Tatur, V Yu; Vesnin, S G; Ivanova, N D; Ziborov, V S; Archakov, A I

    2016-05-01

    A combination of (atomic force microscopy)-based fishing (AFM-fishing) and mass spectrometry allows to capture protein molecules from solutions, concentrate and visualize them on an atomically flat surface of the AFM chip and identify by subsequent mass spectrometric analysis. In order to increase the AFM-fishing efficiency we have applied pulsed voltage with the rise time of the front of about 1 ns to the AFM chip. The AFM-chip was made using a conductive material, highly oriented pyrolytic graphite (HOPG). The increased efficiency of AFM-fishing has been demonstrated using detection of cytochrome b5 protein. Selection of the stimulating pulse with a rise time of 1 ns, corresponding to the GHz frequency range, by the effect of intrinsic emission from water observed in this frequency range during water injection into the cell.

  13. Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging.

    PubMed

    Zhang, Qinnan; Zhong, Liyun; Tang, Ping; Yuan, Yingjie; Liu, Shengde; Tian, Jindong; Lu, Xiaoxu

    2017-05-31

    Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

  14. 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.

  15. On CD-AFM bias related to probe bending

    NASA Astrophysics Data System (ADS)

    Ukraintsev, V. A.; Orji, N. G.; Vorburger, T. V.; Dixson, R. G.; Fu, J.; Silver, R. M.

    2012-03-01

    Critical Dimension AFM (CD-AFM) is a widely used reference metrology. To characterize modern semiconductor devices, very small and flexible probes, often 15 nm to 20 nm in diameter, are now frequently used. Several recent publications have reported on uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements [1,2]. Results obtained in this work suggest that probe bending can be on the order of several nanometers and thus potentially can explain much of the observed CD-AFM probe-to-probe bias variation. We have developed and experimentally tested one-dimensional (1D) and two-dimensional (2D) models to describe the bending of cylindrical probes. An earlier 1D bending model reported by Watanabe et al. [3] was refined. Contributions from several new phenomena were considered, including: probe misalignment, diameter variation near the carbon nanotube tip (CNT) apex, probe bending before snapping, distributed van der Waals-London force, etc. The methodology for extraction of the Hamaker probe-surface interaction energy from experimental probe bending data was developed. To overcome limitations of the 1D model, a new 2D distributed force (DF) model was developed. Comparison of the new model with the 1D single point force (SPF) model revealed about 27 % difference in probe bending bias between the two. A simple linear relation between biases predicted by the 1D SPF and 2D DF models was found. This finding simplifies use of the advanced 2D DF model of probe bending in various CD-AFM applications. New 2D and three-dimensional (3D) CDAFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

  16. 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.

  17. Analysis of photothermally induced vibration in metal coated AFM cantilever

    NASA Astrophysics Data System (ADS)

    Kadri, Shahrul; Fujiwara, Hideki; Sasaki, Keiji

    2010-05-01

    We report the vibration reduction in the optically driven V-shaped AFM cantilever with 70 nm gold surface coating. The driving laser at 780 nm is intensity modulated at 1 kHz to 100 kHz and focused on the AFM cantilever surface. The cantilever vibration amplitude is monitored by HeNe probe laser. Two features are observed: high vibration amplitude of the cantilever (1) at several kHz modulation frequencies regime and (2) at around its mechanical resonance. In addition, we found that vibration at the resonance peak increases when the excitation spot is positioned farther from the free end of the cantilever.

  18. Atomic Force Microscope (AFM) measurements and analysis on Sagem 05R0025 secondary substrate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Soufli, R; Baker, S L; Robinson, J C

    2006-02-22

    The summary of Atomic Force Microscope (AFM) on Sagem 05R0025 secondary substrate: (1) 2 x 2 {micro}m{sup 2} and 10 x 10 {micro}m{sup 2} AFM measurements and analysis on Sagem 05R0025 secondary substrate at LLNL indicate rather uniform and extremely isotropic finish across the surface, with high-spatial frequency roughness {sigma} in the range 5.1-5.5 {angstrom} rms; (2) the marked absence of pronounced long-range polishing marks in any direction, combined with increased roughness in the very high spatial frequencies, are consistent with ion-beam polishing treatment on the surface. These observations are consistent with all earlier mirrors they measured from the samemore » vendor; and (3) all data were obtained with a Digital Instruments Dimension 5000{trademark} atomic force microscope.« less

  19. Probing ternary solvent effect in high V oc 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 V oc 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 C 60 buffer layer, a bulk heterojunction PSC with V oc 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)more » 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.« less

  20. 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...

  1. Stiffness and evolution of interfacial micropancakes revealed by AFM quantitative nanomechanical imaging.

    PubMed

    Zhao, Binyu; Wang, Xingya; Song, Yang; Hu, Jun; Lü, Junhong; Zhou, Xingfei; Tai, Renzhong; Zhang, Xuehua; Zhang, Lijuan

    2015-05-28

    Micropancakes are quasi-two-dimensional micron-sized domains on crystalline substrates (e.g. highly oriented pyrolytic graphite (HOPG)) immersed in water. They are only a few nanometers thick, and are suspected to come from the accumulation of dissolved air at the solid-water interface. However, the exact chemical nature and basic physical properties of micropancakes have been under debate ever since their first observation, primarily due to the lack of a suitable characterization technique. In this study, the stiffness of micropancakes at the interface between HOPG and ethanol-water solutions was investigated by using PeakForce Quantitative NanoMechanics (PF-QNM) mode Atomic Force Microscopy (AFM). Our measurements showed that micropancakes were stiffer than nanobubbles, and for bilayer micropancakes, the bottom layer in contact with the substrate was stiffer than the top one. Interestingly, the micropancakes became smaller and softer with an increase in the ethanol concentration in the solution, and were undetectable by AFM above a critical concentration of ethanol. But they re-appeared after the ethanol concentration in the solution was reduced. Clearly the evolution and stiffness of the micropancakes were dependent on the chemical composition in the solution, which could be attributed to the correlation of the mechanical properties of the micropancakes with the surface tension of the liquid phase. Based on the "go-and-come" behaviors of micropancakes with the ethanol concentration, we found that the micropancakes could actually tolerate the ethanol concentration much higher than 5%, a value reported in the literature. The results from this work may be helpful in alluding the chemical nature of micropancakes.

  2. AFM combined to ATR-FTIR reveals Candida cell wall changes under caspofungin treatment.

    PubMed

    Quilès, Fabienne; Accoceberry, Isabelle; Couzigou, Célia; Francius, Grégory; Noël, Thierry; El-Kirat-Chatel, Sofiane

    2017-09-21

    Fungal pathogens from Candida genus are responsible for severe life-threatening infections and the antifungal arsenal is still limited. Caspofungin, an antifungal drug used for human therapy, acts as a blocking agent of the cell wall synthesis by inhibiting the β-1,3-glucan-synthase encoded by FKS genes. Despite its efficiency, the number of genetic mutants that are resistant to caspofungin is increasing. An important challenge to improve antifungal therapy is to understand cellular phenomenon that are associated with drug resistance. Here we used atomic force microscopy (AFM) combined to Fourier transform infrared spectroscopy in attenuated total reflection mode (ATR-FTIR) to decipher the effect of low and high drug concentration on the morphology, mechanics and cell wall composition of two Candida strains, one susceptible and one resistant to caspofungin. Our results confirm that caspofungin induces a dramatic cell wall remodelling via activation of stress responses, even at high drug concentration. Additionally, we highlighted unexpected changes related to drug resistance, suggesting that caspofungin resistance associated with FKS gene mutations comes from a combination of effects: (i) an overall remodelling of yeast cell wall composition; and (ii) cell wall stiffening through chitin synthesis. This work demonstrates that AFM combined to ATR-FTIR is a valuable approach to understand at the molecular scale the biological mechanisms associated with drug resistance.

  3. 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

  4. Tip in–light on: Advantages, challenges, and applications of combining AFM and Raman microscopy on biological samples

    PubMed Central

    Gierlinger, Notburga

    2016-01-01

    Abstract Scanning probe microscopies and spectroscopies, especially AFM and Confocal Raman microscopy are powerful tools to characterize biological materials. They are both non‐destructive methods and reveal mechanical and chemical properties on the micro and nano‐scale. In the last years the interest for increasing the lateral resolution of optical and spectral images has driven the development of new technologies that overcome the diffraction limit of light. The combination of AFM and Raman reaches resolutions of about 50–150 nm in near‐field Raman and 1.7–50 nm in tip enhanced Raman spectroscopy (TERS) and both give a molecular information of the sample and the topography of the scanned surface. In this review, the mentioned approaches are introduced, the main advantages and problems for application on biological samples discussed and some examples for successful experiments given. Finally the potential of colocated AFM and Raman measurements is shown on a case study of cellulose‐lignin films: the topography structures revealed by AFM can be related to a certain chemistry by the colocated Raman scan and additionally the mechanical properties be revealed by using the digital pulsed force mode. Microsc. Res. Tech. 80:30–40, 2017. © 2016 Wiley Periodicals, Inc. PMID:27514318

  5. 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

  6. SNOM and AFM microscopy techniques to study the effect of non-ionizing radiation on the morphological and biochemical properties of human keratinocytes cell line (HaCaT).

    PubMed

    Rieti, S; Manni, V; Lisi, A; Giuliani, L; Sacco, D; D'Emilia, E; Cricenti, A; Generosi, R; Luce, M; Grimaldi, S

    2004-01-01

    In this study we have employed atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM) techniques to study the effect of the interaction between human keratinocytes (HaCaT) and electromagnetic fields at low frequency. HaCaT cells were exposed to a sinusoidal magnetic field at a density of 50 Hz, 1 mT. AFM analysis revealed modification in shape and morphology in exposed cells with an increase in the areas of adhesion between cells. This latter finding was confirmed by SNOM indirect immunofluorescence analysis performed with a fluorescent antibody against the adhesion marker beta4 integrin, which revealed an increase of beta4 integrin segregation in the cell membrane of 50-Hz exposed cells, suggesting that a higher percentage of these cells shows a modified pattern of this adhesion marker.

  7. AFM feature definition for neural cells on nanofibrillar tissue scaffolds.

    PubMed

    Tiryaki, Volkan M; Khan, Adeel A; Ayres, Virginia M

    2012-01-01

    A diagnostic approach is developed and implemented that provides clear feature definition in atomic force microscopy (AFM) images of neural cells on nanofibrillar tissue scaffolds. Because the cellular edges and processes are on the same order as the background nanofibers, this imaging situation presents a feature definition problem. The diagnostic approach is based on analysis of discrete Fourier transforms of standard AFM section measurements. The diagnostic conclusion that the combination of dynamic range enhancement with low-frequency component suppression enhances feature definition is shown to be correct and to lead to clear-featured images that could change previously held assumptions about the cell-cell interactions present. Clear feature definition of cells on scaffolds extends the usefulness of AFM imaging for use in regenerative medicine. © Wiley Periodicals, Inc.

  8. Biological Applications of FM-AFM in Liquid Environment

    NASA Astrophysics Data System (ADS)

    Fukuma, Takeshi; Jarvis, Suzanne P.

    Atomic force microscopy (AFM) was noted for its potential to study biological materials shortly after its first development in 1986 due to its ability to image insulators in liquid environments. The subsequent application of AFM to biology has included lateral characterization via imaging, unraveling of molecules under a tensile load and application of a force either to measure mechanical properties under the tip or to instigate a biochemical response in living cells. To date, the application of frequency modulation AFM (FM-AFM) specifically to biological materials has been limited to relatively few research groups when compared to the extensive application of AFM to biological materials. This is probably due to the perceived complexity of the technique both by researchers in the life sciences and those manufacturing liquid AFMs for biological research. In this chapter, we aim to highlight the advantages of applying the technique to biological materials.

  9. Tracing the beginning of crystallization of amorphous forsterite thin films using AFM and IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Oehm, B.; Burchard, M.; Lattard, D.; Dohmen, R.; Chakraborty, S.

    2009-12-01

    Observations of accretion disks of Young Stellar Objects revealed dust of crystalline Mg-silicates, in particular of forsterite, which is assumed to result from high temperature annealing of amorphous cosmic dust particles. We are performing annealing experiments to obtain kinetic parameters of the crystallization that are necessary for the numerical modeling of accretion disks. We use thin films obtained by Pulsed Laser Deposition (PLD) on Si (111) wafers. The thin films are completely amorphous, chemically homogeneous (on the Mg2SiO4 composition) and with a continuous and flat surface. They are annealed for 1 to 260 h at 1073K in a vertical furnace and drop-quenched. To monitor the progress of crystallization, the samples are characterized by AFM and SEM imaging and IR spectroscopy. After 2.5 h of annealing AFM images reveal elliptical features, below 1 µm in diameter, with a central elevation and surrounded by a lowering of the surface which indicate material transport within the elliptical domains. These elliptical features most probably represent early nucleation sites in an amorphous matrix. The IR spectra still show the broad bands of Si-O stretching modes typical of amorphous silica without clear evidence for crystalline forsterite. After 6 h of annealing, AFM and SEM images show circular and square features both with a central elevation in the range of 80 to 120 nm. IR spectra show a few weak bands that can be assigned to crystalline forsterite (bending and stretching of tetrahedra). After 10 h of annealing planar faces appear in the former pyramidal features and the surrounding matrix evolves into domains with spherolitic appearance. IR spectra of these samples display typical bands of crystalline forsterite. With increasing annealing time AFM images picture the further growth of the planar faces towards idiomorphic crystals. SEM imaging shows surface roughening with increasing annealing time. The quantitative evaluation of the surface roughness of AFM

  10. AFM PeakForce QNM mode: Evidencing nanometre-scale mechanical properties of chitin-silica hybrid nanocomposites.

    PubMed

    Smolyakov, G; Pruvost, S; Cardoso, L; Alonso, B; Belamie, E; Duchet-Rumeau, J

    2016-10-20

    PeakForce Quantitative Nanomechanical Mapping (QNM) AFM mode was used to explore the mechanical properties of textured chitin-silica hybrid films at the nanoscale. The influence of the force applied by the tip on the sample surface was studied for standard homogeneous samples, for chitin nanorods and for chitin-silica hybrid nanocomposites. Thick films of superimposed chitin nanorods showed a monotonous increase of DMT modulus (based on the Derjaguin-Muller-Toporov model) owing to an increase in modulus at the interface between nanorods due to geometrical constraints of the AFM acquisition. A similar variation of DMT modulus was obtained for chitin-silica hybrid thick films related to mechanical strengthening induced by the presence of silica. This work revealed the role of the organic-inorganic interface, at the nanoscale, in the mechanical behaviour of textured materials using PeakForce QNM mode, with optimized analysis conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Highly sensitive protein detection by biospecific AFM-based fishing with pulsed electrical stimulation.

    PubMed

    Pleshakova, Tatyana O; Malsagova, Kristina A; Kaysheva, Anna L; Kopylov, Arthur T; Tatur, Vadim Yu; Ziborov, Vadim S; Kanashenko, Sergey L; Galiullin, Rafael A; Ivanov, Yuri D

    2017-08-01

    We report here the highly sensitive detection of protein in solution at concentrations from 10 -15 to 10 -18 m using the combination of atomic force microscopy (AFM) and mass spectrometry. Biospecific detection of biotinylated bovine serum albumin was carried out by fishing out the protein onto the surface of AFM chips with immobilized avidin, which determined the specificity of the analysis. Electrical stimulation was applied to enhance the fishing efficiency. A high sensitivity of detection was achieved by application of nanosecond electric pulses to highly oriented pyrolytic graphite placed under the AFM chip. A peristaltic pump-based flow system, which is widely used in routine bioanalytical assays, was employed throughout the analysis. These results hold promise for the development of highly sensitive protein detection methods using nanosensor devices.

  12. 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.

  13. 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.

  14. Improved AFM Mapping of ICF Target Surfaces

    NASA Astrophysics Data System (ADS)

    Olson, D. K.; Drake, T.; Frey, D.; Huang, H.; Stephens, R. B.

    2003-10-01

    Targets for Inertial Confinement Fusion (ICF) research are made from spherical shells with very strict requirements on surface smoothness. Hydrodynamic instabilities are amplified by the presence of surface defects, greatly reducing the gain of ICF targets. Sub-micron variations in the surface can be examined using an Atomic Force Microscope. The current sphere mapping assembly at General Atomics is designed to trace near the equator of a rotating sphere under the AFM head. Spheres are traced on three mutually orthogonal planes. The ˜10 mm piezo-electric actuator range limits how far off the equator we can scan spheres of millimeter diameter. Because only a small fraction of the target's surface can be covered, localized high-mode defects are difficult to detect. In order to meet the needs of ICF research, we need to scan more surface area of the sphere with the AFM. By integrating an additional stepping motor to the sphere mapping assembly, we will be able to recenter the piezo driver of the AFM while mapping. This additional ability allows us to increase the amount of the sphere's surface we are able to scan with the AFM by extending the range of the AFM from the sphere's equator.

  15. Multifrequency AFM: from origins to convergence.

    PubMed

    Santos, Sergio; Lai, Chia-Yun; Olukan, Tuza; Chiesa, Matteo

    2017-04-20

    Since the inception of the atomic force microscope (AFM) in 1986, influential papers have been presented by the community and tremendous advances have been reported. Being able to routinely image conductive and non-conductive surfaces in air, liquid and vacuum environments with nanoscale, and sometimes atomic, resolution, the AFM has long been perceived by many as the instrument to unlock the nanoscale. From exploiting a basic form of Hooke's law to interpret AFM data to interpreting a seeming zoo of maps in the more advanced multifrequency methods however, an inflection point has been reached. Here, we discuss this evolution, from the fundamental dilemmas that arose in the beginning, to the exploitation of computer sciences, from machine learning to big data, hoping to guide the newcomer and inspire the experimenter.

  16. MetaRep, an extended CMAS 3D program to visualize mafic (CMAS, ACF-S, ACF-N) and pelitic (AFM-K, AFM-S, AKF-S) projections

    NASA Astrophysics Data System (ADS)

    France, Lydéric; Nicollet, Christian

    2010-06-01

    MetaRep is a program based on our earlier program CMAS 3D. It is developed in MATLAB ® script. MetaRep objectives are to visualize and project major element compositions of mafic and pelitic rocks and their minerals in the pseudo-quaternary projections of the ACF-S, ACF-N, CMAS, AFM-K, AFM-S and AKF-S systems. These six systems are commonly used to describe metamorphic mineral assemblages and magmatic evolutions. Each system, made of four apices, can be represented in a tetrahedron that can be visualized in three dimensions with MetaRep; the four tetrahedron apices represent oxides or combination of oxides that define the composition of the projected rock or mineral. The three-dimensional representation allows one to obtain a better understanding of the topology of the relationships between the rocks and minerals and relations. From these systems, MetaRep can also project data in ternary plots (for example, the ACF, AFM and AKF ternary projections can be generated). A functional interface makes it easy to use and does not require any knowledge of MATLAB ® programming. To facilitate the use, MetaRep loads, from the main interface, data compiled in a Microsoft Excel ™ spreadsheet. Although useful for scientific research, the program is also a powerful tool for teaching. We propose an application example that, by using two combined systems (ACF-S and ACF-N), provides strong confirmation in the petrological interpretation.

  17. 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.

  18. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies.

    PubMed

    Shlyakhtenko, Luda S; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S; Lyubchenko, Yuri L

    2015-10-27

    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.

  19. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies

    PubMed Central

    Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.

    2015-01-01

    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. PMID:26503602

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ali, Yasir; Kumar, Vijay; Dhaliwal, A. S.

    2013-02-05

    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 {sup 60}Co 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 AFMmore » observations.« less

  1. Gum tragacanth stabilized green gold nanoparticles as cargos for Naringin loading: A morphological investigation through AFM.

    PubMed

    Rao, Komal; Imran, Muhammad; Jabri, Tooba; Ali, Imdad; Perveen, Samina; Shafiullah; Ahmed, Shakil; Shah, Muhammad Raza

    2017-10-15

    Gold nanoparticles (AuNPs) have attracted greater scientific interests for the construction of drugs loading cargos due to their biocompatibility, safety and facile surface modifications. This study deals with the fabrication of gum tragacanth (GT) green AuNPs as carrier for Naringin, a less water soluble therapeutic molecule. The optimized AuNPs were characterized through UV-vis spectroscopy, FT-IR and atomic force microscope (AFM). Naringin loaded nanoparticles were investigated for their bactericidal potentials using Tetrazolium Microplate assay. Morphological studies conducted via AFM revealed spherical shape for AuNPs with nano-range size and stabilized by GT multi-functional groups. The AuNPs acted as carrier for increased amount of Naringin. Upon loading in AuNPs, Naringin An increased in the bactericidal potentials of Naringin was observed after loading on AuNPs against various tested bacterial strains. This was further authenticated by the surface morphological analysis, showing enhanced membrane destabilizing effects of loaded Naringin. The results suggest that GT stabilized green AuNPs can act as effective delivery vehicles for enhancing bactericidal potentials of Naringin. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. 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.

  3. Controlling the electric charge of gold nanoplatelets on an insulator by field emission nc-AFM

    NASA Astrophysics Data System (ADS)

    Baris, Bulent; Alchaar, Mohanad; Prasad, Janak; Gauthier, Sébastien; Dujardin, Erik; Martrou, David

    2018-03-01

    Charging of 2D Au nanoplatelets deposited on an insulating SiO2 substrate to or from the tip of a non-contact atomic force microscope (nc-AFM) is demonstrated. Charge transfer is controlled by monitoring the resonance frequency shift Δf(V) during the bias voltage ramp V applied to the tip-back electrode junction. The onset of charge transfer is revealed by a transition from a capacitive parabolic behavior to a constant Δf(V) region for both polarities. An analytical model, based on charging by electron field emission, shows that the field-emitted current saturates shortly after the onset of the charging, due to the limiting effect of the charge-induced rise of the Au platelet potential. The value of this current plateau depends only on the rate of the bias voltage ramp and on the value of the platelet/SiO2/back electrode capacitance. This analysis is confirmed by numerical simulations based on a virtual nc-AFM model that faithfully matches the experimental data. Our charging protocol could be used to tune the potential of the platelets at the single charge level.

  4. Simultaneous AFM and fluorescence imaging: A method for aligning an AFM-tip with an excitation beam using a 2D galvanometer

    NASA Astrophysics Data System (ADS)

    Moores, A. N.; Cadby, A. J.

    2018-02-01

    Correlative fluorescence and atomic force microscopy (AFM) imaging is a highly attractive technique for use in biological imaging, enabling force and mechanical measurements of particular structures whose locations are known due to the specificity of fluorescence imaging. The ability to perform these two measurements simultaneously (rather than consecutively with post-processing correlation) is highly valuable because it would allow the mechanical properties of a structure to be tracked over time as changes in the sample occur. We present an instrument which allows simultaneous AFM and fluorescence imaging by aligning an incident fluorescence excitation beam with an AFM-tip. Alignment was performed by calibrating a 2D galvanometer present in the excitation beam path and using it to reposition the incident beam. Two programs were developed (one manual and one automated) which correlate sample features between the AFM and fluorescence images, calculating the distance required to translate the incident beam towards the AFM-tip. Using this method, we were able to obtain beam-tip alignment (and therefore field-of-view alignment) from an offset of >15 μm to within one micron in two iterations of the program. With the program running alongside data acquisition for real-time feedback between AFM and optical images, this offset was maintained over a time period of several hours. Not only does this eliminate the need to image large areas with both techniques to ensure that fields-of-view overlap, but it also raises the possibility of using this instrument for tip-enhanced fluorescence applications, a technique in which super-resolution images have previously been achieved.

  5. 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

    α 1-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 onmore » 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 vivo

  6. An AFM-SIMS Nano Tomography Acquisition System

    NASA Astrophysics Data System (ADS)

    Swinford, Richard William

    An instrument, adding the capability to measure 3D volumetric chemical composition, has been constructed by me as a member of the Sanchez Nano Laboratory. The laboratory's in situ atomic force microscope (AFM) and secondary ion mass spectrometry systems (SIMS) are functional and integrated as one instrument. The SIMS utilizes a Ga focused ion beam (FIB) combined with a quadrupole mass analyzer. The AFM is comprised of a 6-axis stage, three coarse axes and three fine. The coarse stage is used for placing the AFM tip anywhere inside a (13x13x5 mm3) (xyz) volume. Thus the tip can be moved in and out of the FIB processing region with ease. The planned range for the Z-axis piezo was 60 microm, but was reduced after it was damaged from arc events. The repaired Z-axis piezo is now operated at a smaller nominal range of 18 microm (16.7 microm after pre-loading), still quite respectable for an AFM. The noise floor of the AFM is approximately 0.4 nm Rq. The voxel size for the combined instrument is targeted at 50 nm or larger. Thus 0.4 nm of xyz uncertainty is acceptable. The instrument has been used for analyzing samples using FIB beam currents of 250 pA and 5.75 nA. Coarse tip approaches can take a long time so an abbreviated technique is employed. Because of the relatively long thro of the Z piezo, the tip can be disengaged by deactivating the servo PID. Once disengaged, it can be moved laterally out of the way of the FIB-SIMS using the coarse stage. This instrument has been used to acquire volumetric data on AlTiC using AFM tip diameters of 18.9 nm and 30.6 nm. Acquisition times are very long, requiring multiple days to acquire a 50-image stack. New features to be added include auto stigmation, auto beam shift, more software automation, etc. Longer term upgrades to include a new lower voltage Z-piezo with strain-gauge feedback and a new design to extend the life for the coarse XY nano-positioners. This AFM-SIMS instrument, as constructed, has proven to be a great proof

  7. SEM and AFM studies of dip-coated CuO nanofilms.

    PubMed

    Dhanasekaran, V; Mahalingam, T; Ganesan, V

    2013-01-01

    Cupric oxide (CuO) semiconducting thin films were prepared at various copper sulfate concentrations by dip coating. The copper sulfate concentration was varied to yield films of thicknesses in the range of 445-685 nm by surface profilometer. X-ray diffraction patterns revealed that the deposited films were polycrystalline in nature with monoclinic structure of (-111) plane. The surface morphology and topography of monoclinic-phase CuO thin films were examined using scanning electron microscopy (SEM) and atomic force microscopy (AFM), respectively. Surface roughness profile was plotted using WSxM software and the estimated surface roughness was about ∼19.4 nm at 30 mM molar concentration. The nanosheets shaped grains were observed by SEM and AFM studies. The stoichiometric compound formation was observed at 30 mM copper sulfate concentration prepared film by EDX. The indirect band gap energy of CuO films was increased from 1.08 to 1.20 eV with the increase of copper sulfate concentrations. Copyright © 2012 Wiley Periodicals, Inc.

  8. 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

  9. Application of focused ion beam for the fabrication of AFM probes

    NASA Astrophysics Data System (ADS)

    Kolomiytsev, A. S.; Lisitsyn, S. A.; Smirnov, V. A.; Fedotov, A. A.; Varzarev, Yu N.

    2017-10-01

    The results of an experimental study of the probe tips fabrication for critical-dimension atomic force microscopy (CD-AFM) using the focused ion beam (FIB) induced deposition are presented. Methods of the FIB-induced deposition of tungsten and carbon onto the tip of an AFM probe are studied. Based on the results obtained in the study, probes for the CD-AFM technique with a tip height about 1 μm and radius of 20 nm were created. The formation of CD-AFM probes by FIB-induced deposition allows creating a high efficiency tool for nanotechnology and nanodiagnostics. The use of modified cantilevers allows minimizing the artefacts of AFM images and increasing the accuracy of the relief measurement. The obtained results can be used for fabrication of AFM probes for express monitoring of the technological process in the manufacturing of the elements for micro- and nanoelectronics.

  10. 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.

  11. A quantitative AFM analysis of nano-scale surface roughness in various orthodontic brackets.

    PubMed

    Lee, Gi-Ja; Park, Ki-Ho; Park, Young-Guk; Park, Hun-Kuk

    2010-10-01

    In orthodontics, the surface roughnesses of orthodontic archwire and brackets affect the effectiveness of arch-guided tooth movement, corrosion behavior, and the aesthetics of orthodontic components. Atomic force microscopy (AFM) measurements were used to provide quantitative information on the surface roughness of the orthodontic material. In this study, the changes in surface roughness of various orthodontic bracket slots before and after sliding movement of archwire in vitro and in vivo were observed through the utilization of AFM. Firstly, we characterized the surface of four types of brackets slots as follows: conventional stainless steel (Succes), conventional ceramic (Perfect), self-ligating stainless steel (Damon) and self-ligating ceramic (Clippy-C) brackets. Succes) and Damon brackets showed relatively smooth surfaces, while Perfect had the roughest surface among the four types of brackets used. Secondly, after in vitro sliding test with beta titanium wire in two conventional brackets (Succes and Perfect), there were significant increases in only stainless steel bracket, Succes. Thirdly, after clinical orthodontic treatment for a maximum of 2 years, the self-ligating stainless steel bracket, Damon, showed a significant increase in surface roughness. But self-ligating ceramic brackets, Clippy-C, represented less significant changes in roughness parameters than self-ligating stainless steel ones. Based on the results of the AFM measurements, it is suggested that the self-ligating ceramic bracket has great possibility to exhibit less friction and better biocompatibility than the other tested brackets. This implies that these bracket slots will aid in the effectiveness of arch-guided tooth movement.

  12. Determination of Mechanical Properties of Spatially Heterogeneous Breast Tissue Specimens Using Contact Mode Atomic Force Microscopy (AFM)

    PubMed Central

    Roy, Rajarshi; Desai, Jaydev P.

    2016-01-01

    This paper outlines a comprehensive parametric approach for quantifying mechanical properties of spatially heterogeneous thin biological specimens such as human breast tissue using contact-mode Atomic Force Microscopy. Using inverse finite element (FE) analysis of spherical nanoindentation, the force response from hyperelastic material models is compared with the predicted force response from existing analytical contact models, and a sensitivity study is carried out to assess uniqueness of the inverse FE solution. Furthermore, an automation strategy is proposed to analyze AFM force curves with varying levels of material nonlinearity with minimal user intervention. Implementation of our approach on an elastic map acquired from raster AFM indentation of breast tissue specimens indicates that a judicious combination of analytical and numerical techniques allow more accurate interpretation of AFM indentation data compared to relying on purely analytical contact models, while keeping the computational cost associated an inverse FE solution with reasonable limits. The results reported in this study have several implications in performing unsupervised data analysis on AFM indentation measurements on a wide variety of heterogeneous biomaterials. PMID:25015130

  13. University of Maryland MRSEC - Facilities: SEM/STM/AFM

    Science.gov Websites

    MRSEC Templates Opportunities Search Home » Facilities » SEM/STM/AFM Shared Experimental Facilities conducting and non conducting samples. The sample stage permits electronic device imaging under operational Specifications: Image Modes - STM, STS, MFM, EFM, SKPM, contact- and non-contact AFM Three Sample Contacts 0.1 nm

  14. Analysis of effect of nanoporous alumina substrate coated with polypyrrole nanowire on cell morphology based on AFM topography.

    PubMed

    El-Said, Waleed Ahmed; Yea, Cheol-Heon; Jung, Mi; Kim, Hyuncheol; Choi, Jeong-Woo

    2010-05-01

    In this study, in situ electrochemical synthesis of polypyrrole nanowires with nanoporous alumina template was described. The formation of highly ordered porous alumina substrate was demonstrated with Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). In addition, Fourier transform infrared analysis confirmed that polypyrrole (PP) nanowires were synthesized by direct electrochemical oxidation of pyrrole. HeLa cancer cells and HMCF normal cells were immobilized on the polypyrrole nanowires/nanoporous alumina substrates to determine the effects of the substrate on the cell morphology, adhesion and proliferation as well as the biocompatibility of the substrate. Cell adhesion and proliferation were characterized using a standard MTT assay. The effects of the polypyrrole nanowires/nanoporous alumina substrate on the cell morphology were studied by AFM. The nanoporous alumina coated with polypyrrole nanowires was found to exhibit better cell adhesion and proliferation than polystyrene petridish, aluminum foil, 1st anodized and uncoated 2nd anodized alumina substrate. This study showed the potential of the polypyrrole nanowires/nanoporous alumina substrate as biocompatibility electroactive polymer substrate for both healthy and cancer cell cultures applications.

  15. Investigating Oil-Prone Kerogen Conversion to Hydrocarbons Using AFM-based Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Eoghan, D.; Cook, D.; Hackley, P. C.; Kjoller, K.; Dawson, D.; Shetty, R.

    2016-12-01

    Understanding in situ chemical changes occurring during thermal conversion of oil-prone kerogen to hydrocarbons can provide fundamental information regarding the origin of the earth's fossil fuel endowment and reduce uncertainty in hydrocarbon prospecting and resource assessment. Tasmanites algal bodies were studied using an Atomic Force Microscope-based IR spectroscopy technique (AFM-IR) that offers chemical characterization of organic materials with spatial resolution below the diffraction limit. The AFM allows precise positioning within the algal bodies. A tunable IR laser irradiates the sample under the AFM probe. At absorbing wavenumbers, the sample heats up and expands. The AFM detects the expansion of the material under the probe tip to generate local IR spectra. The Tasmanites algal bodies from the Devonian-Mississippian Woodford Shale were contained in two polished rock fragment pellets. To simulate maturation, one was subjected to isothermal hydrous pyrolysis at 320 °C for 72 hours. AFM-IR spectra were collected at multiple sites on algal bodies in both samples (Figure 1). The aromatic C=C ring stretching at 1600 cm-1 (unheated) shifted to 1606 cm-1 with increased absorption in the heated algal bodies, indicating development of increased aromaticity with thermal maturation. The ratio of the 1606 cm-1 peak to peaks at 1708 cm-1 (C=O stretching) and 1460 cm-1 (CH2 wag) was higher in the heated sample, indicating loss of oxygenated functional groups and aliphatic components with thermal advance. A shift of the 1372 cm-1 peak to 1376 cm-1 with lower absorption in the heated samples suggests reduction in the abundance of methyl substituents and development of preferred localization. These results are consistent with extant information from FTIR analysis and demonstrate the ability of AFM-IR to provide in situ characterization of organic matter with respect to thermal maturity advance, and its application to understanding conversion of oil-prone kerogen to

  16. Characterization of the interaction between AFM tips and surface nanobubbles.

    PubMed

    Walczyk, Wiktoria; Schönherr, Holger

    2014-06-24

    While the presence of gaseous enclosures observed at various solid-water interfaces, the so-called "surface nanobubles", has been confirmed by many groups in recent years, their formation, properties, and stability have not been convincingly and exhaustively explained. Here we report on an atomic force microscopy (AFM) study of argon nanobubbles on highly oriented pyrolitic graphite (HOPG) in water to elucidate the properties of nanobubble surfaces and the mechanism of AFM tip-nanobubble interaction. In particular, the deformation of the nanobubble-water interface by the AFM tip and the question whether the AFM tip penetrates the nanobubble during scanning were addressed by this combined intermittent contact (tapping) mode and force volume AFM study. We found that the stiffness of nanobubbles was smaller than the cantilever spring constant and comparable with the surface tension of water. The interaction with the AFM tip resulted in severe quasi-linear deformation of the bubbles; however, in the case of tip-bubble attraction, the interface deformed toward the tip. We tested two models of tip-bubble interaction, namely, the capillary force and the dynamic interaction model, and found, depending on the tip properties, good agreement with experimental data. The results showed that the tip-bubble interaction strength and the magnitude of the bubble deformation depend strongly on tip and bubble geometry and on tip and substrate material, and are very sensitive to the presence of contaminations that alter the interfacial tension. In particular, nanobubbles interacted differently with hydrophilic and hydrophobic AFM tips, which resulted in qualitatively and quantitatively different force curves measured on the bubbles in the experiments. To minimize bubble deformation and obtain reliable AFM results, nanobubbles must be measured with a sharp hydrophilic tip and with a cantilever having a very low spring constant in a contamination-free system.

  17. In-Process Atomic-Force Microscopy (AFM) Based Inspection

    PubMed Central

    Mekid, Samir

    2017-01-01

    A new in-process atomic-force microscopy (AFM) based inspection is presented for nanolithography to compensate for any deviation such as instantaneous degradation of the lithography probe tip. Traditional method used the AFM probes for lithography work and retract to inspect the obtained feature but this practice degrades the probe tip shape and hence, affects the measurement quality. This paper suggests a second dedicated lithography probe that is positioned back-to-back to the AFM probe under two synchronized controllers to correct any deviation in the process compared to specifications. This method shows that the quality improvement of the nanomachining, in progress probe tip wear, and better understanding of nanomachining. The system is hosted in a recently developed nanomanipulator for educational and research purposes. PMID:28561747

  18. Recent developments in dimensional nanometrology using AFMs

    NASA Astrophysics Data System (ADS)

    Yacoot, Andrew; Koenders, Ludger

    2011-12-01

    Scanning probe microscopes, in particular the atomic force microscope (AFM), have developed into sophisticated instruments that, throughout the world, are no longer used just for imaging, but for quantitative measurements. A role of the national measurement institutes has been to provide traceable metrology for these instruments. This paper presents a brief overview as to how this has been achieved, highlights the future requirements for metrology to support developments in AFM technology and describes work in progress to meet this need.

  19. High-resolution AFM structure of DNA G-wires in aqueous solution.

    PubMed

    Bose, Krishnashish; Lech, Christopher J; Heddi, Brahim; Phan, Anh Tuân

    2018-05-17

    We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G 4 T 2 G 4 ] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

  20. MDI: integrity index of cytoskeletal fibers observed by AFM

    NASA Astrophysics Data System (ADS)

    Manghi, Massimo; Bruni, Luca; Croci, Simonetta

    2016-06-01

    The Modified Directional Index (MDI) is a form factor of the angular spectrum computed from the 2D Fourier transform of an image marking the prevalence of rectilinear features throughout the picture. We study some properties of the index and we apply it to AFM images of cell cytoskeleton regions featuring patterns of rectilinear nearly parallel actin filaments as in the case of microfilaments grouped in bundles. The analysis of AFM images through MDI calculation quantifies the fiber directionality changes which could be related to fiber damages. This parameter is applied to the images of Hs 578Bst cell line, non-tumoral and not immortalized human epithelial cell line, irradiated with X-rays at doses equivalent to typical radiotherapy treatment fractions. In the reported samples, we could conclude that the damages are mainly born to the membrane and not to the cytoskeleton. It could be interesting to test the parameter also using other kinds of chemical or physical agents.

  1. 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.

  2. AFM probing in aqueous environment of Staphylococcus epidermidis cells naturally immobilised on glass: physico-chemistry behind the successful immobilisation.

    PubMed

    Méndez-Vilas, A; Gallardo-Moreno, A M; Calzado-Montero, R; González-Martín, M L

    2008-05-01

    AFM probing of microbial cells in liquid environments usually requires them to be physically or chemically attached to a solid surface. The fixation mechanisms may influence the nanomechanical characterization done by force curve mapping using an AFM. To study the response of a microbial cell surface to this kind of local measurement this study attempts to overcome the problem associated to the uncertainties introduced by the different fixation treatments by analysing the surface of Staphylococcus epidermidis cells naturally (non-artificially mediated) immobilised on a glass support surface. The particularities of this natural bacterial fixation process for AFM surface analysis are discussed in terms of theoretical predictions of the XDLVO model applied to the systems bacteria/support substratum and bacteria/AFM tip immersed in water. In this sense, in the first part of this study the conditions for adequate natural fixation of three S. epidermidis strains have been analyzed by taking into account the geometries of the bacterium, substrate and tip. In the second part, bacteria are probed without the risk of any possible artefacts due to the mechanical or chemical fixation procedures. Forces measured over the successfully adhered cells have (directly) shown that the untreated bacterial surface suffers from a combination of both reversible and non-reversible deformations during acquisition of force curves all taken under the same operational conditions. This is revealed directly through high-resolution tapping-mode imaging of the bacterial surface immediately following force curve mapping. The results agree with the two different types of force curves that were repeatedly obtained. Interestingly, one type of these force curves suggests that the AFM tip is breaking (rather than pushing) the cell surface during acquisition of the force curve. In this case, adhesive peaks were always observed, suggesting a mechanical origin of the measured pull-off forces. The other

  3. Design and Realization of 3D Printed AFM Probes.

    PubMed

    Alsharif, Nourin; Burkatovsky, Anna; Lissandrello, Charles; Jones, Keith M; White, Alice E; Brown, Keith A

    2018-05-01

    Atomic force microscope (AFM) probes and AFM imaging by extension are the product of exceptionally refined silicon micromachining, but are also restricted by the limitations of these fabrication techniques. Here, the nanoscale additive manufacturing technique direct laser writing is explored as a method to print monolithic cantilevered probes for AFM. Not only are 3D printed probes found to function effectively for AFM, but they also confer several advantages, most notably the ability to image in intermittent contact mode with a bandwidth approximately ten times larger than analogous silicon probes. In addition, the arbitrary structural control afforded by 3D printing is found to enable programming the modal structure of the probe, a capability that can be useful in the context of resonantly amplifying nonlinear tip-sample interactions. Collectively, these results show that 3D printed probes complement those produced using conventional silicon micromachining and open the door to new imaging techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Dehomogenized Elastic Properties of Heterogeneous Layered Materials in AFM Indentation Experiments.

    PubMed

    Lee, Jia-Jye; Rao, Satish; Kaushik, Gaurav; Azeloglu, Evren U; Costa, Kevin D

    2018-06-05

    Atomic force microscopy (AFM) is used to study mechanical properties of biological materials at submicron length scales. However, such samples are often structurally heterogeneous even at the local level, with different regions having distinct mechanical properties. Physical or chemical disruption can isolate individual structural elements but may alter the properties being measured. Therefore, to determine the micromechanical properties of intact heterogeneous multilayered samples indented by AFM, we propose the Hybrid Eshelby Decomposition (HED) analysis, which combines a modified homogenization theory and finite element modeling to extract layer-specific elastic moduli of composite structures from single indentations, utilizing knowledge of the component distribution to achieve solution uniqueness. Using finite element model-simulated indentation of layered samples with micron-scale thickness dimensions, biologically relevant elastic properties for incompressible soft tissues, and layer-specific heterogeneity of an order of magnitude or less, HED analysis recovered the prescribed modulus values typically within 10% error. Experimental validation using bilayer spin-coated polydimethylsiloxane samples also yielded self-consistent layer-specific modulus values whether arranged as stiff layer on soft substrate or soft layer on stiff substrate. We further examined a biophysical application by characterizing layer-specific microelastic properties of full-thickness mouse aortic wall tissue, demonstrating that the HED-extracted modulus of the tunica media was more than fivefold stiffer than the intima and not significantly different from direct indentation of exposed media tissue. Our results show that the elastic properties of surface and subsurface layers of microscale synthetic and biological samples can be simultaneously extracted from the composite material response to AFM indentation. HED analysis offers a robust approach to studying regional micromechanics of

  5. Accurate Calibration and Uncertainty Estimation of the Normal Spring Constant of Various AFM Cantilevers

    PubMed Central

    Song, Yunpeng; Wu, Sen; Xu, Linyan; Fu, Xing

    2015-01-01

    Measurement of force on a micro- or nano-Newton scale is important when exploring the mechanical properties of materials in the biophysics and nanomechanical fields. The atomic force microscope (AFM) is widely used in microforce measurement. The cantilever probe works as an AFM force sensor, and the spring constant of the cantilever is of great significance to the accuracy of the measurement results. This paper presents a normal spring constant calibration method with the combined use of an electromagnetic balance and a homemade AFM head. When the cantilever presses the balance, its deflection is detected through an optical lever integrated in the AFM head. Meanwhile, the corresponding bending force is recorded by the balance. Then the spring constant can be simply calculated using Hooke’s law. During the calibration, a feedback loop is applied to control the deflection of the cantilever. Errors that may affect the stability of the cantilever could be compensated rapidly. Five types of commercial cantilevers with different shapes, stiffness, and operating modes were chosen to evaluate the performance of our system. Based on the uncertainty analysis, the expanded relative standard uncertainties of the normal spring constant of most measured cantilevers are believed to be better than 2%. PMID:25763650

  6. Accurate calibration and uncertainty estimation of the normal spring constant of various AFM cantilevers.

    PubMed

    Song, Yunpeng; Wu, Sen; Xu, Linyan; Fu, Xing

    2015-03-10

    Measurement of force on a micro- or nano-Newton scale is important when exploring the mechanical properties of materials in the biophysics and nanomechanical fields. The atomic force microscope (AFM) is widely used in microforce measurement. The cantilever probe works as an AFM force sensor, and the spring constant of the cantilever is of great significance to the accuracy of the measurement results. This paper presents a normal spring constant calibration method with the combined use of an electromagnetic balance and a homemade AFM head. When the cantilever presses the balance, its deflection is detected through an optical lever integrated in the AFM head. Meanwhile, the corresponding bending force is recorded by the balance. Then the spring constant can be simply calculated using Hooke's law. During the calibration, a feedback loop is applied to control the deflection of the cantilever. Errors that may affect the stability of the cantilever could be compensated rapidly. Five types of commercial cantilevers with different shapes, stiffness, and operating modes were chosen to evaluate the performance of our system. Based on the uncertainty analysis, the expanded relative standard uncertainties of the normal spring constant of most measured cantilevers are believed to be better than 2%.

  7. Modeling the Interaction between AFM Tips and Pinned Surface Nanobubbles.

    PubMed

    Guo, Zhenjiang; Liu, Yawei; Xiao, Qianxiang; Schönherr, Holger; Zhang, Xianren

    2016-01-26

    Although the morphology of surface nanobubbles has been studied widely with different AFM modes, AFM images may not reflect the real shapes of the nanobubbles due to AFM tip-nanobubble interactions. In addition, the interplay between surface nanobubble deformation and induced capillary force has not been well understood in this context. In our work we used constraint lattice density functional theory to investigate the interaction between AFM tips and pinned surface nanobubbles systematically, especially concentrating on the effects of tip hydrophilicity and shape. For a hydrophilic tip contacting a nanobubble, its hydrophilic nature facilitates its departure from the bubble surface, displaying a weak and intermediate-range attraction. However, when the tip squeezes the nanobubble during the approach process, the nanobubble shows an elastic effect that prevents the tip from penetrating the bubble, leading to a strong nanobubble deformation and repulsive interactions. On the contrary, a hydrophobic tip can easily pierce the vapor-liquid interface of the nanobubble during the approach process, leading to the disappearance of the repulsive force. In the retraction process, however, the adhesion between the tip and the nanobubble leads to a much stronger lengthening effect on nanobubble deformation and a strong long-range attractive force. The trends of force evolution from our simulations agree qualitatively well with recent experimental AFM observations. This favorable agreement demonstrates that our model catches the main intergradient of tip-nanobubble interactions for pinned surface nanobubbles and may therefore provide important insight into how to design minimally invasive AFM experiments.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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.

  9. Applications of AFM for atomic manipulation and spectroscopy

    NASA Astrophysics Data System (ADS)

    Custance, Oscar

    2009-03-01

    Since the first demonstration of atom-by-atom assembly [1], atomic manipulation with scanning tunneling microscopy has yielded stunning realizations in nanoscience. A new exciting panorama has been recently opened with the possibility of manipulating atoms at surfaces using atomic force microscopy (AFM) [2-5]. In this talk, we will present two different approaches that enable patterning structures at semiconductor surfaces by manipulating individual atoms with AFM and at room temperature [2, 3]. We will discuss the physics behind each protocol through the analysis of the measured forces associated with these manipulations [3-5]. Another challenging issue in scanning probe microscopy is the ability to disclose the local chemical composition of a multi-element system at atomic level. Here, we will introduce a single-atom chemical identification method, which is based on detecting the forces between the outermost atom of the AFM tip and the atoms at a surface [6]. We demonstrate this identification procedure on a particularly challenging system, where any discrimination attempt based solely on topographic measurements would be impossible to achieve. [4pt] References: [0pt] [1] D. M. Eigler and E. K. Schweizer, Nature 344, 524 (1990); [0pt] [2] Y. Sugimoto, M. Abe, S. Hirayama, N. Oyabu, O. Custance and S. Morita, Nature Materials 4, 156 (2005); [0pt] [3] Y. Sugimoto, P. Pou, O. Custance, P. Jelinek, M. Abe, R. Perez and S. Morita, Science 322, 413 (2008); [0pt] [4] Y. Sugimoto, P. Jelinek, P. Pou, M. Abe, S. Morita, R. Perez and O. Custance, Phys. Rev. Lett. 98, 106104 (2007); [0pt] [5] M. Ternes, C. P. Lutz, C. F. Hirjibehedin, F. J. Giessibl and A. J. Heinrich, Science 319, 1066 (2008); [0pt] [6] Y. Sugimoto, P. Pou, M. Abe, P. Jelinek, R. Perez, S. Morita, and O. Custance, Nature 446, 64 (2007)

  10. 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

  11. Noise in NC-AFM measurements with significant tip-sample interaction.

    PubMed

    Lübbe, Jannis; Temmen, Matthias; Rahe, Philipp; Reichling, Michael

    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.

  12. Wettability of AFM tip influences the profile of interfacial nanobubbles

    NASA Astrophysics Data System (ADS)

    Teshima, Hideaki; Takahashi, Koji; Takata, Yasuyuki; Nishiyama, Takashi

    2018-02-01

    To accurately characterize the shape of interfacial nanobubbles using atomic force microscopy (AFM), we investigated the effect of wettability of the AFM tip while operating in the peak force tapping (PFT) mode. The AFM tips were made hydrophobic and hydrophilic by Teflon AF coating and oxygen plasma treatment, respectively. It was found that the measured base radius of nanobubbles differed between AFM height images and adhesion images, and that this difference depended on the tip wettability. The force curves obtained during the measurements were also different depending on the wettability, especially in the range of the tip/nanobubble interaction and in the magnitude of the maximum attractive force in the retraction period. The difference suggests that hydrophobic tips penetrate the gas/liquid interface of the nanobubbles, with the three phase contact line being pinned on the tip surface; hydrophilic tips on the other hand do not penetrate the interface. We then quantitatively estimated the pinning position and recalculated the true profiles of the nanobubbles by comparing the height images and adhesion images. As the AFM tip was made more hydrophilic, the penetration depth decreased and eventually approached zero. This result suggests that the PFT measurement using a hydrophilic tip is vital for the acquisition of reliable nanobubble profiles.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. AFM-based detection of glycocalyx degradation and endothelial stiffening in the db/db mouse model of diabetes.

    PubMed

    Targosz-Korecka, Marta; Jaglarz, Magdalena; Malek-Zietek, Katarzyna E; Gregorius, Aleksandra; Zakrzewska, Agnieszka; Sitek, Barbara; Rajfur, Zenon; Chlopicki, Stefan; Szymonski, Marek

    2017-11-21

    Degradation of the glycocalyx and stiffening of endothelium are important pathophysiological components of endothelial dysfunction. However, to our knowledge, these events have not been investigated in tandem in experimental diabetes. Here, the mechanical properties of the glycocalyx and endothelium in ex vivo mouse aorta were determined simultaneously in indentation experiments with an atomic force microscope (AFM) for diabetic db/db and control db/+ mice at ages of 11-19 weeks. To analyze highly heterogeneous aorta samples, we developed a tailored classification procedure of indentation data based on a bi-layer brush model supplemented with Hertz model for quantification of nanomechanics of endothelial regions with and without the glycocalyx surface. In db/db mice, marked endothelial stiffening and reduced glycocalyx coverage were present already in 11-week-old mice and persisted in older animals. In contrast, reduction of the effective glycocalyx length was progressive and was most pronounced in 19-week-old db/db mice. The reduction of the glycocalyx length correlated with an increasing level of glycated haemoglobin and decreased endothelial NO production. In conclusion, AFM nanoindentation analysis revealed that stiffening of endothelial cells and diminished glycocalyx coverage occurred in early diabetes and were followed by the reduction of the glycocalyx length that correlated with diabetes progression.

  18. Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

    NASA Astrophysics Data System (ADS)

    Jarvis, S. P.; Sweetman, A. M.; Lekkas, I.; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2015-02-01

    The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images.

  19. 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

  20. 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

  1. Membrane-based actuation for high-speed single molecule force spectroscopy studies using AFM.

    PubMed

    Sarangapani, Krishna; Torun, Hamdi; Finkler, Ofer; Zhu, Cheng; Degertekin, Levent

    2010-07-01

    Atomic force microscopy (AFM)-based dynamic force spectroscopy of single molecular interactions involves characterizing unbinding/unfolding force distributions over a range of pulling speeds. Owing to their size and stiffness, AFM cantilevers are adversely affected by hydrodynamic forces, especially at pulling speeds >10 microm/s, when the viscous drag becomes comparable to the unbinding/unfolding forces. To circumvent these adverse effects, we have fabricated polymer-based membranes capable of actuating commercial AFM cantilevers at speeds >or=100 microm/s with minimal viscous drag effects. We have used FLUENT, a computational fluid dynamics (CFD) software, to simulate high-speed pulling and fast actuation of AFM cantilevers and membranes in different experimental configurations. The simulation results support the experimental findings on a variety of commercial AFM cantilevers and predict significant reduction in drag forces when membrane actuators are used. Unbinding force experiments involving human antibodies using these membranes demonstrate that it is possible to achieve bond loading rates >or=10(6) pN/s, an order of magnitude greater than that reported with commercial AFM cantilevers and systems.

  2. 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.

  3. A phase 1 study of the bispecific anti-CD30/CD16A antibody construct AFM13 in patients with relapsed or refractory Hodgkin lymphoma

    PubMed Central

    Rothe, Achim; Sasse, Stephanie; Topp, Max S.; Eichenauer, Dennis A.; Hummel, Horst; Reiners, Katrin S.; Dietlein, Markus; Kuhnert, Georg; Kessler, Joerg; Buerkle, Carolin; Ravic, Miroslav; Knackmuss, Stefan; Marschner, Jens-Peter; Pogge von Strandmann, Elke; Borchmann, Peter

    2015-01-01

    AFM13 is a bispecific, tetravalent chimeric antibody construct (TandAb) designed for the treatment of CD30-expressing malignancies. AFM13 recruits natural killer (NK) cells via binding to CD16A as immune effector cells. In this phase 1 dose-escalation study, 28 patients with heavily pretreated relapsed or refractory Hodgkin lymphoma received AFM13 at doses of 0.01 to 7 mg/kg body weight. Primary objectives were safety and tolerability. Secondary objectives included pharmacokinetics, antitumor activity, and pharmacodynamics. Adverse events were generally mild to moderate. The maximum tolerated dose was not reached. Pharmacokinetics assessment revealed a half-life of up to 19 hours. Three of 26 evaluable patients achieved partial remission (11.5%) and 13 patients achieved stable disease (50%), with an overall disease control rate of 61.5%. AFM13 was also active in brentuximab vedotin–refractory patients. In 13 patients who received doses of ≥1.5 mg/kg AFM13, the overall response rate was 23% and the disease control rate was 77%. AFM13 treatment resulted in a significant NK-cell activation and a decrease of soluble CD30 in peripheral blood. In conclusion, AFM13 represents a well-tolerated, safe, and active targeted immunotherapy of Hodgkin lymphoma. A phase 2 study is currently planned to optimize the dosing schedule in order to further improve the therapeutic efficacy. This phase 1 study was registered at www.clinicaltrials.gov as #NCT01221571. PMID:25887777

  4. A phase 1 study of the bispecific anti-CD30/CD16A antibody construct AFM13 in patients with relapsed or refractory Hodgkin lymphoma.

    PubMed

    Rothe, Achim; Sasse, Stephanie; Topp, Max S; Eichenauer, Dennis A; Hummel, Horst; Reiners, Katrin S; Dietlein, Markus; Kuhnert, Georg; Kessler, Joerg; Buerkle, Carolin; Ravic, Miroslav; Knackmuss, Stefan; Marschner, Jens-Peter; Pogge von Strandmann, Elke; Borchmann, Peter; Engert, Andreas

    2015-06-25

    AFM13 is a bispecific, tetravalent chimeric antibody construct (TandAb) designed for the treatment of CD30-expressing malignancies. AFM13 recruits natural killer (NK) cells via binding to CD16A as immune effector cells. In this phase 1 dose-escalation study, 28 patients with heavily pretreated relapsed or refractory Hodgkin lymphoma received AFM13 at doses of 0.01 to 7 mg/kg body weight. Primary objectives were safety and tolerability. Secondary objectives included pharmacokinetics, antitumor activity, and pharmacodynamics. Adverse events were generally mild to moderate. The maximum tolerated dose was not reached. Pharmacokinetics assessment revealed a half-life of up to 19 hours. Three of 26 evaluable patients achieved partial remission (11.5%) and 13 patients achieved stable disease (50%), with an overall disease control rate of 61.5%. AFM13 was also active in brentuximab vedotin-refractory patients. In 13 patients who received doses of ≥1.5 mg/kg AFM13, the overall response rate was 23% and the disease control rate was 77%. AFM13 treatment resulted in a significant NK-cell activation and a decrease of soluble CD30 in peripheral blood. In conclusion, AFM13 represents a well-tolerated, safe, and active targeted immunotherapy of Hodgkin lymphoma. A phase 2 study is currently planned to optimize the dosing schedule in order to further improve the therapeutic efficacy. This phase 1 study was registered at www.clinicaltrials.gov as #NCT01221571. © 2015 by The American Society of Hematology.

  5. Structure, cell wall elasticity and polysaccharide properties of living yeast cells, as probed by AFM

    NASA Astrophysics Data System (ADS)

    Alsteens, David; Dupres, Vincent; McEvoy, Kevin; Wildling, Linda; Gruber, Hermann J.; Dufrêne, Yves F.

    2008-09-01

    Although the chemical composition of yeast cell walls is known, the organization, assembly, and interactions of the various macromolecules remain poorly understood. Here, we used in situ atomic force microscopy (AFM) in three different modes to probe the ultrastructure, cell wall elasticity and polymer properties of two brewing yeast strains, i.e. Saccharomyces carlsbergensis and S. cerevisiae. Topographic images of the two strains revealed smooth and homogeneous cell surfaces, and the presence of circular bud scars on dividing cells. Nanomechanical measurements demonstrated that the cell wall elasticity of S. carlsbergensis is homogeneous. By contrast, the bud scar of S. cerevisiae was found to be stiffer than the cell wall, presumably due to the accumulation of chitin. Notably, single molecule force spectroscopy with lectin-modified tips revealed major differences in polysaccharide properties of the two strains. Polysaccharides were clearly more extended on S. cerevisiae, suggesting that not only oligosaccharides, but also polypeptide chains of the mannoproteins were stretched. Consistent with earlier cell surface analyses, these findings may explain the very different aggregation properties of the two organisms. This study demonstrates the power of using multiple complementary AFM modalities for probing the organization and interactions of the various macromolecules of microbial cell walls.

  6. Measuring nanoscale viscoelastic parameters of cells directly from AFM force-displacement curves.

    PubMed

    Efremov, Yuri M; Wang, Wen-Horng; Hardy, Shana D; Geahlen, Robert L; Raman, Arvind

    2017-05-08

    Force-displacement (F-Z) curves are the most commonly used Atomic Force Microscopy (AFM) mode to measure the local, nanoscale elastic properties of soft materials like living cells. Yet a theoretical framework has been lacking that allows the post-processing of F-Z data to extract their viscoelastic constitutive parameters. Here, we propose a new method to extract nanoscale viscoelastic properties of soft samples like living cells and hydrogels directly from conventional AFM F-Z experiments, thereby creating a common platform for the analysis of cell elastic and viscoelastic properties with arbitrary linear constitutive relations. The method based on the elastic-viscoelastic correspondence principle was validated using finite element (FE) simulations and by comparison with the existed AFM techniques on living cells and hydrogels. The method also allows a discrimination of which viscoelastic relaxation model, for example, standard linear solid (SLS) or power-law rheology (PLR), best suits the experimental data. The method was used to extract the viscoelastic properties of benign and cancerous cell lines (NIH 3T3 fibroblasts, NMuMG epithelial, MDA-MB-231 and MCF-7 breast cancer cells). Finally, we studied the changes in viscoelastic properties related to tumorigenesis including TGF-β induced epithelial-to-mesenchymal transition on NMuMG cells and Syk expression induced phenotype changes in MDA-MB-231 cells.

  7. Hydration states of AFm cement phases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baquerizo, Luis G., E-mail: luis.baquerizoibarra@holcim.com; Matschei, Thomas; Scrivener, Karen L.

    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 AFmmore » 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.« less

  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. Revealing the hidden structural phases of FeRh

    NASA Astrophysics Data System (ADS)

    Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

    2016-11-01

    Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. Beyond topography - enhanced imaging of cometary dust with the MIDAS AFM

    NASA Astrophysics Data System (ADS)

    Bentley, M. S.; Torkar, K.; Jeszenszky, H.; Romstedt, J.

    2013-09-01

    The MIDAS atomic force microscope (AFM) onboard the Rosetta spacecraft is primarily designed to return the 3D shape and structure of cometary dust particles collected at comet 67P/Churyumov-Gerasimenko [1]. Commercial AFMs have, however, been further developed to measure many other sample properties. The possibilities to make such measurements with MIDAS are explored here.

  15. Physical-mechanical image of the cell surface on the base of AFM data in contact mode

    NASA Astrophysics Data System (ADS)

    Starodubtseva, M. N.; Starodubtsev, I. E.; Yegorenkov, N. I.; Kuzhel, N. S.; Konstantinova, E. E.; Chizhik, S. A.

    2017-10-01

    Physical and mechanical properties of the cell surface are well-known markers of a cell state. The complex of the parameters characterizing the cell surface properties, such as the elastic modulus (E), the parameters of adhesive (Fa), and friction (Ff) forces can be measured using atomic force microscope (AFM) in a contact mode and form namely the physical-mechanical image of the cell surface that is a fundamental element of the cell mechanical phenotype. The paper aims at forming the physical-mechanical images of the surface of two types of glutaraldehyde-fixed cancerous cells (human epithelial cells of larynx carcinoma, HEp-2c cells, and breast adenocarcinoma, MCF-7 cells) based on the data obtained by AFM in air and revealing the basic difference between them. The average values of friction, elastic and adhesive forces, and the roughness of lateral force maps, as well as dependence of the fractal dimension of lateral force maps on Z-scale factor have been studied. We have revealed that the response of microscale areas of the HEp-2c cell surface having numerous microvilli to external mechanical forces is less expressed and more homogeneous in comparison with the response of MCF-7 cell surface.

  16. Association between Urinary Aflatoxin (AFM1) and Dietary Intake among Adults in Hulu Langat District, Selangor, Malaysia

    PubMed Central

    Sulaiman, Siti Husna

    2018-01-01

    Aflatoxin is a food contaminant and its exposure through the diet is frequent and ubiquitous. A long-term dietary aflatoxin exposure has been linked to the development of liver cancer in populations with high prevalence of aflatoxin contamination in foods. Therefore, this study was conducted to identify the association between urinary aflatoxin M1 (AFM1), a biomarker of aflatoxin exposure, with the dietary intake among adults in Hulu Langat district, Selangor, Malaysia. Certain food products have higher potential for aflatoxin contamination and these were listed in a Food Frequency Questionnaire, which was given to all study participants. This allowed us to record consumption rates for each food product listed. Concomitantly, urine samples were collected, from adults in selected areas in Hulu Langat district, for the measurement of AFM1 levels using an ELISA kit. Of the 444 urine samples collected and tested, 199 were positive for AFM1, with 37 of them exceeding the limit of detection (LOD) of 0.64 ng/mL. Cereal products showed the highest consumption level among all food groups, with an average intake of 512.54 g per day. Chi-square analysis showed that consumption of eggs (X2 = 4.77, p = 0.03) and dairy products (X2 = 19.36, p < 0.01) had significant associations with urinary AFM1 but both food groups were having a phi and Cramer’s V value that less than 0.3, which indicated that the association between these food groups’ consumption and AFM1 level in urine was weak. PMID:29642443

  17. Pinning effects from substrate and AFM tip surfaces on interfacial nanobubbles

    NASA Astrophysics Data System (ADS)

    Teshima, Hideaki; Takahashi, Koji; Takata, Yasuyuki; Nishiyama, Takashi

    2017-11-01

    Measurement accuracy of atomic force microscopy (AFM) is vital to understand the mechanism of interfacial nanobubbles. In this study, we report the influence of pinning derived from both substrate and AFM tip surfaces on the measured shape of interfacial nanobubbles in peak force tapping mode. First, we pushed the nanobubbles using the AFM tip with high peak force setpoint. As a result, the deformed nanobubbles kept their flat shape for several tens of minutes. We quantitatively discuss the pinning force from substrate surface, which retains the flat shape enhancing the stability of nanobubbles. Next, we prepared three AFM tips with different wettability and measured the nanobubbles with an identical setpoint. By comparing the force curves obtained during the measurements, it seems that the (middle-)hydrophobic tips penetrated the liquid/gas interface and received repulsive force resulting from positive meniscus formed by pinning at the tip surface. In contrast, hydrophilic tip didn't penetrate the interface and received the force from the deformation of the interface of the nanobubbles. In addition, the measurements using the (middle-)hydrophobic tips led to the underestimation of the nanobubbles profile corresponding to the pinning position at the tip surfaces.

  18. The Atomic Force Microscopic (AFM) Characterization of Nanomaterials

    DTIC Science & Technology

    2009-06-01

    Several Types of Microscopes ..................................................................................................7 8 OM on Mica Surface...12 9 AFM on Mica Surface...12 10 OM Images SWNTs on Mica After 1) 30 Minutes, b) 60

  19. Joint Research on Scatterometry and AFM Wafer Metrology

    NASA Astrophysics Data System (ADS)

    Bodermann, Bernd; Buhr, Egbert; Danzebrink, Hans-Ulrich; Bär, Markus; Scholze, Frank; Krumrey, Michael; Wurm, Matthias; Klapetek, Petr; Hansen, Poul-Erik; Korpelainen, Virpi; van Veghel, Marijn; Yacoot, Andrew; Siitonen, Samuli; El Gawhary, Omar; Burger, Sven; Saastamoinen, Toni

    2011-11-01

    Supported by the European Commission and EURAMET, a consortium of 10 participants from national metrology institutes, universities and companies has started a joint research project with the aim of overcoming current challenges in optical scatterometry for traceable linewidth metrology. Both experimental and modelling methods will be enhanced and different methods will be compared with each other and with specially adapted atomic force microscopy (AFM) and scanning electron microscopy (SEM) measurement systems in measurement comparisons. Additionally novel methods for sophisticated data analysis will be developed and investigated to reach significant reductions of the measurement uncertainties in critical dimension (CD) metrology. One final goal will be the realisation of a wafer based reference standard material for calibration of scatterometers.

  20. An AFM-based pit-measuring method for indirect measurements of cell-surface membrane vesicles

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Xiaojun; Department of Biotechnology, Nanchang University, Nanchang, Jiangxi 330031; Chen, Yuan

    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)more » 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.« less

  1. Application of Contact Mode AFM to Manufacturing Processes

    NASA Astrophysics Data System (ADS)

    Giordano, Michael A.; Schmid, Steven R.

    A review of the application of contact mode atomic force microscopy (AFM) to manufacturing processes is presented. A brief introduction to common experimental techniques including hardness, scratch, and wear testing is presented, with a discussion of challenges in the extension of manufacturing scale investigations to the AFM. Differences between the macro- and nanoscales tests are discussed, including indentation size effects and their importance in the simulation of processes such as grinding. The basics of lubrication theory are presented and friction force microscopy is introduced as a method of investigating metal forming lubrication on the nano- and microscales that directly simulates tooling/workpiece asperity interactions. These concepts are followed by a discussion of their application to macroscale industrial manufacturing processes and direct correlations are made.

  2. Estimation of polymer-surface interfacial interaction strength by a contact AFM technique.

    PubMed

    Dvir, H; Jopp, J; Gottlieb, M

    2006-12-01

    Atomic force microscopy (AFM) measurements were employed to assess polymer-surface interfacial interaction strength. The main feature of the measurement is the use of contact-mode AFM as a tool to scratch off the polymer monolayer adsorbed on the solid surface. Tapping-mode AFM was used to determine the depth of the scraped recess. Independent determination of the layer thickness obtained from optical phase interference microscopy (OPIM) confirmed the depth of the AFM scratch. The force required for the complete removal of the polymer layer with no apparent damage to the substrate surface was determined. Polypropylene (PP), low-density polyethylene (PE), and PP-grafted-maleic anhydride (PP-g-ma) were scraped off silane-treated glass slabs, and the strength of surface interaction of the polymer layer was determined. In all cases it was determined that the magnitude of surface interaction force is of the order of van der Waals (VDW) interactions. The interaction strength is influenced either by polymer ability to wet the surface (hydrophobic or hydrophilic interactions) or by hydrogen bonding between the polymer and the surface treatment.

  3. Finite element modeling of trolling-mode AFM.

    PubMed

    Sajjadi, Mohammadreza; Pishkenari, Hossein Nejat; Vossoughi, Gholamreza

    2018-06-01

    Trolling mode atomic force microscopy (TR-AFM) has overcome many imaging problems in liquid environments by considerably reducing the liquid-resonator interaction forces. The finite element model of the TR-AFM resonator considering the effects of fluid and nanoneedle flexibility is presented in this research, for the first time. The model is verified by ABAQUS software. The effect of installation angle of the microbeam relative to the horizon and the effect of fluid on the system behavior are investigated. Using the finite element model, frequency response curve of the system is obtained and validated around the frequency of the operating mode by the available experimental results, in air and liquid. The changes in the natural frequencies in the presence of liquid are studied. The effects of tip-sample interaction on the excitation of higher order modes of the system are also investigated in air and liquid environments. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Fast and controlled fabrication of porous graphene oxide: application of AFM tapping for mechano-chemistry

    NASA Astrophysics Data System (ADS)

    Chu, Liangyong; Korobko, Alexander V.; Bus, Marcel; Boshuizen, Bart; Sudhölter, Ernst J. R.; Besseling, Nicolaas A. M.

    2018-05-01

    This paper describes a novel method to fabricate porous graphene oxide (PGO) from GO by exposure to oxygen plasma. Compared to other methods to fabricate PGO described so far, e.g. the thermal and steam etching methods, oxygen plasma etching method is much faster. We studied the development of the porosity with exposure time using atomic force microscopy (AFM). It was found that the development of PGO upon oxygen-plasma exposure can be controlled by tapping mode AFM scanning using a Si tip. AFM tapping stalls the growth of pores upon further plasma exposure at a level that coincides with the fraction of sp2 carbons in the GO starting material. We suggest that AFM tapping procedure changes the bond structure of the intermediate PGO structure, and these stabilized PGO structures cannot be further etched by oxygen plasma. This constitutes the first report of tapping AFM as a tool for local mechano-chemistry.

  5. Fast and controlled fabrication of porous graphene oxide: application of AFM tapping for mechano-chemistry.

    PubMed

    Chu, Liangyong; Korobko, Alexander V; Bus, Marcel; Boshuizen, Bart; Sudhölter, Ernst J R; Besseling, Nicolaas A M

    2018-05-04

    This paper describes a novel method to fabricate porous graphene oxide (PGO) from GO by exposure to oxygen plasma. Compared to other methods to fabricate PGO described so far, e.g. the thermal and steam etching methods, oxygen plasma etching method is much faster. We studied the development of the porosity with exposure time using atomic force microscopy (AFM). It was found that the development of PGO upon oxygen-plasma exposure can be controlled by tapping mode AFM scanning using a Si tip. AFM tapping stalls the growth of pores upon further plasma exposure at a level that coincides with the fraction of sp 2 carbons in the GO starting material. We suggest that AFM tapping procedure changes the bond structure of the intermediate PGO structure, and these stabilized PGO structures cannot be further etched by oxygen plasma. This constitutes the first report of tapping AFM as a tool for local mechano-chemistry.

  6. [Coupling AFM fluid imaging with micro-flocculation filtration process for the technological optimization].

    PubMed

    Zheng, Bei; Ge, Xiao-peng; Yu, Zhi-yong; Yuan, Sheng-guang; Zhang, Wen-jing; Sun, Jing-fang

    2012-08-01

    Atomic force microscope (AFM) fluid imaging was applied to the study of micro-flocculation filtration process and the optimization of micro-flocculation time and the agitation intensity of G values. It can be concluded that AFM fluid imaging proves to be a promising tool in the observation and characterization of floc morphology and the dynamic coagulation processes under aqueous environmental conditions. Through the use of AFM fluid imaging technique, optimized conditions for micro-flocculation time of 2 min and the agitation intensity (G value) of 100 s(-1) were obtained in the treatment of dye-printing industrial tailing wastewater by the micro-flocculation filtration process with a good performance.

  7. 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.

  8. AFM Studies of Lunar Soils and Application to the Mars 2001 Mission

    NASA Technical Reports Server (NTRS)

    Weitz, C. M.; Anderson, M. S.; Marshall, J.

    1999-01-01

    The upcoming Mars 01 mission will carry an Atomic Force Microscope (AFM) as part of the Mars Environmental Compatibility Assessment (MECA) instrument. By operating in a tapping mode, the AFM is capable of sub-nanometer resolution in three dimensions and can distinguish between substances of different compositions by employing phase contrast imaging. To prepare for the Mars 01 mission, we are testing the AFM on a lunar soil to determine its ability to define particle shapes and sizes and grain-surface textures. The test materials are from the Apollo 17 soil 79221, which is a mixture of agglutinates, impact and volcanic beads, and mare and highland rock and mineral fragments. The majority of the lunar soil particles are less than 100 microns in size, comparable to the sizes estimated for martian dust. We have used the AFM to examine several different soil particles at various resolutions. The instrument has demonstrated the ability to identify parallel ridges characteristic of twinning on a 150 micron plagioclase feldspar particle. Extremely small (10-100 nanometer) adhering particles are visible on the surface of the feldspar grain, and they appear elongate with smooth surfaces. Phase contrast imaging of the nanometer particles shows several compositions to be present. When the AFM was applied to a 100 micron glass spherule, it was possible to define an extremely smooth surface; this is in clear contrast to results from a basalt fragment which exhibited a rough surface texture. Also visible on the surface of the glass spherule were chains of 100 nanometer and smaller impact melt droplets. For the '01 Mars mission, the AFM is intended to define the size and shape distributions of soil particles, in combination with the NMCA optical microscope system and images from the Robot Arm Camera (RAC). These three data sets will provide a means of assessing potentially hazardous soil and dust properties. The study that we have conducted on the lunar soils now suggests that the

  9. AFMS Flight Path: Building Future Leaders

    DTIC Science & Technology

    2009-02-12

    small numbers of deactivated squadrons were reactivated. In general, the Flight Path maintains the four squadron framework of OMG with an additional...MC fill all but two. Vast differences in rank and promotion rates further bias the AFMS to a non-DOPMA corps led entity . The Flight Path has done...Aeromedical Squadron (AMDS) can combine into an Aeromedical Dental Squadron ( ADOS ) or can reside as flights under the Medical Operations Squadron

  10. 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

  11. 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.

  12. AFM-porosimetry: density and pore volume measurements of particulate materials.

    PubMed

    Sörensen, Malin H; Valle-Delgado, Juan J; Corkery, Robert W; Rutland, Mark W; Alberius, Peter C

    2008-06-01

    We introduced the novel technique of AFM-porosimetry and applied it to measure the total pore volume of porous particles with a spherical geometry. The methodology is based on using an atomic force microscope as a balance to measure masses of individual particles. Several particles within the same batch were measured, and by plotting particle mass versus particle volume, the bulk density of the sample can be extracted from the slope of the linear fit. The pore volume is then calculated from the densities of the bulk and matrix materials, respectively. In contrast to nitrogen sorption and mercury porosimetry, this method is capable of measuring the total pore volume regardless of pore size distribution and pore connectivity. In this study, three porous samples were investigated by AFM-porosimetry: one ordered mesoporous sample and two disordered foam structures. All samples were based on a matrix of amorphous silica templated by a block copolymer, Pluronic F127, swollen to various degrees with poly(propylene glycol). In addition, the density of silica spheres without a template was measured by two independent techniques: AFM and the Archimedes principle.

  13. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. AFM and SFG studies of pHEMA-based hydrogel contact lens surfaces in saline solution: adhesion, friction, and the presence of non-crosslinked polymer chains at the surface.

    PubMed

    Kim, Seong Han; Opdahl, Aric; Marmo, Chris; Somorjai, Gabor A

    2002-04-01

    The surfaces of two types of soft contact lenses neutral and ionic hydrogels--were characterized by atomic force microscopy (AFM) and sum-frequency-generation (SFG) vibrational spectroscopy. AFM measurements in saline solution showed that the presence of ionic functional groups at the surface lowered the friction and adhesion to a hydrophobic polystyrene tip. This was attributed to the specific interactions of water and the molecular orientation of hydrogel chains at the surface. Friction and adhesion behavior also revealed the presence of domains of non-crosslinked polymer chains at the lens surface. SFG showed that the lens surface became partially dehydrated upon exposure to air. On this partially dehydrated lens surface, the non-crosslinked domains exhibited low friction and adhesion in AFM. Fully hydrated in saline solution, the non-crosslinked domains extended more than tens of nanometers into solution and were mobile.

  15. 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).

  16. Tip-enhanced Raman mapping with top-illumination AFM.

    PubMed

    Chan, K L Andrew; Kazarian, Sergei G

    2011-04-29

    Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of ∼ 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

  17. Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

    PubMed

    Edwards, Devin T; Faulk, Jaevyn K; LeBlanc, Marc-André; Perkins, Thomas T

    2017-12-19

    Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm 2 cantilever into one terminated with a gold-coated, 4 × 4 μm 2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM. Published by Elsevier Inc.

  18. 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.

  19. 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

  20. Microfluidic chip for non-invasive analysis of tumor cells interaction with anti-cancer drug doxorubicin by AFM and Raman spectroscopy.

    PubMed

    Zhang, Han; Xiao, Lifu; Li, Qifei; Qi, Xiaojun; Zhou, Anhong

    2018-03-01

    Raman spectroscopy has been playing an increasingly significant role for cell classification. Here, we introduce a novel microfluidic chip for non-invasive Raman cell natural fingerprint collection. Traditional Raman spectroscopy measurement of the cells grown in a Polydimethylsiloxane (PDMS) based microfluidic device suffers from the background noise from the substrate materials of PDMS when intended to apply as an in vitro cell assay. To overcome this disadvantage, the current device is designed with a middle layer of PDMS layer sandwiched by two MgF 2 slides which minimize the PDMS background signal in Raman measurement. Three cancer cell lines, including a human lung cancer cell A549, and human breast cancer cell lines MDA-MB-231 and MDA-MB-231/BRMS1, were cultured in this microdevice separately for a period of three days to evaluate the biocompatibility of the microfluidic system. In addition, atomic force microscopy (AFM) was used to measure the Young's modulus and adhesion force of cancer cells at single cell level. The AFM results indicated that our microchannel environment did not seem to alter the cell biomechanical properties. The biochemical responses of cancer cells exposed to anti-cancer drug doxorubicin (DOX) up to 24 h were assessed by Raman spectroscopy. Principal component analysis over the Raman spectra indicated that cancer cells untreated and treated with DOX can be distinguished. This PDMS microfluidic device offers a non-invasive and reusable tool for in vitro Raman measurement of living cells, and can be potentially applied for anti-cancer drug screening.

  1. 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.

  2. 3D Nanofabrication Using AFM-Based Ultrasonic Vibration Assisted Nanomachining

    NASA Astrophysics Data System (ADS)

    Deng, Jia

    Nanolithography and nanofabrication processes have significant impact on the recent development of fundamental research areas such as physics, chemistry and biology, as well as the modern electronic devices that have reached nanoscale domain such as optoelectronic devices. Many advanced nanofabrication techniques have been developed and reported to satisfy different requirements in both research areas and applications such as electron-beam lithography. However, it is expensive to use and maintain the equipment. Atomic Force Microscope (AFM) based nanolithography processes provide an alternative approach to nanopatterning with significantly lower cost. Recently, three dimensional nanostructures have attracted a lot of attention, motivated by many applications in various fields including optics, plasmonics and nanoelectromechanical systems. AFM nanolithography processes are able to create not only two dimensional nanopatterns but also have the great potential to fabricate three dimensional nanostructures. The objectives of this research proposal are to investigate the capability of AFM-based three dimensional nanofabrication processes, to transfer the three dimensional nanostructures from resists to silicon surfaces and to use the three dimensional nanostructures on silicon in applications. Based on the understanding of literature, a novel AFM-based ultrasonic vibration assisted nanomachining system is utilized to develop three dimensional nanofabrication processes. In the system, high-frequency in plane circular xy-vibration was introduced to create a virtual tool, whose diameter is controlled by the amplitude of xy-vibration and is larger than that of a regular AFM tip. Therefore, the feature width of a single trench is tunable. Ultrasonic vibration of sample in z-direction was introduced to control the depth of single trenches, creating a high-rate 3D nanomachining process. Complicated 3D nanostructures on PMMA are fabricated under both the setpoint force and z

  3. AFM study of adsorption of protein A on a poly(dimethylsiloxane) surface

    NASA Astrophysics Data System (ADS)

    Yu, Ling; Lu, Zhisong; Gan, Ye; Liu, Yingshuai; Li, Chang Ming

    2009-07-01

    In this paper, the morphology and kinetics of adsorption of protein A on a PDMS surface is studied by AFM. The results of effects of pH, protein concentration and contact time of the adsorption reveal that the morphology of adsorbed protein A is significantly affected by pH and adsorbed surface concentration, in which the pH away from the isoelectric point (IEP) of protein A could produce electrical repulsion to change the protein conformation, while the high adsorbed surface protein volume results in molecular networks. Protein A can form an adsorbed protein film on PDMS with a maximum volume of 2.45 × 10-3 µm3. This work enhances our fundamental understanding of protein A adsorption on PDMS, a frequently used substrate component in miniaturized immunoassay devices.

  4. Simultaneous noncontact AFM and STM of Ag:Si(111)-(3×3)R30∘

    NASA Astrophysics Data System (ADS)

    Sweetman, Adam; Stannard, Andrew; Sugimoto, Yoshiaki; Abe, Masayuki; Morita, Seizo; Moriarty, Philip

    2013-02-01

    The Ag:Si(111)-(3×3)R30∘ surface structure has attracted considerable debate concerning interpretation of scanning tunneling microscope (STM) and noncontact atomic force microscope (NC-AFM) images. In particular, the accepted interpretation of atomic resolution images in NC-AFM has been questioned by theoretical and STM studies. In this paper, we use combined NC-AFM and STM to conclusively show that the inequivalent trimer (IET) configuration best describes the surface ground state. Thermal-averaging effects result in a honeycomb-chained-trimer (HCT) appearance at room temperature, in contrast to studies suggesting that the IET configuration remains stable at higher temperatures [Zhang, Gustafsson, and Johansson, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.201304 74, 201304(R) (2006) and J. Phys.: Conf. Ser.1742-658810.1088/1742-6596/61/1/264 61, 1336 (2007)]. We also comment on results obtained at an intermediate temperature that suggest an intriguing difference between the imaging mechanisms of NC-AFM and STM on structurally fluctuating samples.

  5. Restoration of high-resolution AFM images captured with broken probes

    NASA Astrophysics Data System (ADS)

    Wang, Y. F.; Corrigan, D.; Forman, C.; Jarvis, S.; Kokaram, A.

    2012-03-01

    A type of artefact is induced by damage of the scanning probe when the Atomic Force Microscope (AFM) captures a material surface structure with nanoscale resolution. This artefact has a dramatic form of distortion rather than the traditional blurring artefacts. Practically, it is not easy to prevent the damage of the scanning probe. However, by using natural image deblurring techniques in image processing domain, a comparatively reliable estimation of the real sample surface structure can be generated. This paper introduces a novel Hough Transform technique as well as a Bayesian deblurring algorithm to remove this type of artefact. The deblurring result is successful at removing blur artefacts in the AFM artefact images. And the details of the fibril surface topography are well preserved.

  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. The effect of PeakForce tapping mode AFM imaging on the apparent shape of surface nanobubbles.

    PubMed

    Walczyk, Wiktoria; Schön, Peter M; Schönherr, Holger

    2013-05-08

    Until now, TM AFM (tapping mode or intermittent contact mode atomic force microscopy) has been the most often applied direct imaging technique to analyze surface nanobubbles at the solid-aqueous interface. While the presence and number density of nanobubbles can be unequivocally detected and estimated, it remains unclear how much the a priori invasive nature of AFM affects the apparent shapes and dimensions of the nanobubbles. To be able to successfully address the unsolved questions in this field, the accurate knowledge of the nanobubbles' dimensions, radii of curvature etc is necessary. In this contribution we present a comparative study of surface nanobubbles on HOPG (highly oriented pyrolytic graphite) in water acquired with (i) TM AFM and (ii) the recently introduced PFT (PeakForce tapping) mode, in which the force exerted on the nanobubbles rather than the amplitude of the resonating cantilever is used as the AFM feedback parameter during imaging. In particular, we analyzed how the apparent size and shape of nanobubbles depend on the maximum applied force in PFT AFM. Even for forces as small as 73 pN, the nanobubbles appeared smaller than their true size, which was estimated from an extrapolation of the bubble height to zero applied force. In addition, the size underestimation was found to be more pronounced for larger bubbles. The extrapolated true nanoscopic contact angles for nanobubbles on HOPG, measured in PFT AFM, ranged from 145° to 175° and were only slightly underestimated by scanning with non-zero forces. This result was comparable to the nanoscopic contact angles of 160°-175° measured using TM AFM in the same set of experiments. Both values disagree, in accordance with the literature, with the macroscopic contact angle of water on HOPG, measured here to be 63° ± 2°.

  8. High-stress study of bioinspired multifunctional PEDOT:PSS/nanoclay nanocomposites using AFM, SEM and numerical simulation.

    PubMed

    Diaz, Alfredo J; Noh, Hanaul; Meier, Tobias; Solares, Santiago D

    2017-01-01

    Bioinspired design has been central in the development of hierarchical nanocomposites. Particularly, the nacre-mimetic brick-and-mortar structure has shown excellent mechanical properties, as well as gas-barrier properties and optical transparency. Along with these intrinsic properties, the layered structure has also been utilized in sensing devices. Here we extend the multifunctionality of nacre-mimetics by designing an optically transparent and electron conductive coating based on PEDOT:PSS and nanoclays Laponite RD and Cloisite Na + . We carry out extensive characterization of the nanocomposite using transmittance spectra (transparency), conductive atomic force microscopy (conductivity), contact-resonance force microscopy (mechanical properties), and SEM combined with a variety of stress-strain AFM experiments and AFM numerical simulations (internal structure). We further study the nanoclay's response to the application of pressure with multifrequency AFM and conductive AFM, whereby increases and decreases in conductivity can occur for the Laponite RD composites. We offer a possible mechanism to explain the changes in conductivity by modeling the coating as a 1-dimensional multibarrier potential for electron transport, and show that conductivity can change when the separation between the barriers changes under the application of pressure, and that the direction of the change depends on the energy of the electrons. We did not observe changes in conductivity under the application of pressure with AFM for the Cloisite Na + nanocomposite, which has a large platelet size compared with the AFM probe diameter. No pressure-induced changes in conductivity were observed in the clay-free polymer either.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 amore » 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.« less

  10. The detection of hepatitis c virus core antigen using afm chips with immobolized aptamers.

    PubMed

    Pleshakova, T O; Kaysheva, A L; Bayzyanova, J М; Anashkina, А S; Uchaikin, V F; Ziborov, V S; Konev, V A; Archakov, A I; Ivanov, Y D

    2018-01-01

    In the present study, the possibility of hepatitis C virus core antigen (HCVcoreAg) detection in buffer solution, using atomic force microscope chip (AFM-chip) with immobilized aptamers, has been demonstrated. The target protein was detected in 1mL of solution at concentrations from 10 -10 М to 10 -13 М. The registration of aptamer/antigen complexes on the chip surface was carried out by atomic force microscopy (AFM). The further mass-spectrometric (MS) identification of AFM-registered objects on the chip surface allowed reliable identification of HCVcoreAg target protein in the complexes. Aptamers, which were designed for therapeutic purposes, have been shown to be effective in HCVcoreAg detection as probe molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Metrological AFMs and its application for versatile nano-dimensional metrology tasks

    NASA Astrophysics Data System (ADS)

    Dai, Gaoliang; Dziomba, T.; Pohlenz, F.; Danzebrink, H.-U.; Koenders, L.

    2010-08-01

    Traceable calibrations of various micro and nano measurement devices are crucial tasks for ensuring reliable measurements for micro and nanotechnology. Today metrological AFM are widely used for traceable calibrations of nano dimensional standards. In this paper, we introduced the developments of metrological force microscopes at PTB. Of the three metrological AFMs described here, one is capable of measuring in a volume of 25 mm x 25 mm x 5 mm. All instruments feature interferometers and the three-dimensional position measurements are thus directly traceable to the metre definition. Some calibration examples on, for instance, flatness standards, step height standards, one and two dimensional gratings are demonstrated.

  12. 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

  13. Crystal structures of Boro-AFm and sBoro-AFt phases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Champenois, Jean-Baptiste; Mesbah, Adel; Clermont Universite, ENSCCF, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand

    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 themore » 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.« less

  14. QCM-D on mica for parallel QCM-D-AFM studies.

    PubMed

    Richter, Ralf P; Brisson, Alain

    2004-05-25

    Quartz crystal microbalance with dissipation monitoring (QCM-D) has developed into a recognized method to study adsorption processes in liquid, such as the formation of supported lipid bilayers and protein adsorption. However, the large intrinsic roughness of currently used gold-coated or silica-coated QCM-D sensors limits parallel structural characterization by atomic force microscopy (AFM). We present a method for coating QCM-D sensors with thin mica sheets operating in liquid with high stability and sensitivity. We define criteria to objectively assess the reliability of the QCM-D measurements and demonstrate that the mica-coated sensors can be used to follow the formation of supported lipid membranes and subsequent protein adsorption. This method allows combining QCM-D and AFM investigations on identical supports, providing detailed physicochemical and structural characterization of model membranes.

  15. Silicon nanowires reliability and robustness investigation using AFM-based techniques

    NASA Astrophysics Data System (ADS)

    Bieniek, Tomasz; Janczyk, Grzegorz; Janus, Paweł; Grabiec, Piotr; Nieprzecki, Marek; Wielgoszewski, Grzegorz; Moczała, Magdalena; Gotszalk, Teodor; Buitrago, Elizabeth; Badia, Montserrat F.; Ionescu, Adrian M.

    2013-07-01

    Silicon nanowires (SiNWs) have undergone intensive research for their application in novel integrated systems such as field effect transistor (FET) biosensors and mass sensing resonators profiting from large surface-to-volume ratios (nano dimensions). Such devices have been shown to have the potential for outstanding performances in terms of high sensitivity, selectivity through surface modification and unprecedented structural characteristics. This paper presents the results of mechanical characterization done for various types of suspended SiNWs arranged in a 3D array. The characterization has been performed using techniques based on atomic force microscopy (AFM). This investigation is a necessary prerequisite for the reliable and robust design of any biosensing system. This paper also describes the applied investigation methodology and reports measurement results aggregated during series of AFM-based tests.

  16. 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

  17. Ultra-high aspect ratio replaceable AFM tips using deformation-suppressed focused ion beam milling.

    PubMed

    Savenko, Alexey; Yildiz, Izzet; Petersen, Dirch Hjorth; Bøggild, Peter; Bartenwerfer, Malte; Krohs, Florian; Oliva, Maria; Harzendorf, Torsten

    2013-11-22

    Fabrication of ultra-high aspect ratio exchangeable and customizable tips for atomic force microscopy (AFM) using lateral focused ion beam (FIB) milling is presented. While on-axis FIB milling does allow high aspect ratio (HAR) AFM tips to be defined, lateral milling gives far better flexibility in terms of defining the shape and size of the tip. Due to beam-induced deformation, it has so far not been possible to define HAR structures using lateral FIB milling. In this work we obtain aspect ratios of up to 45, with tip diameters down to 9 nm, by a deformation-suppressing writing strategy. Several FIB milling strategies for obtaining sharper tips are discussed. Finally, assembly of the HAR tips on a custom-designed probe as well as the first AFM scanning is shown.

  18. 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).

  19. High-stress study of bioinspired multifunctional PEDOT:PSS/nanoclay nanocomposites using AFM, SEM and numerical simulation

    PubMed Central

    Diaz, Alfredo J; Noh, Hanaul; Meier, Tobias

    2017-01-01

    Bioinspired design has been central in the development of hierarchical nanocomposites. Particularly, the nacre-mimetic brick-and-mortar structure has shown excellent mechanical properties, as well as gas-barrier properties and optical transparency. Along with these intrinsic properties, the layered structure has also been utilized in sensing devices. Here we extend the multifunctionality of nacre-mimetics by designing an optically transparent and electron conductive coating based on PEDOT:PSS and nanoclays Laponite RD and Cloisite Na+. We carry out extensive characterization of the nanocomposite using transmittance spectra (transparency), conductive atomic force microscopy (conductivity), contact-resonance force microscopy (mechanical properties), and SEM combined with a variety of stress-strain AFM experiments and AFM numerical simulations (internal structure). We further study the nanoclay’s response to the application of pressure with multifrequency AFM and conductive AFM, whereby increases and decreases in conductivity can occur for the Laponite RD composites. We offer a possible mechanism to explain the changes in conductivity by modeling the coating as a 1-dimensional multibarrier potential for electron transport, and show that conductivity can change when the separation between the barriers changes under the application of pressure, and that the direction of the change depends on the energy of the electrons. We did not observe changes in conductivity under the application of pressure with AFM for the Cloisite Na+ nanocomposite, which has a large platelet size compared with the AFM probe diameter. No pressure-induced changes in conductivity were observed in the clay-free polymer either. PMID:29090109

  20. Closer look at the effect of AFM imaging conditions on the apparent dimensions of surface nanobubbles.

    PubMed

    Walczyk, Wiktoria; Schönherr, Holger

    2013-01-15

    To date, TM AFM (tapping mode or intermittent contact mode atomic force microscopy) is the most frequently applied direct imaging technique to visualize surface nanobubbles at the solid-aqueous interface. On one hand, AFM is the only profilometric technique that provides estimates of the bubbles' nanoscopic dimensions. On the other hand, the nanoscopic contact angles of surface nanobubbles estimated from their apparent dimensions that are deduced from AFM "height" images of nanobubbles differ markedly from the macrocopic water contact angles on the identical substrates. Here we show in detail how the apparent bubble height and width of surface nanobubbles on highly oriented pyrolytic graphite (HOPG) depend on the free amplitude of the cantilever oscillations and the amplitude setpoint ratio. (The role of these two AFM imaging parameters and their interdependence has not been studied so far for nanobubbles in a systematic way.) In all experiments, even with optimal scanning parameters, nanobubbles at the HOPG-water interface appeared to be smaller in the AFM images than their true size, which was estimated using a method presented herein. It was also observed that the severity of the underestimate increased with increasing bubble height and radius of curvature. The nanoscopic contact angle of >130° for nanobubbles on HOPG extrapolated to zero interaction force was only slightly overestimated and hence significantly higher than the macroscopic contact angle of water on HOPG (63 ± 2°). Thus, the widely reported contact angle discrepancy cannot be solely attributed to inappropriate AFM imaging conditions.

  1. A Novel Method to Reconstruct the Force Curve by Higher Harmonics of the First Two Flexural Modes in Frequency Modulation Atomic Force Microscope (FM-AFM).

    PubMed

    Zhang, Suoxin; Qian, Jianqiang; Li, Yingzi; Zhang, Yingxu; Wang, Zhenyu

    2018-06-04

    Atomic force microscope (AFM) is an idealized tool to measure the physical and chemical properties of the sample surfaces by reconstructing the force curve, which is of great significance to materials science, biology, and medicine science. Frequency modulation atomic force microscope (FM-AFM) collects the frequency shift as feedback thus having high force sensitivity and it accomplishes a true noncontact mode, which means great potential in biological sample detection field. However, it is a challenge to establish the relationship between the cantilever properties observed in practice and the tip-sample interaction theoretically. Moreover, there is no existing method to reconstruct the force curve in FM-AFM combining the higher harmonics and the higher flexural modes. This paper proposes a novel method that a full force curve can be reconstructed by any order higher harmonics of the first two flexural modes under any vibration amplitude in FM-AFM. Moreover, in the small amplitude regime, short range forces are reconstructed more accurately by higher harmonics analysis compared with fundamental harmonics using the Sader-Jarvis formula.

  2. Temperature-Controlled High-Speed AFM: Real-Time Observation of Ripple Phase Transitions.

    PubMed

    Takahashi, Hirohide; Miyagi, Atsushi; Redondo-Morata, Lorena; Scheuring, Simon

    2016-11-01

    With nanometer lateral and Angstrom vertical resolution, atomic force microscopy (AFM) has contributed unique data improving the understanding of lipid bilayers. Lipid bilayers are found in several different temperature-dependent states, termed phases; the main phases are solid and fluid phases. The transition temperature between solid and fluid phases is lipid composition specific. Under certain conditions some lipid bilayers adopt a so-called ripple phase, a structure where solid and fluid phase domains alternate with constant periodicity. Because of its narrow regime of existence and heterogeneity ripple phase and its transition dynamics remain poorly understood. Here, a temperature control device to high-speed atomic force microscopy (HS-AFM) to observe dynamics of phase transition from ripple phase to fluid phase reversibly in real time is developed and integrated. Based on HS-AFM imaging, the phase transition processes from ripple phase to fluid phase and from ripple phase to metastable ripple phase to fluid phase could be reversibly, phenomenologically, and quantitatively studied. The results here show phase transition hysteresis in fast cooling and heating processes, while both melting and condensation occur at 24.15 °C in quasi-steady state situation. A second metastable ripple phase with larger periodicity is formed at the ripple phase to fluid phase transition when the buffer contains Ca 2+ . The presented temperature-controlled HS-AFM is a new unique experimental system to observe dynamics of temperature-sensitive processes at the nanoscopic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Direct AFM observation of an opening event of a DNA cuboid constructed via a prism structure.

    PubMed

    Endo, Masayuki; Hidaka, Kumi; Sugiyama, Hiroshi

    2011-04-07

    A cuboid structure was constructed using a DNA origami design based on a square prism structure. The structure was characterized by atomic force microscopy (AFM) and dynamic light scattering. The real-time opening event of the cuboid was directly observed by high-speed AFM.

  4. 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

  5. High-resolution AFM topographs of Rubrivivax gelatinosus light-harvesting complex LH2

    PubMed Central

    Scheuring, Simon; Reiss-Husson, Francoise; Engel, Andreas; Rigaud, Jean-Louis; Ranck, Jean-Luc

    2001-01-01

    Light-harvesting complexes 2 (LH2) are the accessory antenna proteins in the bacterial photosynthetic apparatus and are built up of αβ-heterodimers containing three bacteriochlorophylls and one carotenoid each. We have used atomic force microscopy (AFM) to investigate reconstituted LH2 from Rubrivivax gelatinosus, which has a C-terminal hydrophobic extension of 21 amino acids on the α-subunit. High-resolution topographs revealed a nonameric organization of the regularly packed cylindrical complexes incorporated into the membrane in both orientations. Native LH2 showed one surface which protruded by ∼6 Å and one that protruded by ∼14 Å from the membrane. Topographs of samples reconstituted with thermolysin-digested LH2 revealed a height reduction of the strongly protruding surface to ∼9 Å, and a change of its surface appearance. These results suggested that the α-subunit of R.gelatinosus comprises a single transmembrane helix and an extrinsic C-terminus, and allowed the periplasmic surface to be assigned. Occasionally, large rings (∼120 Å diameter) surrounded by LH2 rings were observed. Their diameter and appearance suggest the large rings to be LH1 complexes. PMID:11406579

  6. High-speed AFM and the reduction of tip-sample forces

    NASA Astrophysics Data System (ADS)

    Miles, Mervyn; Sharma, Ravi; Picco, Loren

    High-speed DC-mode AFM has been shown to be routinely capable of imaging at video rate, and, if required, at over 1000 frames per second. At sufficiently high tip-sample velocities in ambient conditions, the tip lifts off the sample surface in a superlubricity process which reduces the level of shear forces imposed on the sample by the tip and therefore reduces the potential damage and distortion of the sample being imaged. High-frequency mechanical oscillations, both lateral and vertical, have been reported to reduced the tip-sample frictional forces. We have investigated the effect of combining linear high-speed scanning with these small amplitude high-frequency oscillations with the aim of reducing further the force interaction in high-speed imaging. Examples of this new version of high-speed AFM imaging will be presented for biological samples.

  7. Manufacturing and advanced characterization of sub-25nm diameter CD-AFM probes with sub-10nm tip edges radius

    NASA Astrophysics Data System (ADS)

    Foucher, Johann; Filippov, Pavel; Penzkofer, Christian; Irmer, Bernd; Schmidt, Sebastian W.

    2013-04-01

    Atomic force microscopy (AFM) is increasingly used in the semiconductor industry as a versatile monitoring tool for highly critical lithography and etching process steps. Applications range from the inspection of the surface roughness of new materials, over accurate depth measurements to the determination of critical dimension structures. The aim to address the rapidly growing demands on measurement uncertainty and throughput more and more shifts the focus of attention to the AFM tip, which represents the crucial link between AFM tool and the sample to be monitored. Consequently, in order to reach the AFM tool's full potential, the performance of the AFM tip has to be considered as a determining parameter. Currently available AFM tips made from silicon are generally limited by their diameter, radius, and sharpness, considerably restricting the AFM measurement capabilities on sub-30nm spaces. In addition to that, there's lack of adequate characterization structures to accurately characterize sub-25nm tip diameters. Here, we present and discuss a recently introduced AFM tip design (T-shape like design) with precise tip diameters down to 15nm and tip radii down to 5nm fabricated from amorphous, high density diamond-like carbon (HDC/DLC) using electron beam induced processing (EBIP). In addition to that advanced design, we propose a new characterizer structure, which allows for accurate characterization and design control of sub-25nm tip diameters and sub-10nm tip edges radii. We demonstrate the potential advantages of combining a small tip shape design, i.e. tip diameter and tip edge radius, and an advanced tip characterizer for the semiconductor industry by the measurement of advanced lithography patterns.

  8. 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. PMID:28348337

  9. Phenotypic Heterogeneity in Attachment of Marine Bacteria toward Antifouling Copolymers Unraveled by AFM.

    PubMed

    El-Kirat-Chatel, Sofiane; Puymege, Aurore; Duong, The H; Van Overtvelt, Perrine; Bressy, Christine; Belec, Lénaïk; Dufrêne, Yves F; Molmeret, Maëlle

    2017-01-01

    Up to recent years, bacterial adhesion has mostly been evaluated at the population level. Single cell level has improved in the past few years allowing a better comprehension of the implication of individual behaviors as compared to the one of a whole community. A new approach using atomic force microscopy (AFM) to measure adhesion forces between a live bacterium attached via a silica microbead to the AFM tipless cantilever and the surface has been recently developed. The objectives of this study is to examine the bacterial adhesion to a surface dedicated to ship hulls at the population and the cellular level to understand to what extent these two levels could be correlated. Adhesion of marine bacteria on inert surfaces are poorly studied in particular when substrata are dedicated to ship hulls. Studying these interactions in this context are worthwhile as they may involve different adhesion behaviors, taking place in salty conditions, using different surfaces than the ones usually utilized in the literacy. FRC (fouling release coatings)-SPC (self-polishing coatings) hybrids antifouling coatings have been used as substrata and are of particular interest for designing environmentally friendly surfaces, combining progressive surface erosion and low adhesion properties. In this study, a hybrid coating has been synthetized and used to study the adhesion of three marine bacteria, displaying different surface characteristics, using microplate assays associated with confocal scanning laser microscopy (CSLM) and AFM. This study shows that the bacterial strain that appeared to have the weakest adhesion and biofilm formation abilities when evaluated at the population level using microplates assays and CSLM, displayed stronger adhesion forces on the same surfaces at the single cell level using AFM. In addition, one of the strains tested which presented a strong ability to adhere and to form biofilm at the population level, displayed a heterogeneous phenotypic behavior at the

  10. High-field magnetoconductance in La-Sr manganites of FM and AFM ground states

    NASA Astrophysics Data System (ADS)

    Jirák, Zdeněk; Kaman, Ondřej; Knížek, Karel; Levinský, Petr; Míšek, Martin; Veverka, Pavel; Hejtmánek, Jiří

    2018-06-01

    Large-grain La1-xSrxMnO3 ceramic samples of compositions x = 0.45 and 0.55, representing the ferromagnetic (FM) and A-type antiferromagnetic (AFM) ground states, were produced via classical sintering at 1500 °C of cold-pressed sol-gel prepared single-phase nanoparticles. Using the same precursors, nanogranular forms of both manganite ceramics were prepared by fast spark plasma sintering at low temperature of 900 °C, which limits the growth of crystal grains. The magnetotransport of both the bulk and nanogranular forms was investigated in a broad range of magnetic fields up to 130 kOe and analyzed on the basis of detailed magnetic measurements. Both the large-grain and nanogranular systems with x = 0.45, possessing a pure FM state with similar Curie tempereature TC ≈ 345 K), show nearly the same conductivity enhancement in external fields when expressed relatively to the zero-field values. This positive magnetoconductance (MC) can be separated into two terms: (i) the hysteretic low-field MC that reflects the field-induced orientation of magnetic moments of individual grains, and (ii) the high-field MC that depends linearly on external field. In the case of large-grain ceramics with x = 0.55, a partially ordered FM state formed below TC = 264 K is replaced by pure A-type AFM ground state below 204 K. This A-type AFM state is characterized by positive magnetoconductance that is essentially of quadratic dependence on external field in the investigated range up to 130 kOe. On contrary, the nanogranular product with x = 0.55 exhibits a mixed FM/AFM state at low temperatures, and, as a consequence, its magnetotransport combines the features of FM and A-type AFM systems, in which the quadratic term is much enhanced and clearly dominates at high fields. For interpretation of observed behaviors, the theory of grain-boundary tunneling is revisited.

  11. Force-controlled manipulation of single cells: from AFM to FluidFM.

    PubMed

    Guillaume-Gentil, Orane; Potthoff, Eva; Ossola, Dario; Franz, Clemens M; Zambelli, Tomaso; Vorholt, Julia A

    2014-07-01

    The ability to perturb individual cells and to obtain information at the single-cell level is of central importance for addressing numerous biological questions. Atomic force microscopy (AFM) offers great potential for this prospering field. Traditionally used as an imaging tool, more recent developments have extended the variety of cell-manipulation protocols. Fluidic force microscopy (FluidFM) combines AFM with microfluidics via microchanneled cantilevers with nano-sized apertures. The crucial element of the technology is the connection of the hollow cantilevers to a pressure controller, allowing their operation in liquid as force-controlled nanopipettes under optical control. Proof-of-concept studies demonstrated a broad spectrum of single-cell applications including isolation, deposition, adhesion and injection in a range of biological systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. 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.

  13. Corrosion process monitoring by AFM higher harmonic imaging

    NASA Astrophysics Data System (ADS)

    Babicz, S.; Zieliński, A.; Smulko, J.; Darowicki, K.

    2017-11-01

    The atomic force microscope (AFM) was invented in 1986 as an alternative to the scanning tunnelling microscope, which cannot be used in studies of non-conductive materials. Today the AFM is a powerful, versatile and fundamental tool for visualizing and studying the morphology of material surfaces. Moreover, additional information for some materials can be recovered by analysing the AFM’s higher cantilever modes when the cantilever motion is inharmonic and generates frequency components above the excitation frequency, usually close to the resonance frequency of the lowest oscillation mode. This method has been applied and developed to monitor corrosion processes. The higher-harmonic imaging is especially helpful for sharpening boundaries between objects in heterogeneous samples, which can be used to identify variations in steel structures (e.g. corrosion products, steel heterogeneity). The corrosion products have different chemical structures because they are composed of chemicals other than the original metal base (mainly iron oxides). Thus, their physicochemical properties are different from the primary basis. These structures have edges at which higher harmonics should be more intense because of stronger interference between the tip and the specimen structure there. This means that the AFM’s higher-harmonic imaging is an excellent tool for monitoring surficial effects of the corrosion process.

  14. 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).

  15. 3D Structural Model of High-Performance Non-Fullerene Polymer Solar Cells as Revealed by High-Resolution AFM.

    PubMed

    Shi, Shaowei; Chen, Xiaofeng; Liu, Xubo; Wu, Xuefei; Liu, Feng; Zhang, Zhi-Guo; Li, Yongfang; Russell, Thomas P; Wang, Dong

    2017-07-26

    Rapid improvements in nonfullerene polymer solar cells (PSCs) have brought power conversion efficiencies to greater than 12%. To further improve device performance, a fundamental understanding of the correlations between structure and performance is essential. In this paper, based on a typical high-performance system consisting of J61(one donor-acceptor (D-A) copolymer of benzodithiophene and fluorine substituted benzotriazole) and ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone)-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), a 3D structural model is directly imaged by employing high-resolution atomic force microscopy (AFM). Hierarchical morphologies ranging from fiberlike crystallites, several nanometers in size, to a bicontinuous morphology, having domains tens of nanometers in size, are observed. A fibrillar interpenetrating networks of J61-rich domains embedded in a matrix comprised of a J61/ITIC is seen, reflecting the partial miscibility of J61 with ITIC. These hierarchical nanostructural characteristics are coupled to significantly enhanced exciton dissociation, and further contribute to photocurrent and final device performance.

  16. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  17. Radiation pressure excitation of Low Temperature Atomic Force & Magnetic Force Microscope (LT-AFM/MFM) for Imaging

    NASA Astrophysics Data System (ADS)

    Karci, Ozgur; Celik, Umit; Oral, Ahmet; NanoMagnetics Instruments Ltd. Team; Middle East Tech Univ Team

    2015-03-01

    We describe a novel method for excitation of Atomic Force Microscope (AFM) cantilevers by means of radiation pressure for imaging in an AFM for the first time. Piezo excitation is the most common method for cantilever excitation, but it may cause spurious resonance peaks. A fiber optic interferometer with 1310 nm laser was used both to measure the deflection of cantilever and apply a force to the cantilever in a LT-AFM/MFM from NanoMagnetics Instruments. The laser power was modulated at the cantilever`s resonance frequency by a digital Phase Lock Loop (PLL). The force exerted by the radiation pressure on a perfectly reflecting surface by a laser beam of power P is F = 2P/c. We typically modulate the laser beam by ~ 800 μW and obtain 10nm oscillation amplitude with Q ~ 8,000 at 2.5x10-4 mbar. The cantilever's stiffness can be accurately calibrated by using the radiation pressure. We have demonstrated performance of the radiation pressure excitation in AFM/MFM by imaging a hard disk sample between 4-300K and Abrikosov vortex lattice in BSCCO single crystal at 4K to for the first time.

  18. Nano Cu interaction with single amino acid tyrosine derived self-assemblies; study through XRD, AFM, confocal Raman microscopy, SERS and DFT methods

    NASA Astrophysics Data System (ADS)

    Govindhan, Raman; Karthikeyan, Balakrishnan

    2017-12-01

    3,5-Bis(trifluoromethyl)benzylamine derivatives of single amino acid tyrosine produced self-assembled nanotubes (BTTNTs) as simple Phe-Phe. It has been observed that tyrosine derivative gives exclusively micro and nano tubes irrespective of the concentration of the precursor monomer. However, the introduced xenobiotic trifluoromethyl group (TFM) present in key backbone positionsof the self assembly gives the specific therapeutic function has been highlighted. Herein this work study of such self assembled nanotubes were studied through experimental and theoretical methods. The interaction of nanocopper cluster with the nanotubes (Cu@BTTNTs) were extensively studied by various methods like XRD, AFM, confocal Raman microscopy, SERS and theoretical methods like Mulliken's atomic charge analysis. SERS reveals that the interactions of Cu cluster with NH2, OH, NH and phenyl ring π-electrons system of BTTNTs. DFT studies gave the total dipole moment values of Cu@BTTNTs and explained the nature of interaction.

  19. Tendon exhibits complex poroelastic behavior at the nanoscale as revealed by high-frequency AFM-based rheology.

    PubMed

    Connizzo, Brianne K; Grodzinsky, Alan J

    2017-03-21

    Tendons transmit load from muscle to bone by utilizing their unique static and viscoelastic tensile properties. These properties are highly dependent on the composition and structure of the tissue matrix, including the collagen I hierarchy, proteoglycans, and water. While the role of matrix constituents in the tensile response has been studied, their role in compression, particularly in matrix pressurization via regulation of fluid flow, is not well understood. Injured or diseased tendons and tendon regions that naturally experience compression are known to have alterations in glycosaminoglycan content, which could modulate fluid flow and ultimately mechanical function. While recent theoretical studies have predicted tendon mechanics using poroelastic theory, no experimental data have directly demonstrated such behavior. In this study, we use high-bandwidth AFM-based rheology to determine the dynamic response of tendons to compressive loading at the nanoscale and to determine the presence of poroelastic behavior. Tendons are found to have significant characteristic dynamic relaxation behavior occurring at both low and high frequencies. Classic poroelastic behavior is observed, although we hypothesize that the full dynamic response is caused by a combination of flow-dependent poroelasticity as well as flow-independent viscoelasticity. Tendons also demonstrate regional dependence in their dynamic response, particularly near the junction of tendon and bone, suggesting that the structural and compositional heterogeneity in tendon may be responsible for regional poroelastic behavior. Overall, these experiments provide the foundation for understanding fluid-flow-dependent poroelastic mechanics of tendon, and the methodology is valuable for assessing changes in tendon matrix compressive behavior at the nanoscale. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Characterization of surface roughness of laser deposited titanium alloy and copper using AFM

    NASA Astrophysics Data System (ADS)

    Erinosho, M. F.; Akinlabi, E. T.; Johnson, O. T.

    2018-03-01

    Laser Metal Deposition (LMD) is the process of using the laser beam of a nozzle to produce a melt pool on a metal surface usually the substrate and metal powder is been deposited into it thereby creating a fusion bond with the substrate to form a new material layer against the force gravity. A good metal laminate is formed when the wettability between the dropping metal powder and the substrate adheres. This paper reports the surface roughness of laser deposited titanium alloy and copper (Ti6Al4V + Cu) using the Atomic Force Microscopy (AFM). This AFM is employed in order to sense the surface and produce different manipulated images using the micro-fabricated mechanical tip under a probe cartridge of high resolution. The process parameters employed during the deposition routine determines the output of the deposit. A careful attention is given to the laser deposited Ti6Al4V + Cu samples under the AFM probe because of their single tracked layers with semi-circular pattern of deposition. This research work can be applicable in the surface modification of laser deposited samples for the marine industry.

  1. On the nonlinear dynamics of trolling-mode AFM: Analytical solution using multiple time scales method

    NASA Astrophysics Data System (ADS)

    Sajjadi, Mohammadreza; Pishkenari, Hossein Nejat; Vossoughi, Gholamreza

    2018-06-01

    Trolling mode atomic force microscopy (TR-AFM) has resolved many imaging problems by a considerable reduction of the liquid-resonator interaction forces in liquid environments. The present study develops a nonlinear model of the meniscus force exerted to the nanoneedle of TR-AFM and presents an analytical solution to the distributed-parameter model of TR-AFM resonator utilizing multiple time scales (MTS) method. Based on the developed analytical solution, the frequency-response curves of the resonator operation in air and liquid (for different penetration length of the nanoneedle) are obtained. The closed-form analytical solution and the frequency-response curves are validated by the comparison with both the finite element solution of the main partial differential equations and the experimental observations. The effect of excitation angle of the resonator on horizontal oscillation of the probe tip and the effect of different parameters on the frequency-response of the system are investigated.

  2. Influence of smectite suspension structure on sheet orientation in dry sediments: XRD and AFM applications.

    PubMed

    Zbik, Marek S; Frost, Ray L

    2010-06-15

    The structure-building phenomena within clay aggregates are governed by forces acting between clay particles. Measurements of such forces are important to understand in order to manipulate the aggregate structure for applications such as dewatering of mineral processing tailings. A parallel particle orientation is required when conducting XRD investigation on the oriented samples and conduct force measurements acting between basal planes of clay mineral platelets using atomic force microscopy (AFM). To investigate how smectite clay platelets were oriented on silicon wafer substrate when dried from suspension range of methods like SEM, XRD and AFM were employed. From these investigations, we conclude that high clay concentrations and larger particle diameters (up to 5 microm) in suspension result in random orientation of platelets in the substrate. The best possible laminar orientation in the clay dry film, represented in the XRD 001/020 intensity ratio of 47 was obtained by drying thin layers from 0.02 wt.% clay suspensions of the natural pH. Conducted AFM investigations show that smectite studied in water based electrolytes show very long-range repulsive forces lower in strength than electrostatic forces from double-layer repulsion. It was suggested that these forces may have structural nature. Smectite surface layers rehydrate in water environment forms surface gel with spongy and cellular texture which cushion approaching AFM probe. This structural effect can be measured in distances larger than 1000 nm from substrate surface and when probe penetrate this gel layer, structural linkages are forming between substrate and clay covered probe. These linkages prevent subsequently smooth detachments of AFM probe on way back when retrieval. This effect of tearing new formed structure apart involves larger adhesion-like forces measured in retrieval. It is also suggested that these effect may be enhanced by the nano-clay particles interaction. 2010 Elsevier Inc. All

  3. Phenotypic and genotypic characterization of biofilm formation among Staphylococcus aureus isolates from clinical specimens, an Atomic Force Microscopic (AFM) study.

    PubMed

    Bazari, Pelin Aslani Menareh; Honarmand Jahromy, Sahar; Zare Karizi, Shohreh

    2017-09-01

    Staphylococcus aureus is a major cause of nosocomial infections. Biofilm formation is an important factor for bacterial pathogenesis. Its mechanisms are complex and include of many genes depends on expression of icaADBC operon involved in the synthesis of a polysaccharide intercellular adhesion. The aim of study was to investigate biofilm forming ability of Staphylococcus aureus strains by phenotypic and genotypic methods. Also Atomic Force microscope (AFM) was used to visualize biofilm formation. 140 Isolates were collected from clinical specimens of patients in Milad Hospital, Tehran and diagnosed by biochemical tests. The ability of strains to produce slime was evaluated by CRA method. For diagnosing of bacterial EPS, Indian ink staining were used and finally biofilm surface of 3 isolates observed by AFM. The prevalence of icaA and icaD genes was determined by PCR. By CRA method 15% of samples considered as positive slime producers, 44.28% as intermediate and 40.71% indicative as negative slime producers. 118 staphylococcus aureus strains showed a distinct halo transparent zone but 22 strains showed no halo zone. AFM analysis of Slime positive isolates showed a distinct and complete biofilm formation. In slime negative strain, there was not observed biofilm. The prevalence of icaA, icaD genes was 44.2% and 10% of the isolates had both genes simultaneously. There is a relationship between exopolysaccharide layer and biofilm formation of Staphylococcus aureus isolates. The presence of icaAD genes among isolates is not associated with in vitro formation of biofilm. AFM is a useful tool for observation of bacterial biofilm formation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Adiabatic Compression Sensitivity of AF-M315E

    DTIC Science & Technology

    2015-07-01

    the current work is to expand the knowledge base from previous experiments completed at AFRL for AF-M315E in stainless steel U-tubes at room...addressed, to some degree, with the use of clamps and a large stainless steel plate to dissipate any major vibrations. A large preheated bath of 50:50 v/v...autocatalytic chain decomposition in the propellant. This exothermic decomposition decreases the fume -off initiation temperature of the propellant and its

  5. 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.

  6. 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.

  7. Surface electrical properties of stainless steel fibres: An AFM-based study

    NASA Astrophysics Data System (ADS)

    Yin, Jun; D'Haese, Cécile; Nysten, Bernard

    2015-03-01

    Atomic force microscopy (AFM) electrical modes were used to study the surface electrical properties of stainless steel fibres. The surface electrical conductivity was studied by current sensing AFM and I-V spectroscopy. Kelvin probe force microscopy was used to measure the surface contact potential. The oxide film, known as passivation layer, covering the fibre surface gives rise to the observation of an apparently semiconducting behaviour. The passivation layer generally exhibits a p-type semiconducting behaviour, which is attributed to the predominant formation of chromium oxide on the surface of the stainless steel fibres. At the nanoscale, different behaviours are observed from points to points, which may be attributed to local variations of the chemical composition and/or thickness of the passivation layer. I-V curves are well fitted with an electron tunnelling model, indicating that electron tunnelling may be the predominant mechanism for electron transport.

  8. Magnetocaloric effect and negative thermal expansion in hexagonal Fe doped MnNiGe compounds with a magnetoelastic AFM-FM-like transition

    PubMed Central

    Xu, Kun; Li, Zhe; Liu, Enke; Zhou, Haichun; Zhang, Yuanlei; Jing, Chao

    2017-01-01

    We report a detailed study of two successive first-order transitions, including a martensitic transition (MT) and an antiferromagnetic (AFM)-ferromagnetic (FM)-like transition, in Mn1-xFexNiGe (x = 0, 0.06, 0.11) alloys by X-ray diffraction, differential scanning calorimetry, magnetization and linear thermal expansion measurements. Such an AFM-FM-like transition occurring in the martensitic state has seldom been observed in the M(T) curves. The results of Arrott plot and linear relationship of the critical temperature with M2 provide explicit evidence of its first-order magnetoelastic nature. On the other hand, their performances as magnetocaloric and negative thermal expansion materials were characterized. The isothermal entropy change for a field change of 30 kOe reaches an impressive value of −25.8 J/kg K at 203 K for x = 0.11 compared to the other two samples. It demonstrates that the magneto-responsive ability has been significantly promoted since an appropriate amount of Fe doping can break the local Ni-6Mn AFM configuration. Moreover, the Fe-doped samples reveal both the giant negative thermal expansion and near-zero thermal expansion for different temperature ranges. For instance, the average thermal expansion coefficient ā of x = 0.06 reaches −60.7 × 10−6/K over T = 231–338 K and 0.6 × 10−6/K over T = 175–231 K during cooling. PMID:28134355

  9. 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

  10. Lateral Tip Control Effects in CD-AFM Metrology: The Large Tip Limit

    PubMed Central

    Dixson, Ronald G.; Orji, Ndubuisi G.; Goldband, Ryan S.

    2016-01-01

    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

  11. Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Fukuma, Takeshi; Mostaert, Anika S.; Serpell, Louise C.; Jarvis, Suzanne P.

    2008-09-01

    We have investigated the surface structure of islet amyloid polypeptide (IAPP) fibrils and α-synuclein protofibrils in liquid by means of frequency modulation atomic force microscopy (FM-AFM). Ångström-resolution FM-AFM imaging of isolated macromolecules in liquid is demonstrated for the first time. Individual β-strands aligned perpendicular to the fibril axis with a spacing of 0.5 nm are resolved in FM-AFM images, which confirms cross-β structure of IAPP fibrils in real space. FM-AFM images also reveal the existence of 4 nm periodic domains along the axis of IAPP fibrils. Stripe features with 0.5 nm spacing are also found in images of α-synuclein protofibrils. However, in contrast to the case for IAPP fibrils, the stripes are oriented 30° from the axis, suggesting the possibility of β-strand alignment in protofibrils different from that in mature fibrils or the regular arrangement of thioflavin T molecules present during the fibril preparation aligned at the surface of the protofibrils.

  12. Single cell assessment of yeast metabolic engineering for enhanced lipid production using Raman and AFM-IR imaging.

    PubMed

    Kochan, Kamila; Peng, Huadong; Wood, Bayden R; Haritos, Victoria S

    2018-01-01

    Biodiesel is a valuable renewable fuel made from derivatized fatty acids produced in plants, animals, and oleaginous microbes. Of the latter, yeasts are of special interest due to their wide use in biotechnology, ability to synthesize fatty acids and store large amounts of triacylglycerols while utilizing non-food carbon sources. While yeast efficiently produce lipids, genetic modification and indeed, lipid pathway metabolic engineering, is usually required for cost-effective production. Traditionally, gas chromatography (GC) is used to measure fatty acid production and to track the success of a metabolic engineering strategy in a microbial culture; here we have employed vibrational spectroscopy approaches at population and single cell level of engineered yeast while simultaneously investigating metabolite levels in subcellular structures. Firstly, a strong correlation ( r 2  > 0.99) was established between Fourier transform infrared (FTIR) lipid in intact cells and GC analysis of fatty acid methyl esters in the differently engineered strains. Confocal Raman spectroscopy of individual cells carrying genetic modifications to enhance fatty acid synthesis and lipid accumulation revealed changes to the lipid body (LB), the storage organelle for lipids in yeast, with their number increasing markedly (up to tenfold higher); LB size was almost double in the strain that also expressed a LB stabilizing gene but considerable variation was also noted between cells. Raman spectroscopy revealed a clear trend toward reduced unsaturated fatty acid content in lipids of cells carrying more complex metabolic engineering. Atomic force microscopy-infrared spectroscopy (AFM-IR) analysis of individual cells indicated large differences in subcellular constituents between strains: cells of the most highly engineered strain had elevated lipid and much reduced carbohydrate in their cytoplasm compared with unmodified cells. Vibrational spectroscopy analysis allowed the simultaneous

  13. Single cell adhesion force measurement for cell viability identification using an AFM cantilever-based micro putter

    NASA Astrophysics Data System (ADS)

    Shen, Yajing; Nakajima, Masahiro; Kojima, Seiji; Homma, Michio; Kojima, Masaru; Fukuda, Toshio

    2011-11-01

    Fast and sensitive cell viability identification is a key point for single cell analysis. To address this issue, this paper reports a novel single cell viability identification method based on the measurement of single cell shear adhesion force using an atomic force microscopy (AFM) cantilever-based micro putter. Viable and nonviable yeast cells are prepared and put onto three kinds of substrate surfaces, i.e. tungsten probe, gold and ITO substrate surfaces. A micro putter is fabricated from the AFM cantilever by focused ion beam etching technique. The spring constant of the micro putter is calibrated using the nanomanipulation approach. The shear adhesion force between the single viable or nonviable cell and each substrate is measured using the micro putter based on the nanorobotic manipulation system inside an environmental scanning electron microscope. The adhesion force is calculated based on the deflection of the micro putter beam. The results show that the adhesion force of the viable cell to the substrate is much larger than that of the nonviable cell. This identification method is label free, fast, sensitive and can give quantitative results at the single cell level.

  14. 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

  15. Surface analysis of glass fibres using XPS and AFM: case study of glass fibres recovered from the glass fibre reinforced polymer using chemical recycling

    NASA Astrophysics Data System (ADS)

    Nzioka, A. M.; Kim, Y. J.

    2018-01-01

    In this study, we present the results of an experimental study of the use of the X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) to characterise the coatings of the recovered E - glass fibres. The recovered E - glass fibres were obtained using chemical recycling process coupled with ultrasound cavitation. The objective of this study was to analyse the impact of chemical recycling and the ultrasound cavitation process on the sizing properties of the recovered fibres. We obtained the recovered fibres and sized using 1 wt% 3 - aminopropyltriethoxysilane (APS). Part of the sized fibres was washed with acetone and analysed all the sample fibres using AFM and XPS. Results showed the different composition of sizing after extraction using acetone. We compared the results of this study with that of virgin clean glass fibres.

  16. Cell mechanics as a marker for diseases: Biomedical applications of AFM

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rianna, Carmela; Radmacher, Manfred, E-mail: mr@biophysik.uni-bremen.de

    Many diseases are related to changes in cell mechanics. Atomic Force Microscopy (AFM) is one of the most suitable techniques allowing the investigation of both topography and mechanical properties of adherent cells with high spatial resolution under physiological conditions. Over the years the use of this technique in medical and clinical applications has largely increased, resulting in the notion of cell mechanics as a biomarker to discriminate between different physiological and pathological states of cells. Cell mechanics has proven to be a biophysical fingerprint able discerning between cell phenotypes, unraveling processes in aging or diseases, or even detecting and diagnosingmore » cellular pathologies. We will review in this report some of the works on cell mechanics investigated by AFM with clinical and medical relevance in order to clarify the state of research in this field and to highlight the role of cell mechanics in the study of pathologies, focusing on cancer, blood and cardiovascular diseases.« less

  17. 3D assembly of upconverting NaYF4 nanocrystals by AFM nanoxerography: creation of anti-counterfeiting microtags

    NASA Astrophysics Data System (ADS)

    Sangeetha, Neralagatta M.; Moutet, Pierre; Lagarde, Delphine; Sallen, Gregory; Urbaszek, Bernhard; Marie, Xavier; Viau, Guillaume; Ressier, Laurence

    2013-09-01

    Formation of 3D close-packed assemblies of upconverting NaYF4 colloidal nanocrystals (NCs) on surfaces, by Atomic Force Microscopy (AFM) nanoxerography is presented. The surface potential of the charge patterns, the NC concentration, the polarizability of the NCs and the polarity of the dispersing solvent are identified as the key parameters controlling the assembly of NaYF4 NCs into micropatterns of the desired 3D architecture. This insight allowed us to fabricate micrometer sized Quick Response (QR) codes encoded in terms of upconversion luminescence intensity or color. Topographically hidden messages could also be readily incorporated within these microtags. This work demonstrates that AFM nanoxerography has enormous potential for generating high-security anti-counterfeiting microtags.Formation of 3D close-packed assemblies of upconverting NaYF4 colloidal nanocrystals (NCs) on surfaces, by Atomic Force Microscopy (AFM) nanoxerography is presented. The surface potential of the charge patterns, the NC concentration, the polarizability of the NCs and the polarity of the dispersing solvent are identified as the key parameters controlling the assembly of NaYF4 NCs into micropatterns of the desired 3D architecture. This insight allowed us to fabricate micrometer sized Quick Response (QR) codes encoded in terms of upconversion luminescence intensity or color. Topographically hidden messages could also be readily incorporated within these microtags. This work demonstrates that AFM nanoxerography has enormous potential for generating high-security anti-counterfeiting microtags. Electronic supplementary information (ESI) available: Detailed experimental procedures for the synthesis of upconverting NaYF4 nanocrystals and their transmission electron microscopy images. KFM and AFM images corresponding to the assembly of positively charged β-NaYF4:Er3+,Yb3+ nanocrystals from water suspensions by AFM nanoxerography. Photoluminescence spectra of β-NaYF4:Er3+,Yb3+ nanocrystals

  18. KPFM/AFM imaging on TiO2(110) surface in O2 gas

    NASA Astrophysics Data System (ADS)

    Arima, Eiji; Wen, Huan Fei; Naitoh, Yoshitaka; Li, Yan Jun; Sugawara, Yasuhiro

    2018-03-01

    We have carried out high-speed imaging of the topography and local contact potential difference (LCPD) on rutile TiO2(110) in O2 gas by atomic force microscopy (AFM) and Kelvin probe force microscopy (KPFM). We succeeded in KPFM/AFM imaging with atomic resolution at 1 frame min-1 and observed the adsorbate on a hydroxylated TiO2(110) surface. The observed adsorbate is considered to be oxygen adatoms (Oa), hydroperoxyls (HO2), or terminal hydroxyls (OHt). After adsorption, changes in the topography and the LCPD of the adsorbate were observed. This phenomenon is thought to be caused by the charge transfer of the adsorbate. This technique has the potential to observe catalytic behavior with atomic resolution.

  19. Study of mesoporous CdS-quantum-dot-sensitized TiO2 films by using X-ray photoelectron spectroscopy and AFM

    PubMed Central

    Wojcieszak, Robert; Raj, Gijo

    2014-01-01

    Summary CdS quantum dots were grown on mesoporous TiO2 films by successive ionic layer adsorption and reaction processes in order to obtain CdS particles of various sizes. AFM analysis shows that the growth of the CdS particles is a two-step process. The first step is the formation of new crystallites at each deposition cycle. In the next step the pre-deposited crystallites grow to form larger aggregates. Special attention is paid to the estimation of the CdS particle size by X-ray photoelectron spectroscopy (XPS). Among the classical methods of characterization the XPS model is described in detail. In order to make an attempt to validate the XPS model, the results are compared to those obtained from AFM analysis and to the evolution of the band gap energy of the CdS nanoparticles as obtained by UV–vis spectroscopy. The results showed that XPS technique is a powerful tool in the estimation of the CdS particle size. In conjunction with these results, a very good correlation has been found between the number of deposition cycles and the particle size. PMID:24605274

  20. Experimentally validated 3D MD model for AFM-based tip-based nanomanufacturing

    NASA Astrophysics Data System (ADS)

    Promyoo, Rapeepan

    In order to control AFM-based TBN to produce precise nano-geometry efficiently, there is a need to conduct a more focused study of the effects of different parameters, such as feed, speed, and depth of cut on the process performance and outcome. This is achieved by experimentally validating a MD simulation model of nanomachining, and using it to conduct parametric studies to guide AFM-based TBN. A 3D MD model with a larger domain size was developed and used to gain a unique insight into the nanoindentation and nanoscratching processes such as the effect of tip speed (e.g. effect of tip speed on indentation force above 10 nm of indentation depth). The model also supported a more comprehensive parametric study (than other published work) in terms of number of parameters and ranges of values investigated, as well as a more cost effective design of experiments. The model was also used to predict material properties at the nanoscale (e.g. hardness of gold predicted within 6% error). On the other hand, a comprehensive experimental parametric study was conducted to produce a database that is used to select proper machining conditions for guiding the fabrication of nanochannels (e.g. scratch rate = 0.996 Hz, trigger threshold = 1 V, for achieving a nanochannel depth = 50 nm for the case of gold device). Similar trends for the variation of indentation force with depth of cut, pattern of the material pile-up around the indentation mark or scratched groove were found. The parametric studies conducted using both MD model simulations and AFM experiments showed the following: Normal forces for both nanoindentation and nanoscratching increase as the depth of cut increases. The indentation depth increases with tip speed, but the depth of scratch decrease with increasing tip speed. The width and depth of scratched groove also depend on the scratch angle. The recommended scratch angle is at 90°. The surface roughness increases with step over, especially when the step over is larger

  1. Hematite/silica nanoparticle bilayers on mica: AFM and electrokinetic characterization.

    PubMed

    Morga, Maria; Adamczyk, Zbigniew; Kosior, Dominik; Oćwieja, Magdalena

    2018-06-06

    Quantitative studies on self-assembled hematite/silica nanoparticle (NP) bilayers on mica were performed by applying scanning electron microscopy (SEM), atomic force microscopy (AFM), and streaming potential measurements. The coverage of the supporting hematite layers was adjusted by changing the bulk concentration of the suspension and the deposition time. The coverage was determined by direct enumeration of deposited particles from AFM images and SEM micrographs. Afterward, silica nanoparticle monolayers were assembled under diffusion-controlled transport. A unique functional relationship was derived connecting the silica coverage with the hematite precursor layer coverage. The formation of the hematite monolayer and the hematite/silica bilayer was also monitored in situ by streaming potential measurements. It was confirmed that the zeta potential of the bilayers was independent of the supporting layer coverage, exceeding 0.15. These measurements were theoretically interpreted in terms of the general electrokinetic model that allowed for deriving a formula for calculating nanoparticle coverage in the bilayers. Additionally, from desorption experiments, the interactions among hematite/silica particles in the bilayers were determined using DLVO theory. These results facilitate the development of a robust method of preparing nanoparticle bilayers with controlled properties, with potential applications in catalytic processes.

  2. Neural network approximation of tip-abrasion effects in AFM imaging

    NASA Astrophysics Data System (ADS)

    Bakucz, Peter; Yacoot, Andrew; Dziomba, Thorsten; Koenders, Ludger; Krüger-Sehm, Rolf

    2008-06-01

    The abrasion (wear) of tips used in scanning force microscopy (SFM) directly influences SFM image quality and is therefore of great relevance to quantitative SFM measurements. The increasing implementation of automated SFM measurement schemes has become a strong driving force for increasing efforts towards the prediction of tip wear, as it needs to be ensured that the probe is exchanged before a level of tip wear is reached that adversely affects the measurement quality. In this paper, we describe the identification of tip abrasion in a system of SFM measurements. We attempt to model the tip-abrasion process as a concatenation of a mapping from the measured AFM data to a regression vector and a nonlinear mapping from the regressor space to the output space. The mapping is formed as a basis function expansion. Feedforward neural networks are used to approximate this mapping. The one-hidden layer network gave a good quality of fit for the training and test sets for the tip-abrasion system. We illustrate our method with AFM measurements of both fine periodic structures and randomly oriented sharp features and compare our neural network results with those obtained using other methods.

  3. The association between acute flaccid myelitis (AFM) and Enterovirus D68 (EV-D68) - what is the evidence for causation?

    PubMed

    Dyda, Amalie; Stelzer-Braid, Sacha; Adam, Dillon; Chughtai, Abrar A; MacIntyre, C Raina

    2018-01-01

    BackgroundEnterovirus D68 (EV-D68) has historically been a sporadic disease, causing occasional small outbreaks of generally mild infection. In recent years, there has been evidence of an increase in EV-D68 infections globally. Large outbreaks of EV-D68, with thousands of cases, occurred in the United States, Canada and Europe in 2014. The outbreaks were associated temporally and geographically with an increase in clusters of acute flaccid myelitis (AFM).
 Aims: We aimed to evaluate a causal association between EV-D68 and AFM. 
 Methods: Using data from the published and grey literature, we applied the Bradford Hill criteria, a set of nine principles applied to examine causality, to evaluate the relationship between EV-D68 and AFM. Based on available evidence, we defined the Bradford Hill Criteria as being not met, or met minimally, partially or fully. 
 Results: Available evidence applied to EV-D68 and AFM showed that six of the Bradford Hill criteria were fully met and two were partially met. The criterion of biological gradient was minimally met. The incidence of EV-D68 infections is increasing world-wide. Phylogenetic epidemiology showed diversification from the original Fermon and Rhyne strains since the year 2000, with evolution of a genetically distinct outbreak strain, clade B1. Clade B1, but not older strains, is associated with AFM and is neuropathic in animal models. 
 Conclusion: While more research is needed on dose-response relationship, application of the Bradford Hill criteria supported a causal relationship between EV-D68 and AFM.

  4. Atomic Force Microscopy for Soil Analysis

    NASA Astrophysics Data System (ADS)

    gazze, andrea; doerr, stefan; dudley, ed; hallin, ingrid; matthews, peter; quinn, gerry; van keulen, geertje; francis, lewis

    2016-04-01

    Atomic Force Microscopy (AFM) is a high-resolution surface-sensitive technique, which provides 3-dimensional topographical information and material properties of both stiff and soft samples in their natural environments. Traditionally AFM has been applied to samples with low roughness: hence its use for soil analysis has been very limited so far. Here we report the optimization settings required for a standardization of high-resolution and artefact-free analysis of natural soil with AFM: soil immobilization, AFM probe selection, artefact recognition and minimization. Beyond topography, AFM can be used in a spectroscopic mode to evaluate nanomechanical properties, such as soil viscosity, stiffness, and deformation. In this regards, Bruker PeakForce-Quantitative NanoMechanical (QNM) AFM provides a fast and convenient way to extract physical properties from AFM force curves in real-time to obtain soil nanomechanical properties. Here we show for the first time the ability of AFM to describe the topography of natural soil at nanometre resolution, with observation of micro-components, such as clays, and of nano-structures, possibly of biotic origin, the visualization of which would prove difficult with other instrumentations. Finally, nanomechanical profiling has been applied to different wettability states in soil and the respective physical patterns are discussed.

  5. Crystal faces of anhydrite (CaSO 4) and their preferential dissolution in aqueous solutions studied with AFM

    NASA Astrophysics Data System (ADS)

    Shindo, H.; Kaise, M.; Kondoh, H.; Nishihara, C.; Nozoye, H.

    Structures of cleaved surfaces of anhydrite were studied with atomic force microscopy (AFM) before and after partial dissolution in aqueous solutions of NH 4Cl and NaHSO 4. Two crystal faces showed atom-resolved images just after cleavage, (100) and (010), of which the former was roughened by the dissolution, while step structures were developed on the latter. After dissolution, steplines ran along the a- and c-axes on the (010) face, while they ran in directions inclined to these axes before. It was revealed that the arrangement of dipoles is a key factor in determining stabilities of step structures on crystal faces. On the terraces, the arrangement of oxygen atoms of the sulfate groups and calcium ions were clearly observed.

  6. Surface Nanobubbles Studied by Time-Resolved Fluorescence Microscopy Methods Combined with AFM: The Impact of Surface Treatment on Nanobubble Nucleation.

    PubMed

    Hain, Nicole; Wesner, Daniel; Druzhinin, Sergey I; Schönherr, Holger

    2016-11-01

    The impact of surface treatment and modification on surface nanobubble nucleation in water has been addressed by a new combination of fluorescence lifetime imaging microscopy (FLIM) and atomic force microscopy (AFM). In this study, rhodamine 6G (Rh6G)-labeled surface nanobubbles nucleated by the ethanol-water exchange were studied on differently cleaned borosilicate glass, silanized glass as well as self-assembled monolayers on transparent gold by combined AFM-FLIM. While the AFM data confirmed earlier reports on surface nanobubble nucleation, size, and apparent contact angles in dependence of the underlying substrate, the colocalization of these elevated features with highly fluorescent features observed in confocal intensity images added new information. By analyzing the characteristic contributions to the excited state lifetime of Rh6G in decay curves obtained from time-correlated single photon counting (TCSPC) experiments, the characteristic short-lived (<600 ps) component of could be associated with an emission at the gas-water interface. Its colocalization with nanobubble-like features in the AFM height images provides evidence for the observation of gas-filled surface nanobubbles. While piranha-cleaned glass supported nanobubbles, milder UV-ozone or oxygen plasma treatment afforded glass-water interfaces, where no nanobubbles were observed by combined AFM-FLIM. Finally, the number density of nanobubbles scaled inversely with increasing surface hydrophobicity.

  7. AFM surface imaging of AISI D2 tool steel machined by the EDM process

    NASA Astrophysics Data System (ADS)

    Guu, Y. H.

    2005-04-01

    The surface morphology, surface roughness and micro-crack of AISI D2 tool steel machined by the electrical discharge machining (EDM) process were analyzed by means of the atomic force microscopy (AFM) technique. Experimental results indicate that the surface texture after EDM is determined by the discharge energy during processing. An excellent machined finish can be obtained by setting the machine parameters at a low pulse energy. The surface roughness and the depth of the micro-cracks were proportional to the power input. Furthermore, the AFM application yielded information about the depth of the micro-cracks is particularly important in the post treatment of AISI D2 tool steel machined by EDM.

  8. Characterization of the Polycaprolactone Melt Crystallization: Complementary Optical Microscopy, DSC, and AFM Studies

    PubMed Central

    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. PMID:24523644

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    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 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.

  11. 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

  12. Nanospot soldering polystyrene nanoparticles with an optical fiber probe laser irradiating a metallic AFM probe based on the near-field enhancement effect.

    PubMed

    Cui, Jianlei; Yang, Lijun; Wang, Yang; Mei, Xuesong; Wang, Wenjun; Hou, Chaojian

    2015-02-04

    With the development of nanoscience and nanotechnology for the bottom-up nanofabrication of nanostructures formed from polystyrene nanoparticles, joining technology is an essential step in the manufacturing and assembly of nanodevices and nanostructures in order to provide mechanical integration and connection. To study the nanospot welding of polystyrene nanoparticles, we propose a new nanospot-soldering method using the near-field enhancement effect of a metallic atomic force microscope (AFM) probe tip that is irradiated by an optical fiber probe laser. On the basis of our theoretical analysis of the near-field enhancement effect, we set up an experimental system for nanospot soldering; this approach is carried out by using an optical fiber probe laser to irradiate the AFM probe tip to sinter the nanoparticles, providing a promising technical approach for the application of nanosoldering in nanoscience and nanotechnology.

  13. 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).

  14. Surface study of irradiated sapphires from Phrae Province, Thailand using AFM

    NASA Astrophysics Data System (ADS)

    Monarumit, N.; Jivanantaka, P.; Mogmued, J.; Lhuaamporn, T.; Satitkune, S.

    2017-09-01

    The irradiation is one of the gemstone enhancements for improving the gem quality. Typically, there are many varieties of irradiated gemstones in the gem market such as diamond, topaz, and sapphire. However, it is hard to identify the gemstones before and after irradiation. The aim of this study is to analyze the surface morphology for classifying the pristine and irradiated sapphires using atomic force microscope (AFM). In this study, the sapphire samples were collected from Phrae Province, Thailand. The samples were irradiated by high energy electron beam for a dose of ionizing radiation at 40,000 kGy. As the results, the surface morphology of pristine sapphires shows regular atomic arrangement, whereas, the surface morphology of irradiated sapphires shows the nano-channel observed by the 2D and 3D AFM images. The atomic step height and root mean square roughness have changed after irradiation due to the micro-structural defect on the sapphire surface. Therefore, this study is a frontier application for sapphire identification before and after irradiation.

  15. Changes in surface characteristics of two different resin composites after 1 year water storage: An SEM and AFM study.

    PubMed

    Tekçe, Neslihan; Pala, Kansad; Demirci, Mustafa; Tuncer, Safa

    2016-11-01

    To evaluate changes in surface characteristics of two different resin composites after 1 year of water storage using a profilometer, Vickers hardness, scanning electron microscopy (SEM), and atomic force microscopy (AFM). A total of 46 composite disk specimens (10 mm in diameter and 2 mm thick) were fabricated using Clearfil Majesty Esthetic and Clearfil Majesty Posterior (Kuraray Medical Co, Tokyo, Japan). Ten specimens from each composite were used for surface roughness and microhardness tests (n = 10). For each composite, scanning electron microscope (SEM, n = 2) and atomic force microscope (AFM, n = 1) images were obtained after 24 h and 1 year of water storage. The data were analyzed using two-way analysis of variance and a post-hoc Bonferroni test. Microhardness values of Clearfil Majesty Esthetic decreased significantly (78.15-63.74, p = 0.015) and surface roughness values did not change after 1 year of water storage (0.36-0.39, p = 0.464). Clearfil Majesty Posterior microhardness values were quite stable (138.74-137.25, p = 0.784), and surface roughness values increased significantly (0.39-0.48, p = 0.028) over 1 year. One year of water storage caused microhardness values for Clearfil Majesty Esthetic to decrease and the surface roughness of Clearfil Majesty Posterior increased. AFM and SEM images demonstrated surface detoration of the materials after 1 year and ensured similar results with the quantitative test methods. SCANNING 38:694-700, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

  16. Construction of Compact Polyelectrolyte Multilayers Inspired by Marine Mussel: Effects of Salt Concentration and pH As Observed by QCM-D and AFM.

    PubMed

    Wang, Weina; Xu, Yisheng; Backes, Sebastian; Li, Ang; Micciulla, Samantha; Kayitmazer, A Basak; Li, Li; Guo, Xuhong; von Klitzing, Regine

    2016-04-12

    Biomimetic multilayers based on layer-by-layer (LbL) assembly were prepared as functional films with compact structure by incorporating the mussel-inspired catechol cross-linking. Dopamine-modified poly(acrylic acid) (PAADopa) was synthesized as a polyanion to offer electrostatic interaction with the prelayer polyethylenimine (PEI) and consecutively cross-linked by zinc to generate compact multilayers with tunable physicochemical properties. In situ layer-by-layer growth and cross-linking were monitored by a quartz crystal microbalance with dissipation (QCM-D) to reveal the kinetics of the process and the influence of Dopa chemistry. Addition of Dopa enhanced the mass adsorption and led to the formation of a more compact structure. An increase of ionic strength induced an increase in mass adsorption in the Dopa-cross-linked multilayers. This is a universal approach for coating of various surfaces such as Au, SiO2, Ti, and Al2O3. Roughness observed by AFM in both wet and dry conditions was compared to confirm the compact morphology of Dopa-cross-linked multilayers. Because of the pH sensitivity of Dopa moiety, metal-chelated Dopa groups can be turned into softer structure at higher pH as revealed by reduction of Young's modulus determined by MFP-3D AFM. A deeper insight into the growth and mechanical properties of Dopa-cross-linked polyelectrolyte multilayers was addressed in the present study. This allows a better control of these systems for bioapplications.

  17. Functionalized AFM probes for force spectroscopy: eigenmode shapes and stiffness calibration through thermal noise measurements.

    PubMed

    Laurent, Justine; Steinberger, Audrey; Bellon, Ludovic

    2013-06-07

    The functionalization of an atomic force microscope (AFM) cantilever with a colloidal bead is a widely used technique when the geometry between the probe and the sample must be controlled, particularly in force spectroscopy. But some questions remain: how does a bead glued at the end of a cantilever influence its mechanical response? And more importantly for quantitative measurements, can we still determine the stiffness of the AFM probe with traditional techniques?In this paper, the influence of the colloidal mass loading on the eigenmode shape and resonant frequency is investigated by measuring the thermal noise on rectangular AFM microcantilevers with and without beads attached at their extremities. The experiments are performed with a home-made ultra-sensitive AFM, based on differential interferometry. The focused beam from the interferometer probes the cantilever at different positions and the spatial shapes of the modes are determined up to the fifth resonance, without external excitation. The results clearly demonstrate that the first eigenmode is almost unchanged by mass loading. However the oscillation behavior of higher resonances presents a marked difference: with a particle glued at its extremity, the nodes of the modes are displaced towards the free end of the cantilever. These results are compared to an analytical model taking into account the mass and inertial moment of the load in an Euler-Bernoulli framework, where the normalization of the eigenmodes is explicitly worked out in order to allow a quantitative prediction of the thermal noise amplitude of each mode. A good agreement between the experimental results and the analytical model is demonstrated, allowing a clean calibration of the probe stiffness.

  18. 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 TiO 2 ). 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.

  19. A novel AFM-based 5-axis nanoscale machine tool for fabrication of nanostructures on a micro ball

    NASA Astrophysics Data System (ADS)

    Geng, Yanquan; Wang, Yuzhang; Yan, Yongda; Zhao, Xuesen

    2017-11-01

    This paper presents a novel atomic force microscopy (AFM)-based 5-axis nanoscale machine tool developed to fabricate nanostructures on different annuli of the micro ball. Different nanostructures can be obtained by combining the scratching trajectory of the AFM tip with the movement of the high precision air-bearing spindle. The center of the micro ball is aligned to be coincided with the gyration center of the high precision to guarantee the machining process during the rotating of the air-bearing spindle. Processing on different annuli of the micro ball is achieved by controlling the distance between the center of the micro ball and the rotation center of the AFM head. Nanostructures including square cavities, circular cavities, triangular cavities, and an annular nanochannel are machined successfully on the three different circumferences of a micro ball with a diameter of 1500 μm. Moreover, the influences of the error motions of the high precision air-bearing spindle and the eccentric between the micro ball and the gyration center of the high precision air-bearing spindle on the processing position error on the micro ball are also investigated. This proposed machining method has the potential to prepare the inertial confinement fusion target with the expected dimension defects, which would advance the application of the AFM tip-based nanomachining approach.

  20. Localization and force analysis at the single virus particle level using atomic force microscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Chih-Hao; Horng, Jim-Tong; Chang, Jeng-Shian

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer Localization of single virus particle. Black-Right-Pointing-Pointer Force measurements. Black-Right-Pointing-Pointer Force mapping. -- Abstract: Atomic force microscopy (AFM) is a vital instrument in nanobiotechnology. In this study, we developed a method that enables AFM to simultaneously measure specific unbinding force and map the viral glycoprotein at the single virus particle level. The average diameter of virus particles from AFM images and the specificity between the viral surface antigen and antibody probe were integrated to design a three-stage method that sets the measuring area to a single virus particle before obtaining the force measurements, where the influenza virus was usedmore » as the object of measurements. Based on the purposed method and performed analysis, several findings can be derived from the results. The mean unbinding force of a single virus particle can be quantified, and no significant difference exists in this value among virus particles. Furthermore, the repeatability of the proposed method is demonstrated. The force mapping images reveal that the distributions of surface viral antigens recognized by antibody probe were dispersed on the whole surface of individual virus particles under the proposed method and experimental criteria; meanwhile, the binding probabilities are similar among particles. This approach can be easily applied to most AFM systems without specific components or configurations. These results help understand the force-based analysis at the single virus particle level, and therefore, can reinforce the capability of AFM to investigate a specific type of viral surface protein and its distributions.« less

  1. Towards early detection of cervical cancer: Fractal dimension of AFM images of human cervical epithelial cells at different stages of progression to cancer.

    PubMed

    Guz, Nataliia V; Dokukin, Maxim E; Woodworth, Craig D; Cardin, Andrew; Sokolov, Igor

    2015-10-01

    We used AFM HarmoniX modality to analyse the surface of individual human cervical epithelial cells at three stages of progression to cancer, normal, immortal (pre-malignant) and carcinoma cells. Primary cells from 6 normal strains, 6 cancer, and 6 immortalized lines (derived by plasmid DNA-HPV-16 transfection of cells from 6 healthy individuals) were tested. This cell model allowed for good control of the cell phenotype down to the single cell level, which is impractical to attain in clinical screening tests (ex-vivo). AFM maps of physical (nonspecific) adhesion are collected on fixed dried cells. We show that a surface parameter called fractal dimension can be used to segregate normal from both immortal pre-malignant and malignant cells with sensitivity and specificity of more than 99%. The reported method of analysis can be directly applied to cells collected in liquid cytology screening tests and identified as abnormal with regular optical methods to increase sensitivity. Despite cervical smear screening, sometimes it is very difficult to differentiate cancers cells from pre-malignant cells. By using AFM to analyze the surface properties of human cervical epithelial cells, the authors were able to accurately identify normal from abnormal cells. This method could augment existing protocols to increase diagnostic accuracy. Copyright © 2015. Published by Elsevier Inc.

  2. Material property analytical relations for the case of an AFM probe tapping a viscoelastic surface containing multiple characteristic times

    PubMed Central

    López-Guerra, Enrique A

    2017-01-01

    We explore the contact problem of a flat-end indenter penetrating intermittently a generalized viscoelastic surface, containing multiple characteristic times. This problem is especially relevant for nanoprobing of viscoelastic surfaces with the highly popular tapping-mode AFM imaging technique. By focusing on the material perspective and employing a rigorous rheological approach, we deliver analytical closed-form solutions that provide physical insight into the viscoelastic sources of repulsive forces, tip–sample dissipation and virial of the interaction. We also offer a systematic comparison to the well-established standard harmonic excitation, which is the case relevant for dynamic mechanical analysis (DMA) and for AFM techniques where tip–sample sinusoidal interaction is permanent. This comparison highlights the substantial complexity added by the intermittent-contact nature of the interaction, which precludes the derivation of straightforward equations as is the case for the well-known harmonic excitations. The derivations offered have been thoroughly validated through numerical simulations. Despite the complexities inherent to the intermittent-contact nature of the technique, the analytical findings highlight the potential feasibility of extracting meaningful viscoelastic properties with this imaging method. PMID:29114450

  3. 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.

  4. The association between acute flaccid myelitis (AFM) and Enterovirus D68 (EV-D68) – what is the evidence for causation?

    PubMed Central

    Dyda, Amalie; Stelzer-Braid, Sacha; Adam, Dillon; Chughtai, Abrar A; MacIntyre, C Raina

    2018-01-01

    Background Enterovirus D68 (EV-D68) has historically been a sporadic disease, causing occasional small outbreaks of generally mild infection. In recent years, there has been evidence of an increase in EV-D68 infections globally. Large outbreaks of EV-D68, with thousands of cases, occurred in the United States, Canada and Europe in 2014. The outbreaks were associated temporally and geographically with an increase in clusters of acute flaccid myelitis (AFM).
Aims: We aimed to evaluate a causal association between EV-D68 and AFM. 
Methods: Using data from the published and grey literature, we applied the Bradford Hill criteria, a set of nine principles applied to examine causality, to evaluate the relationship between EV-D68 and AFM. Based on available evidence, we defined the Bradford Hill Criteria as being not met, or met minimally, partially or fully. 
Results: Available evidence applied to EV-D68 and AFM showed that six of the Bradford Hill criteria were fully met and two were partially met. The criterion of biological gradient was minimally met. The incidence of EV-D68 infections is increasing world-wide. Phylogenetic epidemiology showed diversification from the original Fermon and Rhyne strains since the year 2000, with evolution of a genetically distinct outbreak strain, clade B1. Clade B1, but not older strains, is associated with AFM and is neuropathic in animal models. 
Conclusion: While more research is needed on dose–response relationship, application of the Bradford Hill criteria supported a causal relationship between EV-D68 and AFM. PMID:29386095

  5. Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).

    PubMed

    Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen

    2016-01-21

    The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

  6. Writing with Fluid: Structuring Hydrogels with Micrometer Precision by AFM in Combination with Nanofluidics.

    PubMed

    Helfricht, Nicolas; Mark, Andreas; Behr, Marina; Bernet, Andreas; Schmidt, Hans-Werner; Papastavrou, Georg

    2017-08-01

    Hydrogels have many applications in biomedical surface modification and tissue engineering. However, the structuring of hydrogels after their formation represents still a major challenge, in particular due to their softness. Here, a novel approach is presented that is based on the combination of atomic force microscopy (AFM) and nanofluidics, also referred to as FluidFM technology. Its applicability is demonstrated for supramolecular hydrogel films that are prepared from low-molecular weight hydrogelators, such as derivates of 1,3,5-benzene tricarboxamides (BTAs). BTA films can be dissolved selectively by ejecting alkaline solution through the aperture of a hollow AFM-cantilever connected to a nanofluidic controller. The AFM-based force control is essential in preventing mechanical destruction of the hydrogels. The resulting "chemical writing" process is studied in detail and the influence of various parameters, such as applied pressure and time, is validated. It is demonstrated that the achievable structuring precision is primarily limited by diffusion and the aperture dimensions. Recently, various additive techniques have been presented to pattern hydrogels. The here-presented subtractive approach can not only be applied to structure hydrogels from the large class of reversibly formed gels with superior resolution but would also allow for the selective loading of the hydrogels with active substances or nanoparticles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  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. The Micro Imaging and Dust Analysis System - New Possibilities for Space Sciences

    NASA Astrophysics Data System (ADS)

    Schmied, R.; Torkar, K..; Jeszenszky, H.; Romstedt, J.; Mannel, T.; Bentley, M. S.

    2015-10-01

    The Rosetta mission addresses a range of fundamental questions in Solar System and cometary science and the MIDAS instrument on-board the orbiter is one of the dust analysis systems. While GIADA analyses the dust flux and spatial distribution as a function of time and space and COSIMA investigates the elemental composition of cometary grains, MIDAS is a unique high resolution Atomic Force Microscope (AFM) combined with a dust collection and handling system designed to reveal the three-dimensional topographical structure of nanoand micrometer sized dust particles [1]. In this work we concentrate on the instrumental functionality and limitations coming from the constcution and operation dealing with an AFM fabricated nearly 20 years ago and operating in a harsh environment.

  9. 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).

  10. 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).

  11. Opposite Surface and Bulk Solvatochromic Effects in a Molecular Spin-Crossover Compound Revealed by Ambient Pressure X-ray Absorption Spectroscopy.

    PubMed

    Borgatti, Francesco; Torelli, Piero; Brucale, Marco; Gentili, Denis; Panaccione, Giancarlo; Castan Guerrero, Celia; Schäfer, Bernhard; Ruben, Mario; Cavallini, Massimiliano

    2018-03-27

    We investigate the solvatochromic effect of a Fe-based spin-crossover (SCO) compound via ambient pressure soft X-ray absorption spectroscopy (AP-XAS) and atomic force microscopy (AFM). AP-XAS provides the direct evidence of the spin configuration for the Fe(II) 3d states of the SCO material upon in situ exposure to specific gas or vapor mixtures; concurrent changes in nanoscale topography and mechanical characteristics are revealed via AFM imaging and AFM-based force spectroscopy, respectively. We find that exposing the SCO material to gaseous helium promotes an effective decrease of the transition temperature of its surface layers, while the exposure to methanol vapor causes opposite surfacial and bulk solvatochromic effects. Surfacial solvatochromism is accompanied by a dramatic reduction of the surface layers stiffness. We propose a rationalization of the observed effects based on interfacial dehydration and solvation phenomena.

  12. Immunoactive two-dimensional self-assembly of monoclonal antibodies in aqueous solution revealed by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ido, Shinichiro; Kimiya, Hirokazu; Kobayashi, Kei; Kominami, Hiroaki; Matsushige, Kazumi; Yamada, Hirofumi

    2014-03-01

    The conformational flexibility of antibodies in solution directly affects their immune function. Namely, the flexible hinge regions of immunoglobulin G (IgG) antibodies are essential in epitope-specific antigen recognition and biological effector function. The antibody structure, which is strongly related to its functions, has been partially revealed by electron microscopy and X-ray crystallography, but only under non-physiological conditions. Here we observed monoclonal IgG antibodies in aqueous solution by high-resolution frequency modulation atomic force microscopy (FM-AFM). We found that monoclonal antibodies self-assemble into hexamers, which form two-dimensional crystals in aqueous solution. Furthermore, by directly observing antibody-antigen interactions using FM-AFM, we revealed that IgG molecules in the crystal retain immunoactivity. As the self-assembled monolayer crystal of antibodies retains immunoactivity at a neutral pH and is functionally stable at a wide range of pH and temperature, the antibody crystal is applicable to new biotechnological platforms for biosensors or bioassays.

  13. 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

  14. Modeling AFM-induced PEVK extension and the reversible unfolding of Ig/FNIII domains in single and multiple titin molecules.

    PubMed Central

    Zhang, B; Evans, J S

    2001-01-01

    Molecular elasticity is associated with a select number of polypeptides and proteins, such as titin, Lustrin A, silk fibroin, and spider silk dragline protein. In the case of titin, the globular (Ig) and non-globular (PEVK) regions act as extensible springs under stretch; however, their unfolding behavior and force extension characteristics are different. Using our time-dependent macroscopic method for simulating AFM-induced titin Ig domain unfolding and refolding, we simulate the extension and relaxation of hypothetical titin chains containing Ig domains and a PEVK region. Two different models are explored: 1) a series-linked WLC expression that treats the PEVK region as a distinct entropic spring, and 2) a summation of N single WLC expressions that simulates the extension and release of a discrete number of parallel titin chains containing constant or variable amounts of PEVK. In addition to these simulations, we also modeled the extension of a hypothetical PEVK domain using a linear Hooke's spring model to account for "enthalpic" contributions to PEVK elasticity. We find that the modified WLC simulations feature chain length compensation, Ig domain unfolding/refolding, and force-extension behavior that more closely approximate AFM, laser tweezer, and immunolocalization experimental data. In addition, our simulations reveal the following: 1) PEVK extension overlaps with the onset of Ig domain unfolding, and 2) variations in PEVK content within a titin chain ensemble lead to elastic diversity within that ensemble. PMID:11159428

  15. 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.

  16. 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.

  17. Ultrasonically synthesized organic liquid-filled chitosan microcapsules: part 2: characterization using AFM (atomic force microscopy) and combined AFM-confocal laser scanning fluorescence microscopy.

    PubMed

    Mettu, Srinivas; Ye, Qianyu; Zhou, Meifang; Dagastine, Raymond; Ashokkumar, Muthupandian

    2018-04-25

    Atomic Force Microscopy (AFM) is used to measure the stiffness and Young's modulus of individual microcapsules that have a chitosan cross-linked shell encapsulating tetradecane. The oil filled microcapsules were prepared using a one pot synthesis via ultrasonic emulsification of tetradecane and crosslinking of the chitosan shell in aqueous solutions of acetic acid. The concentration of acetic acid in aqueous solutions of chitosan was varied from 0.2% to 25% v/v. The effect of acetic acid concentration and size of the individual microcapsules on the strength was probed. The deformations and forces required to rupture the microcapsules were also measured. Three dimensional deformations of microcapsules under large applied loads were obtained by the combination of Laser Scanning Confocal Microscopy (LSCM) with Atomic Force Microscopy (AFM). The stiffness, and hence the modulus, of the microcapsules was found to decrease with an increase in size with the average stiffness ranging from 82 to 111 mN m-1 and average Young's modulus ranging from 0.4 to 6.5 MPa. The forces required to rupture the microcapsules varied from 150 to 250 nN with deformations of the microcapsules up to 62 to 110% relative to their radius, respectively. Three dimensional images obtained using laser scanning confocal microscopy showed that the microcapsules retained their structure and shape after being subjected to large deformations and subsequent removal of the loads. Based on the above observations, the oil filled chitosan crosslinked microcapsules are an ideal choice for use in the food and pharmaceutical industries as they would be able to withstand the process conditions encountered.

  18. Capillary force on a tilted cylinder: Atomic Force Microscope (AFM) measurements.

    PubMed

    Kosgodagan Acharige, Sébastien; Laurent, Justine; Steinberger, Audrey

    2017-11-01

    The capillary force in situations where the liquid meniscus is asymmetric, such as the one around a tilted object, has been hitherto barely investigated even though these situations are very common in practice. In particular, the capillary force exerted on a tilted object may depend on the dipping angle i. We investigate experimentally the capillary force that applies on a tilted cylinder as a function of its dipping angle i, using a home-built tilting Atomic Force Microscope (AFM) with custom made probes. A micrometric-size rod is glued at the end of an AFM cantilever of known stiffness, whose deflection is measured when the cylindrical probe is dipped in and retracted from reference liquids. We show that a torque correction is necessary to understand the measured deflection. We give the explicit expression of this correction as a function of the probes' geometrical parameters, so that its magnitude can be readily evaluated. The results are compatible with a vertical capillary force varying as 1/cosi, in agreement with a recent theoretical prediction. Finally, we discuss the accuracy of the method for measuring the surface tension times the cosine of the contact angle of the liquid on the probe. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

    PubMed

    Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

    2016-03-15

    Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

  20. Computational simulation of subatomic-resolution AFM and STM images for graphene/hexagonal boron nitride heterostructures with intercalated defects

    NASA Astrophysics Data System (ADS)

    Lee, Junsu; Kim, Minjung; Chelikowsky, James R.; Kim, Gunn

    2016-07-01

    Using ab initio density functional calculations, we predict subatomic-resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) images of vertical heterostructures of graphene/hexagonal boron nitride (h-BN) with an intercalated metal atom (Li, K, Cr, Mn, Co, or Cu), and study the effects of the extrinsic metal defect on the interfacial coupling. We find that the structural deformation of the graphene/h-BN layer caused by the metal defect strongly affects the AFM images, whereas orbital hybridization between the metal defect and the graphene/h-BN layer characterizes the STM images.

  1. 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.

  2. Polarization induced conductive AFM on cobalt doped ZnO nanostructures

    NASA Astrophysics Data System (ADS)

    Sahoo, Pradosh Kumar; Mangamma, G.; Rajesh, A.; Kamruddin, M.; Dash, S.

    2017-05-01

    In the present work cobalt doped ZnO (CZO) nanostructures (NS) have been synthesized by of sol-gel and spin coating process. After the crystal phase confirmation by GIXRD and Raman spectroscopy, Conductive Atomic Force Microscopy (C-AFM) measurement was performed on CZO NS which shows the random distribution of electrically conducting zones on the surface of the material exhibiting current in the range 4-170 pA. We provide the possible mechanisms for variation in current distribution essential for quantitative understanding of transport properties of ZnO NS in doped and undoped forms.

  3. PREFACE: NC-AFM 2004: Proceedings of the 7th International Conference on Non-contact Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Schwarz, Udo

    2005-03-01

    With the ongoing miniaturization of devices and controlled nanostructuring of materials, the importance of atomic-scale information on surfaces and surface properties is growing continuously. The astonishing progress in nanoscience and nanotechnology that took place during the last two decades was in many ways related to recent progress in high-resolution imaging techniques such as scanning tunnelling microscopy and transmission electron microscopy. Since the mid-1990s, non-contact atomic force microscopy (NC-AFM) performed in ultrahigh vacuum has evolved as an alternative technique that achieves atomic resolution, but without the restriction to conducting surfaces of the previously established techniques. Advances of the rapidly developing field of NC-AFM are discussed at annual conferences as part of a series that started in 1998 in Osaka, Japan. This special issue of Nanotechnology is a compilation of original work presented at the 7th International Conference on Non-contact Atomic Force Microscopy that took place in Seattle, USA, 12-15 September 2004. Over the years, the conference grew in size and scope. Atomic resolution imaging of oxides and semiconductors remains an issue. Noticeable new developments have been presented in this regard such as, e.g., the demonstrated ability to manipulate individual atoms. Additionally, the investigation of individual molecules, clusters, and organic materials gains more and more attention. In this context, considerable effort is undertaken to transfer the NC-AFM principle based on frequency modulation to applications in air and liquids with the goal of enabling high-resolution surface studies of biological material in native environments, as well as to reduce the experimental complexity, which so far involves the availability of (costly) vacuum systems. Force spectroscopy methods continue to be improved and are applied to topics such as the imaging of the three-dimensional force field as a function of the distance with

  4. 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.

  5. Characterization of opto-electrical enhancement of tandem photoelectrochemical cells by using photoconductive-AFM

    NASA Astrophysics Data System (ADS)

    Park, Sun-Young; Elbersen, Rick; Huskens, Jurriaan; Gardeniers, Han; Lee, Joo-Yul; Mul, Guido; Heo, Jinhee

    2017-07-01

    Solar-to-hydrogen conversion by water splitting in photoelectrochemical cells (PECs) is a promising approach to alleviate problems associated with intermittency in solar energy supply and demand. Several interfacial resistances in photoelectrodes limit the performance of such cells, while the properties of interfaces are not easy to analyze in situ. We applied photoconductive-AFM to analyze the performance of WO3/p+n Si photoanodes, containing an ultra-thin metal interface of either Au or Pt. The Au interface consisted of Au nanoparticles with well-ordered interspacing, while Pt was present in the form of a continuous film. Photoconductive-AFM data show that upon illumination significantly larger currents are measured for the WO3/p+n Si anode equipped with the Au interface, as compared to the WO3/p+n Si anode with the Pt interface, in agreement with the better performance of the former electrode in a photoelectrochemical cell. The remarkable performance of the Au-containing electrode is proposed to be the result of favorable electron-hole recombination rates induced by the Au nanoparticles in a plasmon resonance excited state.

  6. Tribological behavior of micro/nano-patterned surfaces in contact with AFM colloidal probe

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoliang; Wang, Xiu; Kong, Wen; Yi, Gewen; Jia, Junhong

    2011-10-01

    In effort to investigate the influence of the micro/nano-patterning or surface texturing on the nanotribological properties of patterned surfaces, the patterned polydimethylsiloxane (PDMS) surfaces with pillars were fabricated by replica molding technique. The surface morphologies of patterned PDMS surfaces with varying pillar sizes and spacing between pillars were characterized by atomic force microscope (AFM) and scanning electron microscope (SEM). The AFM/FFM was used to acquire the friction force images of micro/nano-patterned surfaces using a colloidal probe. A difference in friction force produced a contrast on the friction force images when the colloidal probe slid over different regions of the patterned polymer surfaces. The average friction force of patterned surface was related to the spacing between the pillars and their size. It decreased with the decreasing of spacing between the pillars and the increasing of pillar size. A reduction in friction force was attributed to the reduced area of contact between patterned surface and colloidal probe. Additionally, the average friction force increased with increasing applied load and sliding velocity.

  7. Sensing inhomogeneous mechanical properties of human corneal Descemet's membrane with AFM nano-indentation.

    PubMed

    Di Mundo, Rosa; Recchia, Giuseppina; Parekh, Mohit; Ruzza, Alessandro; Ferrari, Stefano; Carbone, Giuseppe

    2017-10-01

    The paper describes a highly space-resolved characterization of the surface mechanical properties of the posterior human corneal layer (Descemet's membrane). This has been accomplished with Atomic Force Microscopy (AFM) nano-indentation by using a probe with a sharp tip geometry. Results indicate that the contact with this biological tissue in liquid occurs with no (or very low) adhesion. More importantly, under the same operating conditions, a broad distribution of penetration depth can be measured on different x-y positions of the tissue surface, indicating a high inhomogeneity of surface stiffness, not yet clearly reported in the literature. An important contribution to such inhomogeneity should be ascribed to the discontinuous nature of the collagen/proteoglycans fibers matrix tissue, as can be imaged by AFM when the tissue is semi-dry. Using classical contact mechanics calculations adapted to the specific geometry of the tetrahedral tip it has been found that the elastic modulus E of the material in the very proximity of the surface ranges from 0.23 to 2.6 kPa. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. 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.

  9. AFM force measurements of the gp120-sCD4 and gp120 or CD4 antigen-antibody interactions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chen, Yong, E-mail: dr_yongchen@hotmail.com; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612; Zeng, Gucheng

    2011-04-08

    Highlights: {yields} The unbinding force of sCD4-gp120 interaction was 25.45 {+-} 20.46 pN. {yields} The unbinding force of CD4 antigen-antibody interaction was 51.22 {+-} 34.64 pN. {yields} The unbinding force of gp120 antigen-antibody interaction was 89.87 {+-} 44.63 pN. {yields} The interaction forces between various HIV inhibitors and the target molecules are significantly different. {yields} Functionalizing on AFM tip or substrate of an interaction pair caused different results. -- Abstract: Soluble CD4 (sCD4), anti-CD4 antibody, and anti-gp120 antibody have long been regarded as entry inhibitors in human immunodeficiency virus (HIV) therapy. However, the interactions between these HIV entry inhibitors andmore » corresponding target molecules are still poorly understood. In this study, atomic force microscopy (AFM) was utilized to investigate the interaction forces among them. We found that the unbinding forces of sCD4-gp120 interaction, CD4 antigen-antibody interaction, and gp120 antigen-antibody interaction were 25.45 {+-} 20.46, 51.22 {+-} 34.64, and 89.87 {+-} 44.63 pN, respectively, which may provide important mechanical information for understanding the effects of viral entry inhibitors on HIV infection. Moreover, we found that the functionalization of an interaction pair on AFM tip or substrate significantly influenced the results, implying that we must perform AFM force measurement and analyze the data with more caution.« less

  10. Cell mechanics as a marker for diseases: Biomedical applications of AFM

    NASA Astrophysics Data System (ADS)

    Rianna, Carmela; Radmacher, Manfred

    2016-08-01

    Many diseases are related to changes in cell mechanics. Atomic Force Microscopy (AFM) is one of the most suitable techniques allowing the investigation of both topography and mechanical properties of adherent cells with high spatial resolution under physiological conditions. Over the years the use of this technique in medical and clinical applications has largely increased, resulting in the notion of cell mechanics as a biomarker to discriminate between different physiological and pathological states of cells. Cell mechanics has proven to be a biophysical fingerprint able discerning between cell phenotypes, unraveling processes in aging or diseases, or even detecting and diagnosing cellular pathologies. We will review in this report some of the works on cell mechanics investigated by AFM with clinical and medical relevance in order to clarify the state of research in this field and to highlight the role of cell mechanics in the study of pathologies, focusing on cancer, blood and cardiovascular diseases. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 26 September 2016. The original version supplied to AIP Publishing contained blurred figures introduced during the PDF conversion process. Moreover, Equations (5), (6), and (7) were not correctly cited in the text. These errors have been corrected in the updated and republished article.

  11. AFM of the ultrastructural and mechanical properties of lipid-raft-disrupted and/or cold-treated endothelial cells.

    PubMed

    Wu, Li; Huang, Jie; Yu, Xiaoxue; Zhou, Xiaoqing; Gan, Chaoye; Li, Ming; Chen, Yong

    2014-02-01

    The nonionic detergent extraction at 4 °C and the cholesterol-depletion-induced lipid raft disruption are the two widely used experimental strategies for lipid raft research. However, the effects of raft disruption and/or cold treatment on the ultrastructural and mechanical properties of cells are still unclear. Here, we evaluated the effects of raft disruption and/or cold (4 °C) treatment on these properties of living human umbilical vein endothelial cells (HUVECs). At first, the cholesterol-depletion-induced raft disruption was visualized by confocal microscopy and atomic force microscopy (AFM) in combination with fluorescent quantum dots. Next, the cold-induced cell contraction and the formation of end-branched filopodia were observed by confocal microscopy and AFM. Then, the cell-surface ultrastructures were imaged by AFM, and the data showed that raft disruption and cold treatment induced opposite effects on cell-surface roughness (a significant decrease and a significant increase, respectively). Moreover, the cell-surface mechanical properties (stiffness and adhesion force) of raft-disrupted- and/or cold-treated HUVECs were measured by the force measurement function of AFM. We found that raft disruption and cold treatment induced parallel effects on cell stiffness (increase) or adhesion force (decrease) and that the combination of the two treatments caused dramatically strengthened effects. Finally, raft disruption was found to significantly impair cell migration as previously reported, whereas temporary cold treatment only caused a slight but nonsignificant decrease in cell migration performed at physiological temperature. Although the mechanisms for causing these results might be complicated and more in-depth studies will be needed, our data may provide important information for better understanding the effects of raft disruption or cold treatment on cells and the two strategies for lipid raft research.

  12. 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.

  13. Structural and mechanical heterogeneity of the erythrocyte membrane reveals hallmarks of membrane stability.

    PubMed

    Picas, Laura; Rico, Félix; Deforet, Maxime; Scheuring, Simon

    2013-02-26

    The erythrocyte membrane, a metabolically regulated active structure that comprises lipid molecules, junctional complexes, and the spectrin network, enables the cell to undergo large passive deformations when passing through the microvascular system. Here we use atomic force microscopy (AFM) imaging and quantitative mechanical mapping at nanometer resolution to correlate structure and mechanics of key components of the erythrocyte membrane, crucial for cell integrity and function. Our data reveal structural and mechanical heterogeneity modulated by the metabolic state at unprecedented nanometer resolution. ATP-depletion, reducing skeletal junction phosphorylation in RBC cells, leads to membrane stiffening. Analysis of ghosts and shear-force opened erythrocytes show that, in the absence of cytosolic kinases, spectrin phosphorylation results in membrane stiffening at the extracellular face and a reduced junction remodeling in response to loading forces. Topography and mechanical mapping of single components at the cytoplasmic face reveal that, surprisingly, spectrin phosphorylation by ATP softens individual filaments. Our findings suggest that, besides the mechanical signature of each component, the RBC membrane mechanics is regulated by the metabolic state and the assembly of its structural elements.

  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. Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

    Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

  16. Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

    DOE PAGES

    Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

    2017-03-08

    Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

  17. Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

    PubMed Central

    Noh, Hanaul; Diaz, Alfredo J

    2017-01-01

    Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, and is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules. PMID:28382247

  18. Whole-Cell Electrical Activity Under Direct Mechanical Stimulus by AFM Cantilever Using Planar Patch Clamp Chip Approach

    PubMed Central

    Upadhye, Kalpesh V.; Candiello, Joseph E.; Davidson, Lance A.; Lin, Hai

    2011-01-01

    Patch clamp is a powerful tool for studying the properties of ion-channels and cellular membrane. In recent years, planar patch clamp chips have been fabricated from various materials including glass, quartz, silicon, silicon nitride, polydimethyl-siloxane (PDMS), and silicon dioxide. Planar patch clamps have made automation of patch clamp recordings possible. However, most planar patch clamp chips have limitations when used in combination with other techniques. Furthermore, the fabrication methods used are often expensive and require specialized equipments. An improved design as well as fabrication and characterization of a silicon-based planar patch clamp chip are described in this report. Fabrication involves true batch fabrication processes that can be performed in most common microfabrication facilities using well established MEMS techniques. Our planar patch clamp chips can form giga-ohm seals with the cell plasma membrane with success rate comparable to existing patch clamp techniques. The chip permits whole-cell voltage clamp recordings on variety of cell types including Chinese Hamster Ovary (CHO) cells and pheochromocytoma (PC12) cells, for times longer than most available patch clamp chips. When combined with a custom microfluidics chamber, we demonstrate that it is possible to perfuse the extra-cellular as well as intra-cellular buffers. The chamber design allows integration of planar patch clamp with atomic force microscope (AFM). Using our planar patch clamp chip and microfluidics chamber, we have recorded whole-cell mechanosensitive (MS) currents produced by directly stimulating human keratinocyte (HaCaT) cells using an AFM cantilever. Our results reveal the spatial distribution of MS ion channels and temporal details of the responses from MS channels. The results show that planar patch clamp chips have great potential for multi-parametric high throughput studies of ion channel proteins. PMID:22174731

  19. 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

  20. AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

    PubMed Central

    Ruggeri, Francesco Simone; Habchi, Johnny; Cerreta, Andrea; Dietler, Giovanni

    2016-01-01

    Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases. PMID:27189600

  1. 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).

  2. Automatic hammering of nano-patterns on special polymer film by using a vibrating AFM tip

    PubMed Central

    2012-01-01

    Complicated nano-patterns with linewidth less than 18 nm can be automatically hammered by using atomic force microscopy (AFM) tip in tapping mode with high speed. In this study, the special sample was thin poly(styrene-ethylene/butylenes-styrene) (SEBS) block copolymer film with hexagonal spherical microstructures. An ordinary silicon tip was used as a nano-hammer, and the entire hammering process is controlled by a computer program. Experimental results demonstrate that such structure-tailored thin films enable AFM tip hammering to be performed on their surfaces. Both imprinted and embossed nano-patterns can be generated by using a vibrating tip with a larger tapping load and by using a predefined program to control the route of tip movement as it passes over the sample’s surface. Specific details for the fabrication of structure-tailored SEBS film and the theory for auto-hammering patterns were presented in detail. PMID:22889045

  3. 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.

  4. Leveraging Air Force Medical Service (AFMS) Senior Leadership Corps Diversity to Improve Efficiency

    DTIC Science & Technology

    2013-04-01

    licensing , and board certification requirements . A few of these specialties include physician assistant, physical therapist, optometrist, podiatrist...the Deputy Surgeon General (MC), the AFMS Family Practice consultant (MC), 5 Family Practice physicians (MC), 2 nurses (NC), 2 medical technicians...specifically require clinicians, instead of taking advantage of their valuable clinical training in the MTFs. To illustrate, moving one family practice

  5. Magnetoelectric versus thermal actuation characteristics of shear force AFM probes with piezoresistive detection

    NASA Astrophysics Data System (ADS)

    Sierakowski, Andrzej; Kopiec, Daniel; Majstrzyk, Wojciech; Kunicki, Piotr; Janus, Paweł; Dobrowolski, Rafał; Grabiec, Piotr; Rangelow, Ivo W.; Gotszalk, Teodor

    2017-03-01

    In this paper the authors compare methods used for piezoresistive microcantilevers actuation for the atomic force microscopy (AFM) imaging in the dynamic shear force mode. The piezoresistive detection is an attractive technique comparing the optical beam detection of deflection. The principal advantage is that no external alignment of optical source and detector are needed. When the microcantilever is deflected, the stress is transferred into a change of resistivity of piezoresistors. The integration of piezoresistive read-out provides a promising solution in realizing a compact non-contact AFM. Resolution of piezoresistive read-out is limited by three main noise sources: Johnson, 1/f and thermomechanical noise. In the dynamic shear force mode measurement the method used for cantilever actuation will also affect the recorded noise in the piezoresistive detection circuit. This is the result of a crosstalk between an aluminium path (current loop used for actuation) and piezoresistors located near the base of the beam. In this paper authors described an elaborated in ITE (Institute of Electron Technology) technology of fabrication cantilevers with piezoresistive detection of deflection and compared efficiency of two methods used for cantilever actuation.

  6. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

    PubMed

    Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

    2017-02-21

    Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

  7. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

    PubMed Central

    Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

    2017-01-01

    Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance. PMID:28772570

  8. U.S. Army Training and Testing Area Carrying Capacity (ATTACC) for Munitions (AFM)

    DTIC Science & Technology

    2006-11-01

    Army Training Support Center USDA United States Department of Agriculture USGS United States Geological Survey USLE Universal Soil Loss Equation...Range condition is a function of climate, soil , and hydrology. The munitions impact, constituent load, and range condition are modeled using AFM...For ArcGIS v2 to attain expected concentrations of munitions constituents and corresponding risk due to exposure through soil - and water-related

  9. Phase-Imaging with a Sharpened Multi-Walled Carbon Nanotube AFM Tip: Investigation of Low-k Dielectric Polymer Hybrids

    NASA Technical Reports Server (NTRS)

    Nguyen, Cattien V.; Stevens, Ramsey M.; Meyyappan, M.; Volksen, Willi; Miller, Robert D.

    2005-01-01

    Phase shift tapping mode scanning force microscopy (TMSFM) has evolved into a very powerful technique for the nanoscale surface characterization of compositional variations in heterogeneous samples. Phase shift signal measures the difference between the phase angle of the excitation signal and the phase angle of the cantilever response. The signal correlates to the tip-sample inelastic interactions, identifying the different chemical and/or physical property of surfaces. In general, the resolution and quality of scanning probe microscopic images are highly dependent on the size of the scanning probe tip. In improving AFM tip technology, we recently developed a technique for sharpening the tip of a multi-walled carbon nanotube (CNT) AFM tip, reducing the radius of curvature of the CNT tip to less than 5 nm while still maintaining the inherent stability of multi-walled CNT tips. Herein we report the use of sharpened (CNT) AFM tips for phase-imaging of polymer hybrids, a precursor for generating nanoporous low-k dielectrics for on-chip interconnect applications. Using sharpened CNT tips, we obtained phase-contrast images having domains less than 10 nm. In contrast, conventional Si tips and unsharpened CNT tips (radius greater than 15 nm) were not able to resolve the nanoscale domains in the polymer hybrid films. C1early, the size of the CNT tip contributes significantly to the resolution of phase-contrast imaging. In addition, a study on the nonlinear tapping dynamics of the multi-walled CNT tip indicates that the multi-walled CNT tip is immune to conventional imaging instabilities related to the coexistence of attractive and repulsive tapping regimes. This factor may also contribute to the phase-contrast image quality of multi-walled CNT AFM tips. This presentation will also offer data in support of the stability of the CNT tip for phase shift TMSFM.

  10. Fast and accurate: high-speed metrological large-range AFM for surface and nanometrology

    NASA Astrophysics Data System (ADS)

    Dai, Gaoliang; Koenders, Ludger; Fluegge, Jens; Hemmleb, Matthias

    2018-05-01

    Low measurement speed remains a major shortcoming of the scanning probe microscopic technique. It not only leads to a low measurement throughput, but a significant measurement drift over the long measurement time needed (up to hours or even days). To overcome this challenge, PTB, the national metrology institute of Germany, has developed a high-speed metrological large-range atomic force microscope (HS Met. LR-AFM) capable of measuring speeds up to 1 mm s‑1. This paper has introduced the design concept in detail. After modelling scanning probe microscopic measurements, our results suggest that the signal spectrum of the surface to be measured is the spatial spectrum of the surface scaled by the scanning speed. The higher the scanning speed , the broader the spectrum to be measured. To realise an accurate HS Met. LR-AFM, our solution is to combine different stages/sensors synchronously in measurements, which provide a much larger spectrum area for high-speed measurement capability. Two application examples have been demonstrated. The first is a new concept called reference areal surface metrology. Using the developed HS Met. LR-AFM, surfaces are measured accurately and traceably at a speed of 500 µm s‑1 and the results are applied as a reference 3D data map of the surfaces. By correlating the reference 3D data sets and 3D data sets of tools under calibration, which are measured at the same surface, it has the potential to comprehensively characterise the tools, for instance, the spectrum properties of the tools. The investigation results of two commercial confocal microscopes are demonstrated, indicating very promising results. The second example is the calibration of a kind of 3D nano standard, which has spatially distributed landmarks, i.e. special unique features defined by 3D-coordinates. Experimental investigations confirmed that the calibration accuracy is maintained at a measurement speed of 100 µm s‑1, which improves the calibration efficiency by a

  11. Direct and quantitative AFM measurements of the concentration and temperature dependence of the hydrophobic force law at nanoscopic contacts.

    PubMed

    Stock, Philipp; Utzig, Thomas; Valtiner, Markus

    2015-05-15

    By virtue of its importance for self-organization of biological matter the hydrophobic force law and the range of hydrophobic interactions (HI) have been debated extensively over the last 40 years. Here, we directly measure and quantify the hydrophobic force-distance law over large temperature and concentration ranges. In particular, we study the HI between molecularly smooth hydrophobic self-assembled monolayers, and similarly modified gold-coated AFM tips (radii∼8-50 nm). We present quantitative and direct evidence that the hydrophobic force is both long-ranged and exponential down to distances of about 1-2 nm. Therefore, we introduce a self-consistent radius-normalization for atomic force microscopy data. This approach allows quantitative data fitting of AFM-based experimental data to the recently proposed Hydra-model. With a statistical significance of r(2)⩾0.96 our fitting and data directly reveal an exponential HI decay length of 7.2±1.2 Å that is independent of the salt concentration up to 750 mM. As such, electrostatic screening does not have a significant influence on the HI in electrolyte concentrations ranging from 1 mM to 750 mM. In 1 M solutions the observed instability during approach shifts to longer distances, indicating ion correlation/adsorption effects at high salt concentrations. With increasing temperature the magnitude of HI decreases monotonically, while the range increases slightly. We compare our results to the large body of available literature, and shed new light into range and magnitude of hydrophobic interactions at very close distances and over wide temperature and concentration regimes. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Comparative studies of thin film growth on aluminium by AFM, TEM and GDOES characterization

    NASA Astrophysics Data System (ADS)

    Qi, Jiantao; Thompson, George E.

    2016-07-01

    In this present study, comparative studies of trivalent chromium conversion coating formation, associated with aluminium dissolution process, have been investigated using atomic force microscopy (AFM), transmission electron microscopy (TEM) and glow-discharge optical emission spectroscopy (GDOES). High-resolution electron micrographs revealed the evident and uniform coating initiation on the whole surface after conversion treatment for only 30 s, although a network of metal ridges was created by HF etching pre-treatment. In terms of conversion treatment process on electropolished aluminium, constant kinetics of coating growth, ∼0.30 ± 0.2 nm/s, were found after the prolonged conversion treatment for 600 s. The availability of electrolyte anions for coating deposition determined the growth process. Simultaneously, a proceeding process of aluminium dissolution during conversion treatment, of ∼0.11 ± 0.02 nm/s, was found for the first time, indicating constant kinetics of anodic reactions. The distinct process of aluminium consumption was assigned with loss of corrosion protection of the deposited coating material as evidenced in the electrochemical impedance spectroscopy. Based on the present data, a new mechanism of coating growth on aluminium was proposed, and it consisted of an activation period (0-30 s), a linear growth period (0.30 nm/s, up for 600 s) and limited growth period (0.17 nm/s, 600-1200 s). In addition, the air-drying post-treatment and a high-vacuum environment in the microscope revealed a coating shrinkage, especially in the coatings after conversion treatments for longer time.

  13. Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2).

    PubMed

    Ganbaatar, Narangerel; Imai, Kanae; Yano, Taka-Aki; Hara, Masahiko

    2017-01-01

    Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO 2 ) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO 2 (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO 2 (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO 2 surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

  14. The structure of high-methoxyl sugar acid gels of citrus pectin as determined by AFM

    USDA-ARS?s Scientific Manuscript database

    Images of native high methoxyl sugar acid gels (HMSAG) were obtained by atomic force microscopy (AFM) in the Tapping ModeTM. Electronic thinning of the pectin strands to one pixel wide allowed the pectin network to be viewed in the absence of variable strand widths related to preferentially solvate...

  15. 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. Copyright © 2015 John Wiley & Sons, Ltd.

  16. Proceedings of the 2011 AFMS Medical Research Symposium. Volume 4. Healthcare Informatics Track

    DTIC Science & Technology

    2011-08-02

    pretest and posttest , a survey of 10 five-point Likert scale questions on managing critical children before and after, and 2 videotaped pediatric...critical care simulations with debriefings after each scenario. Results: Fund of knowledge improved from a pretest score of 60% to a posttest score of...02--2012 Proceedings 02-08-2011 to 04-08-2011 Proceedings of the 2011 AFMS Medical Research Symposium. Volume 4. Healthcare Informatics Track Major

  17. Coexistence of antiferromagnetic and ferromagnetic spin correlations in SrCo 2As 2 revealed by 59Co and 75As NMR

    DOE PAGES

    Wiecki, P.; Ogloblichev, V.; Pandey, Abhishek; ...

    2015-06-15

    In nonsuperconducting, metallic paramagnetic SrCo 2As 2, inelastic neutron scattering measurements have revealed strong stripe-type q=(π,0) antiferromagnetic (AFM) spin correlations. Using nuclear magnetic resonance (NMR) measurements on 59Co and 75As nuclei, we demonstrate that stronger ferromagnetic (FM) spin correlations coexist in SrCo 2As 2. Our NMR data are consistent with density functional theory (DFT) calculations which show enhancements at both q=(π,0) and the in-plane FM q=0 wave vectors in static magnetic susceptibility χ(q). We suggest that the strong FM fluctuations prevent superconductivity in SrCo 2As 2, despite the presence of stripe-type AFM fluctuations. Since DFT calculations have consistently revealed similarmore » enhancements of the χ(q) at both q=(π,0) and q=0 in the iron-based superconductors and parent compounds, our observation of FM correlations in SrCo 2As 2 calls for detailed studies of FM correlations in the iron-based superconductors.« less

  18. 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.

  19. AFM and x-ray studies of buffing and uv light induced alignment of liquid crystals on SE610 polyimide films

    NASA Astrophysics Data System (ADS)

    Kim, Jae-Hoon; Shi, Yushan; Ha, Kiryong; West, John L.; Kumar, Satyendra

    1997-03-01

    We have studied the competition between the effects of mechanical buffing of and photo-induced chemical reaction in Nissan SE610 polyimide film on the director orientation of liquid crystals using atomic force microscopy (AFM) and textural study under polarizing miscroscope. It was found that the uv light exposure after buffing significantly alters the degree and the direction of alignment achieved by buffing. Results of our study show that the two techniques can be used to control and fine-tune liquid crystal alignment. A description of the microscopic changes as inferred from AFM and x-ray studies will be presented.

  20. Real-time TIRF observation of vinculin recruitment to stretched α-catenin by AFM.

    PubMed

    Maki, Koichiro; Han, Sung-Woong; Hirano, Yoshinori; Yonemura, Shigenobu; Hakoshima, Toshio; Adachi, Taiji

    2018-01-25

    Adherens junctions (AJs) adaptively change their intensities in response to intercellular tension; therefore, they integrate tension generated by individual cells to drive multicellular dynamics, such as morphogenetic change in embryos. Under intercellular tension, α-catenin, which is a component protein of AJs, acts as a mechano-chemical transducer to recruit vinculin to promote actin remodeling. Although in vivo and in vitro studies have suggested that α-catenin-mediated mechanotransduction is a dynamic molecular process, which involves a conformational change of α-catenin under tension to expose a cryptic vinculin binding site, there are no suitable experimental methods to directly explore the process. Therefore, in this study, we developed a novel system by combining atomic force microscopy (AFM) and total internal reflection fluorescence (TIRF). In this system, α-catenin molecules (residues 276-634; the mechano-sensitive M 1 -M 3 domain), modified on coverslips, were stretched by AFM and their recruitment of Alexa-labeled full-length vinculin molecules, dissolved in solution, were observed simultaneously, in real time, using TIRF. We applied a physiologically possible range of tensions and extensions to α-catenin and directly observed its vinculin recruitment. Our new system could be used in the fields of mechanobiology and biophysics to explore functions of proteins under tension by coupling biomechanical and biochemical information.

  1. Dynamic characterization of AFM probes by laser Doppler vibrometry and stroboscopic holographic methodologies

    NASA Astrophysics Data System (ADS)

    Kuppers, J. D.; Gouverneur, I. M.; Rodgers, M. T.; Wenger, J.; Furlong, C.

    2006-08-01

    In atomic probe microscopy, micro-probes of various sizes, geometries, and materials are used to define the interface between the samples under investigation and the measuring detectors and instrumentation. Therefore, measuring resolution in atomic probe microscopy is highly dependent on the transfer function characterizing the micro-probes used. In this paper, characterization of the dynamic transfer function of specific micro-cantilever probes used in an Atomic Force Microscope (AFM) operating in the tapping mode is presented. Characterization is based on the combined application of laser Doppler vibrometry (LDV) and real-time stroboscopic optoelectronic holographic microscopy (OEHM) methodologies. LDV is used for the rapid measurement of the frequency response of the probes due to an excitation function containing multiple frequency components. Data obtained from the measured frequency response is used to identify the principal harmonics. In order to identify mode shapes corresponding to the harmonics, full-field of view OEHM is applied. This is accomplished by measurements of motion at various points on the excitation curve surrounding the identified harmonics. It is shown that the combined application of LDV and OEHM enables the high-resolution characterization of mode shapes of vibration, damping characteristics, as well as transient response of the micro-cantilever probes. Such characterization is necessary in high-resolution AFM measurements.

  2. Non-contact AFM measurement of the Hamaker constants of solids: Calibrating cantilever geometries.

    PubMed

    Fronczak, Sean G; Browne, Christopher A; Krenek, Elizabeth C; Beaudoin, Stephen P; Corti, David S

    2018-05-01

    Surface effects arising from roughness and deformation can negatively affect the results of AFM contact experiments. Using the non-contact portion of an AFM deflection curve is therefore desirable for estimating the Hamaker constant, A, of a solid material. A previously validated non-contact quasi-dynamic method for estimating A is revisited, in which the cantilever tip is now always represented by an "effective sphere". In addition to simplifying this previous method, accurate estimates of A can still be obtained even though precise knowledge of the nanoscale geometric features of the cantilever tip are no longer required. The tip's "effective" radius of curvature, R eff , is determined from a "calibration" step, in which the tip's deflection at first contact with the surface is measured for a substrate with a known Hamaker constant. After R eff is known for a given tip, estimates of A for other surfaces of interest are then determined. An experimental study was conducted to validate the new method and the obtained results are in good agreement with predictions from the Lifshitz approximation, when available. Since R eff accounts for all geometric uncertainties of the tip through a single fitted parameter, no visual fitting of the tip shape was required. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

    DOE PAGES

    Chae, Jungseok; An, Sangmin; Ramer, Georg; ...

    2017-08-03

    The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

  4. Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chae, Jungseok; An, Sangmin; Ramer, Georg

    The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

  5. Methodological development of topographic correction in 2D/3D ToF-SIMS images using AFM images

    NASA Astrophysics Data System (ADS)

    Jung, Seokwon; Lee, Nodo; Choi, Myungshin; Lee, Jungmin; Cho, Eunkyunng; Joo, Minho

    2018-02-01

    Time-of-flight secondary-ion mass spectrometry (ToF-SIMS) is an emerging technique that provides chemical information directly from the surface of electronic materials, e.g. OLED and solar cell. It is very versatile and highly sensitive mass spectrometric technique that provides surface molecular information with their lateral distribution as a two-dimensional (2D) molecular image. Extending the usefulness of ToF-SIMS, a 3D molecular image can be generated by acquiring multiple 2D images in a stack. These imaging techniques by ToF-SIMS provide an insight into understanding the complex structures of unknown composition in electronic material. However, one drawback in ToF-SIMS is not able to represent topographical information in 2D and 3D mapping images. To overcome this technical limitation, topographic information by ex-situ technique such as atomic force microscopy (AFM) has been combined with chemical information from SIMS that provides both chemical and physical information in one image. The key to combine two different images obtained from ToF-SIMS and AFM techniques is to develop the image processing algorithm, which performs resize and alignment by comparing the specific pixel information of each image. In this work, we present methodological development of the semiautomatic alignment and the 3D structure interpolation system for the combination of 2D/3D images obtained by ToF-SIMS and AFM measurements, which allows providing useful analytical information in a single representation.

  6. Comparison of the Identation and Elasticity of E.coli and its Spheroplasts by AFM

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sullivan, Claretta J; Venkataraman, Sankar; Retterer, Scott T

    2007-01-01

    Atomic force microscopy (AFM) provides a unique opportunity to study live individual bacteria at the nanometer scale. In addition to providing accurate morphological information, AFM can be exploited to investigate membrane protein localization and molecular interactions on the surface of living cells. A prerequisite for these studies is the development of robust procedures for sample preparation. While such procedures are established for intact bacteria, they are only beginning to emerge for bacterial spheroplasts. Spheroplasts are useful research models for studying mechanosensitive ion channels, membrane transport, lipopolysaccharide translocation, solute uptake, and the effects of antimicrobial agents on membranes. Furthermore, given themore » similarities between spheroplasts and cell wall-deficient (CWD) forms of pathogenic bacteria, spheroplast research could be relevant in biomedical research. In this paper, a new technique for immobilizing spheroplasts on mica pretreated with aminopropyltriethoxysilane (APTES) and glutaraldehyde is described. Using this mounting technique, the indentation and cell elasticity of glutaraldehyde-fixed and untreated spheroplasts of E. coli in liquid were measured. These values are compared to those of intact E. coli. Untreated spheroplasts were found to be much softer than the intact cells and the silicon nitride cantilevers used in this study.« less

  7. AFM study of the plastic deformation behavior of poly-synthetically-twinned (PST) titanium aluminide crystals

    NASA Astrophysics Data System (ADS)

    Chen, Yali

    The plastic deformation behavior of PST TiAl crystals was investigated using AFM techniques to reveal the effects of lamellar structure on the deform mechanisms of two-phase TiAl materials. PST crystals with a nominal composition of Ti52Al48 (atomic percent) were grown by the floating zone method and at various orientations deformed in compression at room temperature. Atomic Force Microscopy (AFM) was employed to investigate the deformation structure on the free surfaces. The deformation of the PST crystals is highly anisotropic and the deformation mechanism changes dramatically with sample orientation. When the angle between the loading axis and the lamellar interfaces is below 20°, the gamma lamellae deform by dislocation slip and twinning on planes oblique to the lamellar interfaces, but the Burgers vectors or the resultant shear vectors are parallel to the lamellar interfaces inside each lamella. When the angle is between 20° and 80° the gamma phase deforms by shear on planes parallel to the lamellar interfaces. Some domains deform by a combination of ordinary dislocation slip and twinning. In the domains where twinning cannot be activated, slip occurs by ordinary dislocations or superdislocations. When the loading axis is nearly perpendicular to the lamellar interfaces ordinary dislocation slip and twinning on slip planes inclined with the lamellar interfaces are dominant and the shear is trans-lamellar. The three deformation modes are termed as A, B and N type deformation modes respectively. In the A type mode the alpha2 lamellae concomitantly deform by prismatic slip. In the other two modes, the alpha2 phase does not deform and acts as strong obstacles to the transfer of deformation. Abundant misfit dislocations are emitted from the lamellar interfaces which is beneficial for the plastic deformation. On the other hand, the lamellar interfaces strongly impede trans-lamellar deformation and channel the deformation inside each lamella. The inhomogeneous

  8. Insulated Conducting Cantilevered Nanotips and Two-Chamber Recording System for High Resolution Ion Sensing AFM

    PubMed Central

    Meckes, Brian; Arce, Fernando Teran; Connelly, Laura S.; Lal, Ratnesh

    2014-01-01

    Biological membranes contain ion channels, which are nanoscale pores allowing controlled ionic transport and mediating key biological functions underlying normal/abnormal living. Synthetic membranes with defined pores are being developed to control various processes, including filtration of pollutants, charge transport for energy storage, and separation of fluids and molecules. Although ionic transport (currents) can be measured with single channel resolution, imaging their structure and ionic currents simultaneously is difficult. Atomic force microscopy enables high resolution imaging of nanoscale structures and can be modified to measure ionic currents simultaneously. Moreover, the ionic currents can also be used to image structures. A simple method for fabricating conducting AFM cantilevers to image pore structures at high resolution is reported. Tungsten microwires with nanoscale tips are insulated except at the apex. This allows simultaneous imaging via cantilever deflections in normal AFM force feedback mode as well as measuring localized ionic currents. These novel probes measure ionic currents as small as picoampere while providing nanoscale spatial resolution surface topography and is suitable for measuring ionic currents and conductance of biological ion channels. PMID:24663394

  9. NC-AFM observation of atomic scale structure of rutile-type TiO2(110) surface prepared by wet chemical process.

    PubMed

    Namai, Yoshimichi; Matsuoka, Osamu

    2006-04-06

    We succeeded in observing the atomic scale structure of a rutile-type TiO2(110) single-crystal surface prepared by the wet chemical method of chemical etching in an acid solution and surface annealing in air. Ultrahigh vacuum noncontact atomic force microscopy (UHV-NC-AFM) was used for observing the atomic scale structures of the surface. The UHV-NC-AFM measurements at 450 K, which is above a desorption temperature of molecularly adsorbed water on the TiO2(110) surface, enabled us to observe the atomic scale structure of the TiO2(110) surface prepared by the wet chemical method. In the UHV-NC-AFM measurements at room temperature (RT), however, the atomic scale structure of the TiO2(110) surface was not observed. The TiO2(110) surface may be covered with molecularly adsorbed water after the surface was prepared by the wet chemical method. The structure of the TiO2(110) surface that was prepared by the wet chemical method was consistent with the (1 x 1) bulk-terminated model of the TiO2(110) surface.

  10. Removal of industrial dyes and heavy metals by Beauveria bassiana: FTIR, SEM, TEM and AFM investigations with Pb(II).

    PubMed

    Gola, Deepak; Malik, Anushree; Namburath, Maneesh; Ahammad, Shaikh Ziauddin

    2017-10-01

    Presence of industrial dyes and heavy metal as a contaminant in environment poses a great risk to human health. In order to develop a potential technology for remediation of dyes (Reactive remazol red, Yellow 3RS, Indanthrene blue and Vat novatic grey) and heavy metal [Cu(II), Ni(II), Cd(II), Zn(II), Cr(VI) and Pb(II)] contamination, present study was performed with entomopathogenic fungi, Beauveria bassiana (MTCC no. 4580). High dye removal (88-97%) was observed during the growth of B. bassiana while removal percentage for heavy metals ranged from 58 to 75%. Further, detailed investigations were performed with Pb(II) in terms of growth kinetics, effect of process parameters and mechanism of removal. Growth rate decreased from 0.118 h -1 (control) to 0.031 h -1 , showing 28% reduction in biomass at 30 mg L -1 Pb(II) with 58.4% metal removal. Maximum Pb(II) removal was observed at 30 °C, neutral pH and 30 mg L -1 initial metal concentration. FTIR analysis indicated the changes induced by Pb(II) in functional groups on biomass surface. Further, microscopic analysis (SEM and atomic force microscopy (AFM)) was performed to understand the changes in cell surface morphology of the fungal cell. SEM micrograph showed a clear deformation of fungal hyphae, whereas AFM studies proved the increase in surface roughness (RSM) in comparison to control cell. Homogenous bioaccumulation of Pb(II) inside the fungal cell was clearly depicted by TEM-high-angle annular dark field coupled with EDX. Present study provides an insight into the mechanism of Pb(II) bioremediation and strengthens the significance of using entomopathogenic fungus such as B. bassiana for metal and dye removal.

  11. Atomic force microscopy and tridimensional topography analysis of human enamel after resinous infiltration and storage in water.

    PubMed

    Taher, Nadia M

    2013-04-01

    To evaluate the effect of water storage on surface roughness (Ra) of human enamel after treatment with resin infiltrant and fissure sealant, by utilizing atomic force microscopy (AFM) and microtomography. This study was conducted after registration and ethical approval clarification at the College of Dentistry Research Center, King Saud University, Riyadh, Kingdom of Saudi Arabia between January 2011 and August 2011. Thirty enamel surface specimens were prepared from caries-free human premolar teeth. Specimens were divided into 3 groups: Group I, was the control; Group II, a resin infiltrant (Icon) was applied on the enamel surfaces; and Group III, the teeth were treated with fissure sealant (SealRite). All specimens were stored in distilled water for 6 months and then, subjected to AFM Veeco CP11 1.2 analysis. A few specimens were scanned by skyscan-1072-x-ray microtomography. The Ra mean readings were recorded and statistical analysis was performed with the Statistical Package for Social Sciences Version 16 at the significance level of p<0.05. No significant differences in the mean Ra were recorded among the 3 groups, (Group I = 0.21+/-0.057), (Group II = 0.23+/-0.075), and (Group III = 0.20+/-0.039) at p=0.747. The AFM images of enamel surface show thin and inhomogeneous Icon resin in Group II, meanwhile, the SealRite in Group III showed a homogeneous layer in all specimens. The microtomography supported the findings of the AFM images. The persistence of the SealRite in all specimens revealed its low solubility in water and its protective effect on enamel surface.

  12. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

    PubMed Central

    2018-01-01

    Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins. PMID:29698481

  13. 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.

  14. In situ AFM imaging of apolipoprotein A-I directly derived from plasma HDL.

    PubMed

    Gan, Chaoye; Wang, Zhexuan; Chen, Yong

    2017-04-01

    The major apolipoproteins of plasma lipoproteins play vital roles in the structural integrity and physiological functions of lipoproteins. More than ten structural models of apolipoprotein A-I (apoA-I), the major apolipoprotein of high-density lipoprotein (HDL), have been developed successively. In these models, apoA-I was supposed to organize in a ring-shaped form. To date, however, there is no direct evidence under physiological condition. Here, atomic force microscopy (AFM) was used to in situ visualize the organization of apoA-I, which was exposed via depletion of the lipid component of plasma HDL pre-immobilized on functionalized mica sheets. For the first time, the ring-shaped coarse structure and three detailed structures (crescent-shaped, gapped "O"-shaped, and parentheses-shaped structures, respectively) of apoA-I in plasma HDL, which have the ability of binding scavenger receptors, were directly observed and quantitatively measured by AFM. The three detailed structures probably represent the different extents to which the lipid component of HDL was depleted. Data on lipid depletion of HDL may provide clues to understand lipid insertion of HDL. These data provide important information for the understanding of the structure/maturation of plasma HDL. Moreover, they suggest a powerful method for directly visualizing the major apolipoproteins of plasma lipoproteins or the protein component of lipoprotein-like lipid-protein complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Ultra-large scale AFM of lipid droplet arrays: investigating the ink transfer volume in dip pen nanolithography.

    PubMed

    Förste, Alexander; Pfirrmann, Marco; Sachs, Johannes; Gröger, Roland; Walheim, Stefan; Brinkmann, Falko; Hirtz, Michael; Fuchs, Harald; Schimmel, Thomas

    2015-05-01

    There are only few quantitative studies commenting on the writing process in dip-pen nanolithography with lipids. Lipids are important carrier ink molecules for the delivery of bio-functional patters in bio-nanotechnology. In order to better understand and control the writing process, more information on the transfer of lipid material from the tip to the substrate is needed. The dependence of the transferred ink volume on the dwell time of the tip on the substrate was investigated by topography measurements with an atomic force microscope (AFM) that is characterized by an ultra-large scan range of 800 × 800 μm(2). For this purpose arrays of dots of the phospholipid1,2-dioleoyl-sn-glycero-3-phosphocholine were written onto planar glass substrates and the resulting pattern was imaged by large scan area AFM. Two writing regimes were identified, characterized of either a steady decline or a constant ink volume transfer per dot feature. For the steady state ink transfer, a linear relationship between the dwell time and the dot volume was determined, which is characterized by a flow rate of about 16 femtoliters per second. A dependence of the ink transport from the length of pauses before and in between writing the structures was observed and should be taken into account during pattern design when aiming at best writing homogeneity. The ultra-large scan range of the utilized AFM allowed for a simultaneous study of the entire preparation area of almost 1 mm(2), yielding good statistic results.

  16. Ultra-large scale AFM of lipid droplet arrays: investigating the ink transfer volume in dip pen nanolithography

    NASA Astrophysics Data System (ADS)

    Förste, Alexander; Pfirrmann, Marco; Sachs, Johannes; Gröger, Roland; Walheim, Stefan; Brinkmann, Falko; Hirtz, Michael; Fuchs, Harald; Schimmel, Thomas

    2015-05-01

    There are only few quantitative studies commenting on the writing process in dip-pen nanolithography with lipids. Lipids are important carrier ink molecules for the delivery of bio-functional patters in bio-nanotechnology. In order to better understand and control the writing process, more information on the transfer of lipid material from the tip to the substrate is needed. The dependence of the transferred ink volume on the dwell time of the tip on the substrate was investigated by topography measurements with an atomic force microscope (AFM) that is characterized by an ultra-large scan range of 800 × 800 μm2. For this purpose arrays of dots of the phospholipid1,2-dioleoyl-sn-glycero-3-phosphocholine were written onto planar glass substrates and the resulting pattern was imaged by large scan area AFM. Two writing regimes were identified, characterized of either a steady decline or a constant ink volume transfer per dot feature. For the steady state ink transfer, a linear relationship between the dwell time and the dot volume was determined, which is characterized by a flow rate of about 16 femtoliters per second. A dependence of the ink transport from the length of pauses before and in between writing the structures was observed and should be taken into account during pattern design when aiming at best writing homogeneity. The ultra-large scan range of the utilized AFM allowed for a simultaneous study of the entire preparation area of almost 1 mm2, yielding good statistic results.

  17. Influence of the surface chemistry on TiO2 - TiO2 nanocontact forces as measured by an UHV-AFM

    NASA Astrophysics Data System (ADS)

    Kunze, Christian; Giner, Ignacio; Torun, Boray; Grundmeier, Guido

    2014-03-01

    Particle-wall contact forces between a TiO2 film coated AFM tip and TiO2(1 1 0) single crystal surfaces were analyzed by means of UHV-AFM. As a reference system an octadecylphosphonic acid monolayer covered TiO2(1 1 0) surface was studied. The defect chemistry of the TiO2 substrate was modified by Ar ion bombardment, water dosing at 3 × 10-6 Pa and an annealing step at 473 K which resulted in a varying density of Ti(III) states. The observed contact forces are correlated to the surface defect density and are discussed in terms of the change in the electronic structure and its influence on the Hamaker constant.

  18. Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least

    Science.gov Websites

    Polluting Cities in the U.S. | State, Local, and Tribal Governments | NREL Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least Polluting Cities in the U.S. Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least Polluting Cities in the U.S. September 12, 2016 by Megan Day

  19. Using AFM to probe the complexation of DNA with anionic lipids mediated by Ca(2+): the role of surface pressure.

    PubMed

    Luque-Caballero, Germán; Martín-Molina, Alberto; Sánchez-Treviño, Alda Yadira; Rodríguez-Valverde, Miguel A; Cabrerizo-Vílchez, Miguel A; Maldonado-Valderrama, Julia

    2014-04-28

    Complexation of DNA with lipids is currently being developed as an alternative to classical vectors based on viruses. Most of the research to date focuses on cationic lipids owing to their spontaneous complexation with DNA. Nonetheless, recent investigations have revealed that cationic lipids induce a large number of adverse effects on DNA delivery. Precisely, the lower cytotoxicity of anionic lipids accounts for their use as a promising alternative. However, the complexation of DNA with anionic lipids (mediated by cations) is still in early stages and is not yet well understood. In order to explore the molecular mechanisms underlying the complexation of anionic lipids and DNA we proposed a combined methodology based on the surface pressure-area isotherms, Gibbs elasticity and Atomic Force Microscopy (AFM). These techniques allow elucidation of the role of the surface pressure in the complexation and visualization of the interfacial aggregates for the first time. We demonstrate that the DNA complexes with negatively charged model monolayers (DPPC/DPPS 4 : 1) only in the presence of Ca(2+), but is expelled at very high surface pressures. Also, according to the Gibbs elasticity plot, the complexation of lipids and DNA implies a whole fluidisation of the monolayer and a completely different phase transition map in the presence of DNA and Ca(2+). AFM imaging allows identification for the first time of specific morphologies associated with different packing densities. At low surface coverage, a branched net like structure is observed whereas at high surface pressure fibers formed of interfacial aggregates appear. In summary, Ca(2+) mediates the interaction between DNA and negatively charged lipids and also the conformation of the ternary system depends on the surface pressure. Such observations are important new generic features of the interaction between DNA and anionic lipids.

  20. AFM Study of Charge Transfer Between Metals Due to the Oxygen Redox Couple in Water

    NASA Astrophysics Data System (ADS)

    Trombley, Jeremy; Panthani, Tessie; Sankaran, Mohan; Angus, John; Kash, Kathleen

    2010-03-01

    The oxygen redox couple in an adsorbed water film can pin the Fermi level at the surfaces of diamond, GaN and ZnO.footnotetextV. Chakrapani, C. Pendyala, K. Kash, A. B. Anderson, M. K. Sunkara and J. C. Angus, J. Am. Chem. Soc. 130 (2008) 12944-12952, and ref. 6 therein. We report here preliminary observations of the same phenomenon at metal surfaces. A Pt-coated atomic force microscope (AFM) tip was used to take force-distance measurements on Au, Ag, and Pt surfaces placed in pH-controlled water. The work functions of these surfaces vary over ˜2eV and span the electrochemical potential range of the oxygen redox couple, which varies with pH according to the Nernst equation. Adjusting the pH of the water from 4 to 12 allowed us to change the redox potential energy from -5.42eV to -4.95eV, changing the surface charge and the associated screening charge and modulating the pull-off force. This work has relevance to AFM of many materials in air, and to contact electrification, mechanical friction, and nanoscale corona discharges.

  1. 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

  2. Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

    DOE PAGES

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; ...

    2015-11-20

    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 goldmore » 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. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.« less

  3. Three-channel false colour AFM images for improved interpretation of complex surfaces: a study of filamentous cyanobacteria.

    PubMed

    Kurk, Toby; Adams, David G; Connell, Simon D; Thomson, Neil H

    2010-05-01

    Imaging signals derived from the atomic force microscope (AFM) are typically presented as separate adjacent images with greyscale or pseudo-colour palettes. We propose that information-rich false-colour composites are a useful means of presenting three-channel AFM image data. This method can aid the interpretation of complex surfaces and facilitate the perception of information that is convoluted across data channels. We illustrate this approach with images of filamentous cyanobacteria imaged in air and under aqueous buffer, using both deflection-modulation (contact) mode and amplitude-modulation (tapping) mode. Topography-dependent contrast in the error and tertiary signals aids the interpretation of the topography signal by contributing additional data, resulting in a more detailed image, and by showing variations in the probe-surface interaction. Moreover, topography-independent contrast and topography-dependent contrast in the tertiary data image (phase or friction) can be distinguished more easily as a consequence of the three dimensional colour-space.

  4. 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

  5. Correlative STED and Atomic Force Microscopy on Live Astrocytes Reveals Plasticity of Cytoskeletal Structure and Membrane Physical Properties during Polarized Migration

    PubMed Central

    Curry, Nathan; Ghézali, Grégory; Kaminski Schierle, Gabriele S.; Rouach, Nathalie; Kaminski, Clemens F.

    2017-01-01

    The plasticity of the cytoskeleton architecture and membrane properties is important for the establishment of cell polarity, adhesion and migration. Here, we present a method which combines stimulated emission depletion (STED) super-resolution imaging and atomic force microscopy (AFM) to correlate cytoskeletal structural information with membrane physical properties in live astrocytes. Using STED compatible dyes for live cell imaging of the cytoskeleton, and simultaneously mapping the cell surface topology with AFM, we obtain unprecedented detail of highly organized networks of actin and microtubules in astrocytes. Combining mechanical data from AFM with optical imaging of actin and tubulin further reveals links between cytoskeleton organization and membrane properties. Using this methodology we illustrate that scratch-induced migration induces cytoskeleton remodeling. The latter is caused by a polarization of actin and microtubule elements within astroglial cell processes, which correlates strongly with changes in cell stiffness. The method opens new avenues for the dynamic probing of the membrane structural and functional plasticity of living brain cells. It is a powerful tool for providing new insights into mechanisms of cell structural remodeling during physiological or pathological processes, such as brain development or tumorigenesis. PMID:28469559

  6. Ripple formation in unilamellar-supported lipid bilayer revealed by FRAPP.

    PubMed

    Harb, Frédéric; Simon, Anne; Tinland, Bernard

    2013-12-01

    The mechanisms of formation and conditions of the existence of the ripple phase are fundamental thermodynamic questions with practical implications for medicine and pharmaceuticals. We reveal a new case of ripple formation occurring in unilamellar-supported bilayers in water, which results solely from the bilayer/support interaction, without using lipid mixtures or specific ions. This ripple phase is detected by FRAPP using diffusion coefficient measurements as a function of temperature: a diffusivity plateau is observed. It occurs in the same temperature range where ripple phase existence has been observed using other methods. When AFM experiments are performed in the appropriate temperature range the ripple phase is confirmed.

  7. Chemical Species, Micromorphology, and XRD Fingerprint Analysis of Tibetan Medicine Zuotai Containing Mercury

    PubMed Central

    Li, Cen; Yang, Hongxia; Xiao, Yuancan; Zhandui; Sanglao; Wang, Zhang; Ladan, Duojie; Bi, Hongtao

    2016-01-01

    Zuotai (gTso thal) is one of the famous drugs containing mercury in Tibetan medicine. However, little is known about the chemical substance basis of its pharmacodynamics and the intrinsic link of different samples sources so far. Given this, energy dispersive spectrometry of X-ray (EDX), scanning electron microscopy (SEM), atomic force microscopy (AFM), and powder X-ray diffraction (XRD) were used to assay the elements, micromorphology, and phase composition of nine Zuotai samples from different regions, respectively; the XRD fingerprint features of Zuotai were analyzed by multivariate statistical analysis. EDX result shows that Zuotai contains Hg, S, O, Fe, Al, Cu, and other elements. SEM and AFM observations suggest that Zuotai is a kind of ancient nanodrug. Its particles are mainly in the range of 100–800 nm, which commonly further aggregate into 1–30 μm loosely amorphous particles. XRD test shows that β-HgS, S8, and α-HgS are its main phase compositions. XRD fingerprint analysis indicates that the similarity degrees of nine samples are very high, and the results of multivariate statistical analysis are broadly consistent with sample sources. The present research has revealed the physicochemical characteristics of Zuotai, and it would play a positive role in interpreting this mysterious Tibetan drug. PMID:27738409

  8. Chemical Species, Micromorphology, and XRD Fingerprint Analysis of Tibetan Medicine Zuotai Containing Mercury.

    PubMed

    Li, Cen; Yang, Hongxia; Du, Yuzhi; Xiao, Yuancan; Zhandui; Sanglao; Wang, Zhang; Ladan, Duojie; Bi, Hongtao; Wei, Lixin

    2016-01-01

    Zuotai ( gTso thal ) is one of the famous drugs containing mercury in Tibetan medicine. However, little is known about the chemical substance basis of its pharmacodynamics and the intrinsic link of different samples sources so far. Given this, energy dispersive spectrometry of X-ray (EDX), scanning electron microscopy (SEM), atomic force microscopy (AFM), and powder X-ray diffraction (XRD) were used to assay the elements, micromorphology, and phase composition of nine Zuotai samples from different regions, respectively; the XRD fingerprint features of Zuotai were analyzed by multivariate statistical analysis. EDX result shows that Zuotai contains Hg, S, O, Fe, Al, Cu, and other elements. SEM and AFM observations suggest that Zuotai is a kind of ancient nanodrug. Its particles are mainly in the range of 100-800 nm, which commonly further aggregate into 1-30  μ m loosely amorphous particles. XRD test shows that β -HgS, S 8 , and α -HgS are its main phase compositions. XRD fingerprint analysis indicates that the similarity degrees of nine samples are very high, and the results of multivariate statistical analysis are broadly consistent with sample sources. The present research has revealed the physicochemical characteristics of Zuotai , and it would play a positive role in interpreting this mysterious Tibetan drug.

  9. Comparisons of the topographic characteristics and electrical charge distributions among Babesia-infected erythrocytes and extraerythrocytic merozoites using AFM

    USDA-ARS?s Scientific Manuscript database

    Tick-borne Babesia parasites are responsible for costly diseases worldwide. Improved control and prevention tools are urgently needed, but development of such tools is limited by numerous gaps in knowledge of the parasite-host relationships. We hereby used atomic force microscopy (AFM) and Kelvin pr...

  10. Advanced Compatibility Characterization Of AF-M315E With Spacecraft Propulsion System Materials Project

    NASA Technical Reports Server (NTRS)

    McClure, Mark B.; Greene, Benjamin

    2014-01-01

    All spacecraft require propulsion systems for thrust and maneuvering. Propulsion systems can be chemical, nuclear, electrical, cold gas or combinations thereof. Chemical propulsion has proven to be the most reliable technology since the deployment of launch vehicles. Performance, storability, and handling are three important aspects of liquid chemical propulsion. Bipropellant systems require a fuel and an oxidizer for propulsion, but monopropellants only require a fuel and a catalyst for propulsion and are therefore simpler and lighter. Hydrazine is the state of the art propellant for monopropellant systems, but has drawbacks because it is highly hazardous to human health, which requires extensive care in handling, complex ground ops due to safety and environmental considerations, and lengthy turnaround times for reusable spacecraft. All users of hydrazine monopropellant must contend with these issues and their associated costs. The development of a new monopropellant, intended to replace hydrazine, has been in progress for years. This project will apply advanced techniques to characterize the engineering properties of materials used in AF-M315E propulsion systems after propellant exposure. AF-M315E monopropellant has been selected HQ's Green Propellant Infusion Mission (GPIM) to replace toxic hydrazine for improved performance and reduce safety and health issues that will shorten reusable spacecraft turn-around time. In addition, this project will fundamentally strengthen JSC's core competency to evaluate, use and infuse liquid propellant systems.

  11. Spin liquid state in the disordered triangular lattice Sc 2Ga 2CuO 7 revealed by NMR

    DOE PAGES

    Khuntia, P.; Kumar, R.; Mahajan, A. V.; ...

    2016-04-18

    We present microscopic magnetic properties of a two-dimensional triangular lattice Sc 2Ga 2CuO 7, consisting of single and double triangular Cu planes. An antiferromagnetic (AFM) exchange interaction J/k B ≈ 35 K between Cu 2+ (S = 1/2) spins in the triangular biplane is obtained from the analysis of intrinsic magnetic susceptibility data. The intrinsic magnetic susceptibility, extracted from 71Ga NMR shift data, displays the presence of AFM short range spin correlations and remains finite down to 50 mK, suggesting a nonsinglet ground state. The nuclear spin-lattice relaxation rate (1/T 1) reveals a slowing down of Cu 2+ spin fluctuationsmore » with decreasing T down to 100 mK. Magnetic specific heat (C m) and 1/T 1 exhibit power law behavior at low temperatures, implying the gapless nature of the spin excitation spectrum. The absence of long range magnetic ordering down to ~J/700, nonzero spin susceptibility at low T, and the power law behavior of C m and 1/T 1 suggest a gapless quantum spin liquid (QSL) state. Our results demonstrate that persistent spin dynamics induced by frustration maintain a quantum-disordered state at T → 0 in this triangular lattice antiferromagnet. Furthermore, this suggests that the low energy modes are dominated by spinon excitations in the QSL state due to randomness engendered by disorder and frustration.« less

  12. Improvement of the Correlative AFM and ToF-SIMS Approach Using an Empirical Sputter Model for 3D Chemical Characterization.

    PubMed

    Terlier, T; Lee, J; Lee, K; Lee, Y

    2018-02-06

    Technological progress has spurred the development of increasingly sophisticated analytical devices. The full characterization of structures in terms of sample volume and composition is now highly complex. Here, a highly improved solution for 3D characterization of samples, based on an advanced method for 3D data correction, is proposed. Traditionally, secondary ion mass spectrometry (SIMS) provides the chemical distribution of sample surfaces. Combining successive sputtering with 2D surface projections enables a 3D volume rendering to be generated. However, surface topography can distort the volume rendering by necessitating the projection of a nonflat surface onto a planar image. Moreover, the sputtering is highly dependent on the probed material. Local variation of composition affects the sputter yield and the beam-induced roughness, which in turn alters the 3D render. To circumvent these drawbacks, the correlation of atomic force microscopy (AFM) with SIMS has been proposed in previous studies as a solution for the 3D chemical characterization. To extend the applicability of this approach, we have developed a methodology using AFM-time-of-flight (ToF)-SIMS combined with an empirical sputter model, "dynamic-model-based volume correction", to universally correct 3D structures. First, the simulation of 3D structures highlighted the great advantages of this new approach compared with classical methods. Then, we explored the applicability of this new correction to two types of samples, a patterned metallic multilayer and a diblock copolymer film presenting surface asperities. In both cases, the dynamic-model-based volume correction produced an accurate 3D reconstruction of the sample volume and composition. The combination of AFM-SIMS with the dynamic-model-based volume correction improves the understanding of the surface characteristics. Beyond the useful 3D chemical information provided by dynamic-model-based volume correction, the approach permits us to enhance

  13. Quantitative measurements of intercellular adhesion between a macrophage and cancer cells using a cup-attached AFM chip.

    PubMed

    Kim, Hyonchol; Yamagishi, Ayana; Imaizumi, Miku; Onomura, Yui; Nagasaki, Akira; Miyagi, Yohei; Okada, Tomoko; Nakamura, Chikashi

    2017-07-01

    Intercellular adhesion between a macrophage and cancer cells was quantitatively measured using atomic force microscopy (AFM). Cup-shaped metal hemispheres were fabricated using polystyrene particles as a template, and a cup was attached to the apex of the AFM cantilever. The cup-attached AFM chip (cup-chip) approached a murine macrophage cell (J774.2), the cell was captured on the inner concave of the cup, and picked up by withdrawing the cup-chip from the substrate. The cell-attached chip was advanced towards a murine breast cancer cell (FP10SC2), and intercellular adhesion between the two cells was quantitatively measured. To compare cell adhesion strength, the work required to separate two adhered cells (separation work) was used as a parameter. Separation work was almost 2-fold larger between a J774.2 cell and FP10SC2 cell than between J774.2 cell and three additional different cancer cells (4T1E, MAT-LyLu, and U-2OS), two FP10SC2 cells, or two J774.2 cells. FP10SC2 was established from 4T1E as a highly metastatic cell line, indicates separation work increased as the malignancy of cancer cells became higher. One possible explanation of the strong adhesion of macrophages to cancer cells observed in this study is that the measurement condition mimicked the microenvironment of tumor-associated macrophages (TAMs) in vivo, and J774.2 cells strongly expressed CD204, which is a marker of TAMs. The results of the present study, which were obtained by measuring cell adhesion strength quantitatively, indicate that the fabricated cup-chip is a useful tool for measuring intercellular adhesion easily and quantitatively. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Improving the lateral resolution of quartz tuning fork-based sensors in liquid by integrating commercial AFM tips into the fiber end.

    PubMed

    Gonzalez, Laura; Martínez-Martín, David; Otero, Jorge; de Pablo, Pedro José; Puig-Vidal, Manel; Gómez-Herrero, Julio

    2015-01-14

    The use of quartz tuning fork sensors as probes for scanning probe microscopy is growing in popularity. Working in shear mode, some methods achieve a lateral resolution comparable with that obtained with standard cantilevered probes, but only in experiments conducted in air or vacuum. Here, we report a method to produce and use commercial AFM tips in electrically driven quartz tuning fork sensors operating in shear mode in a liquid environment. The process is based on attaching a standard AFM tip to the end of a fiber probe which has previously been sharpened. Only the end of the probe is immersed in the buffer solution during imaging. The lateral resolution achieved is about 6 times higher than that of the etched microfiber on its own.

  15. The LER/LWR metrology challenge for advance process control through 3D-AFM and CD-SEM

    NASA Astrophysics Data System (ADS)

    Faurie, P.; Foucher, J.; Foucher, A.-L.

    2009-12-01

    The continuous shrinkage in dimensions of microelectronic devices has reached such level, with typical gate length in advance R&D of less than 20nm combine with the introduction of new architecture (FinFET, Double gate...) and new materials (porous interconnect material, 193 immersion resist, metal gate material, high k materials...), that new process parameters have to be well understood and well monitored to guarantee sufficient production yield in a near future. Among these parameters, there are the critical dimensions (CD) associated to the sidewall angle (SWA) values, the line edge roughness (LER) and the line width roughness (LWR). Thus, a new metrology challenge has appeared recently and consists in measuring "accurately" the fabricated patterns on wafers in addition to measure the patterns on a repeatable way. Therefore, a great effort has to be done on existing techniques like CD-SEM, Scatterometry and 3D-AFM in order to develop them following the two previous criteria: Repeatability and Accuracy. In this paper, we will compare the 3D-AFM and CD-SEM techniques as a mean to measure LER and LWR on silicon and 193 resist and point out CD-SEM impact on the material during measurement. Indeed, depending on the material type, the interaction between the electron beam and the material or between the AFM tip and the material can vary a lot and subsequently can generate measurements bias. The first results tend to show that depending on CD-SEM conditions (magnification, number of acquisition frames) the final outputs can vary on a large range and therefore show that accuracy in such measurements are really not obvious to obtain. On the basis of results obtained on various materials that present standard sidewall roughness, we will show the limit of each technique and will propose different ways to improve them in order to fulfil advance roadmap requirements for the development of the next IC generation.

  16. In situ AFM investigation of electrochemically induced surface-initiated atom-transfer radical polymerization.

    PubMed

    Li, Bin; Yu, Bo; Zhou, Feng

    2013-02-12

    Electrochemically induced surface-initiated atom-transfer radical polymerization is traced by in situ AFM technology for the first time, which allows visualization of the polymer growth process. It affords a fundamental insight into the surface morphology and growth mechanism simultaneously. Using this technique, the polymerization kinetics of two model monomers were studied, namely the anionic 3-sulfopropyl methacrylate potassium salt (SPMA) and the cationic 2-(metharyloyloxy)ethyltrimethylammonium chloride (METAC). The growth of METAC is significantly improved by screening the ammonium cations by the addition of ionic liquid electrolyte in aqueous solution. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Optical imaging beyond the diffraction limit by SNEM: effects of AFM tip modifications with thiol monolayers on imaging quality.

    PubMed

    Cumurcu, Aysegul; Diaz, Jordi; Lindsay, Ian D; de Beer, Sissi; Duvigneau, Joost; Schön, Peter; Julius Vancso, G

    2015-03-01

    Tip-enhanced nanoscale optical imaging techniques such as apertureless scanning near-field optical microscopy (a-SNOM) and scanning near-field ellipsometric microscopy (SNEM) applications can suffer from a steady degradation in performance due to adhesion of atmospheric contaminants to the metal coated tip. Here, we demonstrate that a self-assembled monolayer (SAM) of ethanethiol (EtSH) is an effective means of protecting gold-coated atomic force microscopy (AFM) probe tips from accumulation of surface contaminants during prolonged exposure to ambient air. The period over which they yield consistent and reproducible results for scanning near-field ellipsometric microscopy (SNEM) imaging is thus extended. SNEM optical images of a microphase separated polystyrene-block-poly (methylmethacrylate) (PS-b-PMMA) diblock copolymer film, which were captured with bare and SAM-protected gold-coated AFM probes, both immediately after coating and following five days of storage in ambient air, were compared. During this period the intensity of the optical signals from the untreated gold tip fell by 66%, while those from the SAM protected tip fell by 14%. Additionally, gold coated AFM probe tips were modified with various lengths of alkanethiols to measure the change in intensity variation in the optical images with SAM layer thickness. The experimental results were compared to point dipole model calculations. While a SAM of 1-dodecanethiol (DoSH) was found to strongly suppress field enhancement we find that it can be locally removed from the tip apex by deforming the molecules under load, restoring SNEM image contrast. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Probing lipid membrane electrostatics

    NASA Astrophysics Data System (ADS)

    Yang, Yi

    The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive

  19. Imaging viscoelastic properties of live cells by AFM: power-law rheology on the nanoscale.

    PubMed

    Hecht, Fabian M; Rheinlaender, Johannes; Schierbaum, Nicolas; Goldmann, Wolfgang H; Fabry, Ben; Schäffer, Tilman E

    2015-06-21

    We developed force clamp force mapping (FCFM), an atomic force microscopy (AFM) technique for measuring the viscoelastic creep behavior of live cells with sub-micrometer spatial resolution. FCFM combines force-distance curves with an added force clamp phase during tip-sample contact. From the creep behavior measured during the force clamp phase, quantitative viscoelastic sample properties are extracted. We validate FCFM on soft polyacrylamide gels. We find that the creep behavior of living cells conforms to a power-law material model. By recording short (50-60 ms) force clamp measurements in rapid succession, we generate, for the first time, two-dimensional maps of power-law exponent and modulus scaling parameter. Although these maps reveal large spatial variations of both parameters across the cell surface, we obtain robust mean values from the several hundreds of measurements performed on each cell. Measurements on mouse embryonic fibroblasts show that the mean power-law exponents and the mean modulus scaling parameters differ greatly among individual cells, but both parameters are highly correlated: stiffer cells consistently show a smaller power-law exponent. This correlation allows us to distinguish between wild-type cells and cells that lack vinculin, a dominant protein of the focal adhesion complex, even though the mean values of viscoelastic properties between wildtype and knockout cells did not differ significantly. Therefore, FCFM spatially resolves viscoelastic sample properties and can uncover subtle mechanical signatures of proteins in living cells.

  20. Elastic modulus of nanomaterials: resonant contact-AFM measurement and reduced-size effects (Invited Paper)

    NASA Astrophysics Data System (ADS)

    Nysten, Bernard; Fretigny, Christian; Cuenot, Stephane

    2005-05-01

    Resonant contact atomic force microscopy (resonant C-AFM) is used to quantitatively measure the elastic modulus of polymer nanotubes and metallic nanowires. To achieve this, an oscillating electric field is applied between the sample holder and the microscope head to excite the oscillation of the cantilever in contact with the nanostructures suspended over the pores of a membrane. The resonance frequency of the cantilever with the tip in contact with a nanostructure is shifted to higher values with respect to the resonance frequency of the free cantilever. It is demonstrated that the system can simply be modeled by a cantilever with the tip in contact with two springs. The measurement of the frequency shift enables the direct determination of the spring stiffness, i.e. the nanowires or nanotube stiffness. The method also enables the determination of the boundary conditions of the nanobeam on the membrane. The tensile elastic modulus is then simply determined using the classical theory of beam deflection. The obtained results for the larger nanostructures fairly agree to the values reported in the literature for the macroscopic elastic modulus of the corresponding materials. The measured modulus of the nanomaterials with smaller diameters is significantly higher than that of the larger ones. The increase of the apparent elastic modulus for the smaller diameters is attributed to the surface tension effects. It is thus demonstrated that resonant C-AFM enables the measurement of the elastic modulus and of the surface tension of nanomaterials.

  1. Ion-damage-free planarization or shallow angle sectioning of solar cells for mapping grain orientation and nanoscale photovoltaic properties

    NASA Astrophysics Data System (ADS)

    Kutes, Yasemin; Luria, Justin; Sun, Yu; Moore, Andrew; Aguirre, Brandon A.; Cruz-Campa, Jose L.; Aindow, Mark; Zubia, David; Huey, Bryan D.

    2017-05-01

    Ion beam milling is the most common modern method for preparing specific features for microscopic analysis, even though concomitant ion implantation and amorphization remain persistent challenges, particularly as they often modify materials properties of interest. Atomic force microscopy (AFM), on the other hand, can mechanically mill specific nanoscale regions in plan-view without chemical or high energy ion damage, due to its resolution, directionality, and fine load control. As an example, AFM-nanomilling (AFM-NM) is implemented for top-down planarization of polycrystalline CdTe thin film solar cells, with a resulting decrease in the root mean square (RMS) roughness by an order of magnitude, even better than for a low incidence FIB polished surface. Subsequent AFM-based property maps reveal a substantially stronger contrast, in this case of the short-circuit current or open circuit voltage during light exposure. Electron back scattering diffraction (EBSD) imaging also becomes possible upon AFM-NM, enabling direct correlations between the local materials properties and the polycrystalline microstructure. Smooth shallow-angle cross-sections are demonstrated as well, based on targeted oblique milling. As expected, this reveals a gradual decrease in the average short-circuit current and maximum power as the underlying CdS and electrode layers are approached, but a relatively consistent open-circuit voltage through the diminishing thickness of the CdTe absorber. AFM-based nanomilling is therefore a powerful tool for material characterization, uniquely providing ion-damage free, selective area, planar smoothing or low-angle sectioning of specimens while preserving their functionality. This enables novel, co-located advanced AFM measurements, EBSD analysis, and investigations by related techniques that are otherwise hindered by surface morphology or surface damage.

  2. Distinguishing Nanobubbles from Nanodroplets with AFM: The Influence of Vertical and Lateral Imaging Forces.

    PubMed

    An, Hongjie; Tan, Beng Hau; Ohl, Claus-Dieter

    2016-12-06

    The widespread application of surface-attached nanobubbles and nanodroplets in biomedical engineering and nanotechnology is limited by numerous experimental challenges, in particular, the possibility of contamination in nucleation experiments. These challenges are complicated by recent reports that it can be difficult to distinguish between nanoscale drops and bubbles. Here we identify clear differences in the mechanical responses of nanobubbles and nanodroplets under various modes of AFM imaging that subject the objects to predominantly vertical or lateral forces. This allows us to distinguish among nanodroplets, nanobubbles, and oil-covered nanobubbles in water.

  3. Adsorption mechanisms for fatty acids on DLC and steel studied by AFM and tribological experiments

    NASA Astrophysics Data System (ADS)

    Simič, R.; Kalin, M.

    2013-10-01

    Fatty acids are known to affect the friction and wear of steel contacts via adsorption onto the surface, which is one of the fundamental boundary-lubrication mechanisms. The understanding of the lubrication mechanisms of polar molecules on diamond-like carbon (DLC) is, however, still insufficient. In this work we aimed to find out whether such molecules have a similar effect on DLC coatings as they do on steel. The adsorption of hexadecanoic acid in various concentrations (2-20 mmol/l) on DLC was studied under static conditions using an atomic force microscope (AFM). The amount of surface coverage of the adsorbed fatty-acid molecules was analysed. In addition, tribological tests were performed to correlate the wear and friction behaviours in tribological contacts with the adsorption of molecules on the surface under static conditions. A good correlation between the AFM results and the tribological behaviour was observed. We confirmed that fatty acids can adsorb onto the DLC surfaces and are, therefore, potential boundary-lubrication agents for DLC coatings. The adsorption of the fatty acid onto the DLC surfaces reduces the wear of the coatings, but it is less effective in reducing the friction. Tentative adsorption mechanisms that include an environmental species effect, a temperature effect and a tribochemical effect are proposed for DLC and steel surfaces based on our results and few potential mechanisms found in literature.

  4. Integrin-specific mechanoresponses to compression and extension probed by cylindrical flat-ended AFM tips in lung cells.

    PubMed

    Acerbi, Irene; Luque, Tomás; Giménez, Alícia; Puig, Marta; Reguart, Noemi; Farré, Ramon; Navajas, Daniel; Alcaraz, Jordi

    2012-01-01

    Cells from lung and other tissues are subjected to forces of opposing directions that are largely transmitted through integrin-mediated adhesions. How cells respond to force bidirectionality remains ill defined. To address this question, we nanofabricated flat-ended cylindrical Atomic Force Microscopy (AFM) tips with ~1 µm(2) cross-section area. Tips were uncoated or coated with either integrin-specific (RGD) or non-specific (RGE/BSA) molecules, brought into contact with lung epithelial cells or fibroblasts for 30 s to form focal adhesion precursors, and used to probe cell resistance to deformation in compression and extension. We found that cell resistance to compression was globally higher than to extension regardless of the tip coating. In contrast, both tip-cell adhesion strength and resistance to compression and extension were the highest when probed at integrin-specific adhesions. These integrin-specific mechanoresponses required an intact actin cytoskeleton, and were dependent on tyrosine phosphatases and Ca(2+) signaling. Cell asymmetric mechanoresponse to compression and extension remained after 5 minutes of tip-cell adhesion, revealing that asymmetric resistance to force directionality is an intrinsic property of lung cells, as in most soft tissues. Our findings provide new insights on how lung cells probe the mechanochemical properties of the microenvironment, an important process for migration, repair and tissue homeostasis.

  5. Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review.

    PubMed

    Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

    2017-09-01

    Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades has yielded remarkable novel insights in understanding the development and progression of certain diseases, such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine. In this paper, we reviewed the utilization of AFM to characterize cell mechanics. First, the principle and method of AFM single-cell mechanical analysis was presented, along with the mechanical responses of cells to representative external stimuli measured by AFM. Next, the unique changes of cell mechanics in two types of physiological processes (stem cell differentiation, cancer metastasis) revealed by AFM were summarized. After that, the molecular mechanisms guiding cell mechanics were analyzed. Finally the challenges and future directions were discussed.

  6. AFM Investigation of Liquid-Filled Polymer Microcapsules Elasticity.

    PubMed

    Sarrazin, Baptiste; Tsapis, Nicolas; Mousnier, Ludivine; Taulier, Nicolas; Urbach, Wladimir; Guenoun, Patrick

    2016-05-10

    Elasticity of polymer microcapsules (MCs) filled with a liquid fluorinated core is studied by atomic force microscopy (AFM). Accurately characterized spherical tips are employed to obtain the Young's moduli of MCs having four different shell thicknesses. We show that those moduli are effective ones because the samples are composites. The strong decrease of the effective MC elasticity (from 3.0 to 0.1 GPa) as the shell thickness decreases (from 200 to 10 nm) is analyzed using a novel numerical approach. This model describes the evolution of the elasticity of a coated half-space according to the contact radius, the thickness of the film, and the elastic moduli of bulk materials. This numerical model is consistent with the experimental data and allows simulating the elastic behavior of MCs at high frequencies (5 MHz). While the quasi-static elasticity of the MCs is found to be very dependent on the shell thickness, the high frequency (5 MHz) elastic behavior of the core leads to a stable behavior of the MCs (from 2.5 to 3 GPa according to the shell thickness). Finally, the effect of thermal annealing on the MCs elasticity is investigated. The Young's modulus is found to decrease because of the reduction of the shell thickness due to the loss of the polymer.

  7. Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system.

    PubMed

    Rygula, Anna; Oleszkiewicz, Tomasz; Grzebelus, Ewa; Pacia, Marta Z; Baranska, Malgorzata; Baranski, Rafal

    2018-05-15

    Three non-destructive and complementary techniques, Raman imaging, Atomic Force Microscopy and Scanning Near-field Optical Microscopy were used simultaneously to show for the first time chemical and structural differences of carotenoid crystals. Spectroscopic and microscopic scanning probe measurements were applied to the released crystals or to crystals accumulated in a unique, carotenoids rich callus tissue growing in vitro that is considered as a new model system for plant carotenoid research. Three distinct morphological crystal types of various carotenoid composition were identified, a needle-like, rhomboidal and helical. Raman imaging using 532 and 488 nm excitation lines provided evidence that the needle-like and rhomboidal crystals had similar carotenoid composition and that they were composed mainly of β-carotene accompanied by α-carotene. However, the presence of α-carotene was not identified in the helical crystals, which had the characteristic spatial structure. AFM measurements of crystals identified by Raman imaging revealed the crystal topography and showed the needle-like and rhomboidal crystals were planar but they differed in all three dimensions. Combining SNOM and Raman imaging enabled indication of carotenoid rich structures and visualised their distribution in the cell. The morphology of identified subcellular structures was characteristic for crystalline, membraneous and tubular chromoplasts that are plant organelles responsible for carotenoid accumulation in cells. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Ion-damage-free planarization or shallow angle sectioning of solar cells for mapping grain orientation and nanoscale photovoltaic properties

    DOE PAGES

    Kutes, Yasemin; Luria, Justin; Sun, Yu; ...

    2017-04-11

    Ion beam milling is the most common modern method for preparing specific features for microscopic analysis, even though concomitant ion implantation and amorphization remain persistent challenges, particularly as they often modify materials properties of interest. Atomic force microscopy (AFM), on the other hand, can mechanically mill specific nanoscale regions in plan-view without chemical or high energy ion damage, due to its resolution, directionality, and fine load control. As an example, AFM-nanomilling (AFM-NM) is implemented for top-down planarization of polycrystalline CdTe thin film solar cells, with a resulting decrease in the root mean square (RMS) roughness by an order of magnitude,more » even better than for a low incidence FIB polished surface. Subsequently AFM-based property maps reveal a substantially stronger contrast, in this case of the short-circuit current or open circuit voltage during light exposure. Furthermore, electron back scattering diffraction (EBSD) imaging also becomes possible upon AFM-NM, enabling direct correlations between the local materials properties and the polycrystalline microstructure. Smooth shallow-angle cross-sections are demonstrated as well, based on targeted oblique milling. As expected, this reveals a gradual decrease in the average short-circuit current and maximum power as the underlying CdS and electrode layers are approached, but a relatively consistent open-circuit voltage through the diminishing thickness of the CdTe absorber. AFM-based nanomilling is therefore a powerful tool for material characterization, uniquely providing ion-damage free, selective area, planar smoothing or low-angle sectioning of specimens while preserving their functionality. This then enables novel, co-located advanced AFM measurements, EBSD analysis, and investigations by related techniques that are otherwise hindered by surface morphology or surface damage.« less

  9. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kutes, Yasemin; Luria, Justin; Sun, Yu

    Ion beam milling is the most common modern method for preparing specific features for microscopic analysis, even though concomitant ion implantation and amorphization remain persistent challenges, particularly as they often modify materials properties of interest. Atomic force microscopy (AFM), on the other hand, can mechanically mill specific nanoscale regions in plan-view without chemical or high energy ion damage, due to its resolution, directionality, and fine load control. As an example, AFM-nanomilling (AFM-NM) is implemented for top-down planarization of polycrystalline CdTe thin film solar cells, with a resulting decrease in the root mean square (RMS) roughness by an order of magnitude,more » even better than for a low incidence FIB polished surface. Subsequently AFM-based property maps reveal a substantially stronger contrast, in this case of the short-circuit current or open circuit voltage during light exposure. Furthermore, electron back scattering diffraction (EBSD) imaging also becomes possible upon AFM-NM, enabling direct correlations between the local materials properties and the polycrystalline microstructure. Smooth shallow-angle cross-sections are demonstrated as well, based on targeted oblique milling. As expected, this reveals a gradual decrease in the average short-circuit current and maximum power as the underlying CdS and electrode layers are approached, but a relatively consistent open-circuit voltage through the diminishing thickness of the CdTe absorber. AFM-based nanomilling is therefore a powerful tool for material characterization, uniquely providing ion-damage free, selective area, planar smoothing or low-angle sectioning of specimens while preserving their functionality. This then enables novel, co-located advanced AFM measurements, EBSD analysis, and investigations by related techniques that are otherwise hindered by surface morphology or surface damage.« less

  10. Effect of tetramethylammonium hydroxide/isopropyl alcohol wet etching on geometry and surface roughness of silicon nanowires fabricated by AFM lithography

    PubMed Central

    Yusoh, Siti Noorhaniah

    2016-01-01

    Summary The optimization of etchant parameters in wet etching plays an important role in the fabrication of semiconductor devices. Wet etching of tetramethylammonium hydroxide (TMAH)/isopropyl alcohol (IPA) on silicon nanowires fabricated by AFM lithography is studied herein. TMAH (25 wt %) with different IPA concentrations (0, 10, 20, and 30 vol %) and etching time durations (30, 40, and 50 s) were investigated. The relationships between etching depth and width, and etching rate and surface roughness of silicon nanowires were characterized in detail using atomic force microscopy (AFM). The obtained results indicate that increased IPA concentration in TMAH produced greater width of the silicon nanowires with a smooth surface. It was also observed that the use of a longer etching time causes more unmasked silicon layers to be removed. Importantly, throughout this study, wet etching with optimized parameters can be applied in the design of the devices with excellent performance for many applications. PMID:27826521

  11. Application of the Maxwell-Wagner-Hanai effective medium theory to the analysis of the interfacial polarization relaxations in conducting composite films

    NASA Astrophysics Data System (ADS)

    J-P Adohi, B.; Vanga Bouanga, C.; Fatyeyeva, K.; Tabellout, M.

    2009-01-01

    A new approach to explain the interfacial polarization phenomenon in conducting composite films is proposed. HCl-doped poly(ethylene terephthalate) (PET) and polyamide-6 (PA-6) matrices with embedded polyaniline (PANI) particles as filler were investigated and analysed, combining dielectric spectroscopy and AFM electrical images with the effective medium theory analysis. Up to three relaxation peaks attributed to the interfacial polarization phenomena were detected in the studied frequency range (0.1 Hz-1 MHz). The AFM electrical images revealed that the doped PA-6/PANI composite can be modelled as a single-type particle medium and the PET/PANI one as a two-type particle medium. A simple dielectric loss expression was derived from the Maxwell-Wagner-Hanai mixture equation and was applied to the experimental data to identify the interfaces involved in each of the relaxation peaks. The parameter values (permittivity, conductivity, volume fraction of the PANI particles) were found to agree well with the measured one, hence validating the models.

  12. Simultaneous Measurement of Multiple Mechanical Properties of Single Cells Using AFM by Indentation and Vibration.

    PubMed

    Zhang, Chuang; Shi, Jialin; Wang, Wenxue; Xi, Ning; Wang, Yuechao; Liu, Lianqing

    2017-12-01

    The mechanical properties of cells, which are the main characteristics determining their physical performance and physiological functions, have been actively studied in the fields of cytobiology and biomedical engineering and for the development of medicines. In this study, an indentation-vibration-based method is proposed to simultaneously measure the mechanical properties of cells in situ, including cellular mass (m), elasticity (k), and viscosity (c). The proposed measurement method is implemented based on the principle of forced vibration stimulated by simple harmonic force using an atomic force microscope (AFM) system integrated with a piezoelectric transducer as the substrate vibrator. The corresponding theoretical model containing the three mechanical properties is derived and used to perform simulations and calculations. Living and fixed human embryonic kidney 293 (HEK 293) cells were subjected to indentation and vibration to measure and compare their mechanical parameters and verify the proposed approach. The results that the fixed sample cells are more viscous and elastic than the living sample cells and the measured mechanical properties of cell are consistent within, but not outside of the central region of the cell, are in accordance with the previous studies. This work provides an approach to simultaneous measurement of the multiple mechanical properties of single cells using an integrated AFM system based on the principle force vibration and thickness-corrected Hertz model. This study should contribute to progress in biomedical engineering, cytobiology, medicine, early diagnosis, specific therapy and cell-powered robots.

  13. Friction measurements on InAs NWs by AFM manipulation

    NASA Astrophysics Data System (ADS)

    Pettersson, Hakan; Conache, Gabriela; Gray, Struan; Bordag, Michael; Ribayrol, Aline; Froberg, Linus; Samuelson, Lars; Montelius, Lars

    2008-03-01

    We discuss a new approach to measure the friction force between elastically deformed nanowires and a surface. The wires are bent, using an AFM, into an equilibrium shape determined by elastic restoring forces within the wire and friction between the wire and the surface. From measurements of the radius of curvature of the bent wires, elasticity theory allows the friction force per unit length to be calculated. We have studied friction properties of InAs nanowires deposited on SiO2, silanized SiO2 and Si3N4 substrates. The wires were typically from 0.5 to a few microns long, with diameters varying between 20 and 80 nm. Manipulation is done in a `Retrace Lift' mode, where feedback is turned off for the reverse scan and the tip follows a nominal path. The effective manipulation force during the reverse scan can be changed by varying an offset in the height of the tip over the surface. We will report on interesting static- and sliding friction experiments with nanowires on the different substrates, including how the friction force per unit length varies with the diameter of the wires.

  14. GTG banding pattern on human metaphase chromosomes revealed by high resolution atomic-force microscopy.

    PubMed

    Thalhammer, S; Koehler, U; Stark, R W; Heckl, W M

    2001-06-01

    Surface topography of human metaphase chromosomes following GTG banding was examined using high resolution atomic force microscopy (AFM). Although using a completely different imaging mechanism, which is based on the mechanical interaction of a probe tip with the chromosome, the observed banding pattern is comparable to results from light microscopy and a karyotype of the AFM imaged metaphase spread can be generated. The AFM imaging process was performed on a normal 2n = 46, XX karyotype and on a 2n = 46, XY, t(2;15)(q23;q15) karyotype as an example of a translocation of chromosomal bands.

  15. Determination of the attractive force, adhesive force, adhesion energy and Hamaker constant of soot particles generated from a premixed methane/oxygen flame by AFM

    NASA Astrophysics Data System (ADS)

    Liu, Ye; Song, Chonglin; Lv, Gang; Chen, Nan; Zhou, Hua; Jing, Xiaojun

    2018-03-01

    Atomic force microscopy (AFM) was used to characterize the attractive force, adhesive force and adhesion energy between an AFM probe tip and nanometric soot particle generated by a premixed methane/oxygen flame. Different attractive force distributions were found when increasing the height above burner (HAB), with forces ranging from 1.1-3.5 nN. As the HAB was increased, the average attractive force initially increased, briefly decreased, and then underwent a gradual increase, with a maximum of 2.54 nN observed at HAB = 25 mm. The mean adhesive force was 6.5-7.5 times greater than the mean attractive force at the same HAB, and values were in the range of 13.5-24.5 nN. The adhesion energy was in the range of 2.0-5.6 × 10-17 J. The variations observed in the average adhesion energy with increasing HAB were different from those of the average adhesion force, implying that the stretched length of soot particles is an important factor affecting the average adhesion energy. The Hamaker constants of the soot particles generated at different HABs were determined from AFM force-separation curves. The average Hamaker constant exhibited a clear correlation with the graphitization degree of soot particles as obtained from Raman spectroscopy.

  16. Attractive forces between hydrophobic solid surfaces measured by AFM on the first approach in salt solutions and in the presence of dissolved gases.

    PubMed

    Azadi, Mehdi; Nguyen, Anh V; Yakubov, Gleb E

    2015-02-17

    Interfacial gas enrichment of dissolved gases (IGE) has been shown to cover hydrophobic solid surfaces in water. The atomic force microscopy (AFM) data has recently been supported by molecular dynamics simulation. It was demonstrated that IGE is responsible for the unexpected stability and large contact angle of gaseous nanobubbles at the hydrophobic solid-water interface. Here we provide further evidence of the significant effect of IGE on an attractive force between hydrophobic solid surfaces in water. The force in the presence of dissolved gas, i.e., in aerated and nonaerated NaCl solutions (up to 4 M), was measured by the AFM colloidal probe technique. The effect of nanobubble bridging on the attractive force was minimized or eliminated by measuring forces on the first approach of the AFM probe toward the flat hydrophobic surface and by using high salt concentrations to reduce gas solubility. Our results confirm the presence of three types of forces, two of which are long-range attractive forces of capillary bridging origin as caused by either surface nanobubbles or gap-induced cavitation. The third type is a short-range attractive force observed in the absence of interfacial nanobubbles that is attributed to the IGE in the form of a dense gas layer (DGL) at hydrophobic surfaces. Such a force was found to increase with increasing gas saturation and to decrease with decreasing gas solubility.

  17. Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

    PubMed Central

    Kulik, Andrzej J; Lee, Kyumin; Pyka-Fościak, Grazyna; Nowak, Wieslaw

    2015-01-01

    Summary The first experiment showing the effects of specific interaction forces using lateral force microscopy (LFM) was demonstrated for lectin–carbohydrate interactions some years ago. Such measurements are possible under the assumption that specific forces strongly dominate over the non-specific ones. However, obtaining quantitative results requires the complex and tedious calibration of a torsional force. Here, a new and relatively simple method for the calibration of the torsional force is presented. The proposed calibration method is validated through the measurement of the interaction forces between human fibronectin and its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions. PMID:26114080

  18. 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.

  19. Wideband digital frequency detector with subtraction-based phase comparator for frequency modulation atomic force microscopy.

    PubMed

    Mitani, Yuji; Kubo, Mamoru; Muramoto, Ken-ichiro; Fukuma, Takeshi

    2009-08-01

    We have developed a wideband digital frequency detector for high-speed frequency modulation atomic force microscopy (FM-AFM). We used a subtraction-based phase comparator (PC) in a phase-locked loop circuit instead of a commonly used multiplication-based PC, which has enhanced the detection bandwidth to 100 kHz. The quantitative analysis of the noise performance revealed that the internal noise from the developed detector is small enough to provide the theoretically limited noise performance in FM-AFM experiments in liquid. FM-AFM imaging of mica in liquid was performed with the developed detector, showing its stability and applicability to true atomic-resolution imaging in liquid.

  20. Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

    PubMed

    Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

    2017-08-24

    Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

  1. The isolated MUC5AC gene product from human ocular mucin displays intramolecular conformational heterogeneity.

    PubMed

    Round, Andrew N; McMaster, Terence J; Miles, Mervyn J; Corfield, Anthony P; Berry, Monica

    2007-06-01

    Atomic force microscopy (AFM) has been used to show that human ocular mucins contain at least three distinct polymer conformations, separable by isopycnic density gradient centrifugation. In this work we have used affinity purification against the anti(mucin peptide core) monoclonal antibody 45M1 to isolate MUC5AC gene products, a major component of human ocular mucins. AFM images confirm that the affinity-purified polymers adopt distinct conformations that coidentify with two of those observed in the parent population, and further reveal that these two different conformations can be present within the same polymer. AFM images of the complexes formed after incubation of 45M1 with the parent sample reveal different rates of binding to the two MUC5AC polymer types. The variability of gene products within a mucin population was revealed by analyzing the height distributions along the polymer contour and periodicities in distances between occupied antibody binding sites. AFM analysis of mucin polymers at the single molecule level provides new information about the genetic origins of individual polymers and the contributions of glycosylation to the physicochemical properties of mucins, which can be correlated with information obtained from biochemistry, antibody binding assays, and molecular biology techniques.

  2. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

    PubMed

    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  3. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    PubMed Central

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  4. Fabrication and characterization of ultrathin dextran layers: Time dependent nanostructure in aqueous environments revealed by OWLS.

    PubMed

    Saftics, Andras; Kurunczi, Sándor; Szekrényes, Zsolt; Kamarás, Katalin; Khánh, Nguyen Quoc; Sulyok, Attila; Bősze, Szilvia; Horvath, Robert

    2016-10-01

    Surface coatings of the polysaccharide dextran and its derivatives are key ingredients especially in label-free biosensors for the suppression of non-specific binding and for receptor immobilization. Nevertheless, the nanostructure of these ultrathin coatings and its tailoring by the variation of the preparation conditions have not been profoundly characterized and understood. In this work carboxymethylated dextran (CMD) was prepared and used for fabricating ultrathin surface coatings. A grafting method based on covalent coupling to aminosilane- and epoxysilane-functionalized surfaces was applied to obtain thin CMD layers. The carboxyl moiety of the CMD was coupled to the aminated surface by EDC-NHS reagents, while CMD coupling through epoxysilane molecules was performed without any additional reagents. The surface analysis following the grafting procedures consisted of X-ray photoelectron spectroscopy (XPS), attenuated total reflection infrared spectroscopy (ATR-IR), spectroscopic ellipsometry, atomic force microscopy (AFM) and optical waveguide lightmode spectroscopy (OWLS). The XPS and AFM measurements showed that the grafting resulted in a very thin dextran layer of a few nanometers. The OWLS method allowed devising the structure of the interfacial dextran layers by the evaluation of the optogeometrical parameters. The alteration in the nanostructure of the CMD layer with the chemical composition of the silane coverage and the pH of the grafting solution was revealed by in situ OWLS, specifically, lain down chains were found to be prevalent on the surface under neutral and basic conditions on epoxysilylated surfaces. The developed methodologies allowed to design and fabricate nanometer scale CMD layers with well-controlled surface structure, which are very difficult to characterize in aqueous environments using present instrumentations and highly hydrated surface layers. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Nanomechanical characterization of nanostructured bainitic steel: Peak Force Microscopy and Nanoindentation with AFM.

    PubMed

    Morales-Rivas, Lucia; González-Orive, Alejandro; Garcia-Mateo, Carlos; Hernández-Creus, Alberto; Caballero, Francisca G; Vázquez, Luis

    2015-11-25

    The full understanding of the deformation mechanisms in nanostructured bainite requires the local characterization of its mechanical properties, which are expected to change from one phase, bainitic ferrite, to another, austenite. This study becomes a challenging process due to the bainitic nanostructured nature and high Young's modulus. In this work, we have carried out such study by means of the combination of AFM-based techniques, such as nanoindentation and Peak Force Quantitative Nanomechanical Mapping (PF-QNM) measurements. We have addressed critically the limits and advantages of these techniques and been able to measure some elastoplastic parameters of both phases. Specifically, we have analyzed by PF-QNM two nanostructured bainitic steels, with a finer and a coarser structure, and found that both phases have a similar Young's modulus.

  6. Characterization of prepared In2O3 thin films: The FT-IR, FT-Raman, UV-Visible investigation and optical analysis.

    PubMed

    Panneerdoss, I Joseph; Jeyakumar, S Johnson; Ramalingam, S; Jothibas, M

    2015-08-05

    In this original work, the Indium oxide (In2O3) thin film is deposited cleanly on microscope glass substrate at different temperatures by spray pyrolysis technique. The physical properties of the films are characterized by XRD, SEM, AFM and AFM measurements. The spectroscopic investigation has been carried out on the results of FT-IR, FT-Raman and UV-Visible. XRD analysis exposed that the structural transformation of films from stoichiometric to non-stoichiometric orientation of the plane vice versa and also found that, the film is polycrystalline in nature having cubic crystal structure with a preferred grain orientation along (222) plane. SEM and AFM studies revealed that, the film with 0.1M at 500°C has spherical grains with uniform dimension. The complete vibrational analysis has been carried out and the optimized parameters are calculated using HF and DFT (CAM-B3LYP, B3LYP and B3PW91) methods with 3-21G(d,p) basis set. Furthermore, NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) technique. The molecular electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, molecular electrostatic potential energy (MEP) analysis and Polarizability first order hyperpolarizability calculations are performed by time dependent DFT (TD-DFT) approach. The energy excitation on electronic structure is investigated and the assignment of the absorption bands in the electronic spectra of steady compound is discussed. The calculated HOMO and LUMO energies showed the enhancement of energy gap by the addition of substitutions with the base molecule. The thermodynamic properties (heat capacity, entropy, and enthalpy) at different temperatures are calculated and interpreted in gas phase. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

  7. Detection of aflatoxin M1 in milk using spectroscopy and multivariate analyses.

    PubMed

    Jaiswal, Pranita; Jha, Shyam Narayan; Kaur, Jaspreet; Borah, Anjan; Ramya, H G

    2018-01-01

    Aflatoxin M1 (AFM1), a potentially carcinogenic compound, is found in milk obtained from animals that consume contaminated feed. Spectra of bovine milk, spiked with AFM1 (0, 0.02, 0.04, 0.06, 0.08 and 0.1μg/l) were acquired using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometer. Spectra revealed significant differences among pure and AFM1 spiked samples in spectral regions 1800-650cm -1 and 3689-3499cm -1 , which may be attributed to complex chemical structure of AFM1. Principal component analysis (PCA) showed clear clustering of samples (p⩽0.05). The models could successfully classify (>86%) and detect even 0.02μg/l AFM1 in milk (p⩽0.05) using SIMCA. AFM1 was best predicted in wavenumber range of 1800-650cm -1 with coefficient of determination (R 2 ) of 0.99 and 0.98, for calibration and validation, respectively, using partial least square (PLS) regression. The study indicated feasibility of ATR-FTIR spectroscopy and chemometrics in rapid detection and quantification of AFM1 in milk. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Dissolution of uranophane: An AFM, XPS, SEM and ICP study

    NASA Astrophysics Data System (ADS)

    Schindler, Michael; Freund, Michael; Hawthorne, Frank C.; Burns, Peter C.; Maurice, Patricia A.

    2009-05-01

    Dissolution experiments on single crystals of uranophane and uranophane-β, Ca(H 2O) 5[(UO 2)(SiO 3(OH)] 2, from the Shinkolobwe mine of the Democratic Republic of Congo, were done in an aqueous HCl solution of pH 3.5 for 3 h, in HCl solutions of pH 2 for 5, 10 and 30 min, and in Pb 2+-, Ba-, Sr-, Ca- and Mg-HCl solutions of pH 2 for 30 min. The basal surfaces of the treated uranophane crystals were examined using atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Solutions after dissolution experiments on single crystals and synthetic powders were analysed with inductively coupled plasma-optical emission spectroscopy (ICP-OES) and mass spectroscopy (ICP-MS). The morphology of the observed etch pits (measured by AFM) were compared to the morphology, predicted on the basis of the bond-valence deficiency of polyhedron chains along the edges of the basal surface. Etch pits form in HCl solutions of pH 2. Their decrease in depth with the duration of the dissolution experiment is explained with the stepwave dissolution model, which describes the lowering of the surrounding area of an etch pit with continuous waves of steps emanated from the etch pit into the rest of the crystal surface. Hillocks form in an HCl solution of pH 3.5, and the chemical composition of the surface (as indicated by XPS) shows that these hillocks are the result of the precipitation of a uranyl-hydroxy-hydrate phase. Well-orientated hillocks form on the surface of uranophane in a SrCl 2-HCl solution of pH 2. They are part of an aged silica coating of composition Si 2O 2(OH) 4(H 2O) n. An amorphous layer forms on the surface of uranophane in a MgCl 2-HCl solution of pH 2, which has a composition and structure similar to silicic acid. Small crystallites of uranyl-hydroxy-hydrate phases form on the surface of uranophane after treatment in Pb(NO 3) 2-HCl and BaCl 2-HCl solutions of pH 2. Dissolution experiments on synthetic uranophane powders

  9. Acquire an Bruker Dimension FastScanTM Atomic Force Microscope (AFM) for Materials, Physical and Biological Science Research and Education

    DTIC Science & Technology

    2016-04-14

    study dynamic events such as melting, evaporation, crystallization, dissolution, self-assembly, membrane disruption, sample movement tracking. To... polymeric hairy nanopraticle, suprastructures REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR/MONITOR’S ACRONYM(S...the AFM will permit us to study dynamic events such as melting, evaporation, crystallization, dissolution, self-assembly, membrane disruption, sample

  10. Predictive Modeling and Optimization of Vibration-assisted AFM Tip-based Nanomachining

    NASA Astrophysics Data System (ADS)

    Kong, Xiangcheng

    The tip-based vibration-assisted nanomachining process offers a low-cost, low-effort technique in fabricating nanometer scale 2D/3D structures in sub-100 nm regime. To understand its mechanism, as well as provide the guidelines for process planning and optimization, we have systematically studied this nanomachining technique in this work. To understand the mechanism of this nanomachining technique, we firstly analyzed the interaction between the AFM tip and the workpiece surface during the machining process. A 3D voxel-based numerical algorithm has been developed to calculate the material removal rate as well as the contact area between the AFM tip and the workpiece surface. As a critical factor to understand the mechanism of this nanomachining process, the cutting force has been analyzed and modeled. A semi-empirical model has been proposed by correlating the cutting force with the material removal rate, which was validated using experimental data from different machining conditions. With the understanding of its mechanism, we have developed guidelines for process planning of this nanomachining technique. To provide the guideline for parameter selection, the effect of machining parameters on the feature dimensions (depth and width) has been analyzed. Based on ANOVA test results, the feature width is only controlled by the XY vibration amplitude, while the feature depth is affected by several machining parameters such as setpoint force and feed rate. A semi-empirical model was first proposed to predict the machined feature depth under given machining condition. Then, to reduce the computation intensity, linear and nonlinear regression models were also proposed and validated using experimental data. Given the desired feature dimensions, feasible machining parameters could be provided using these predictive feature dimension models. As the tip wear is unavoidable during the machining process, the machining precision will gradually decrease. To maintain the machining

  11. Analysis of DNA interactions using single-molecule force spectroscopy.

    PubMed

    Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

    2013-06-01

    Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

  12. Single cell active force generation under dynamic loading - Part I: AFM experiments.

    PubMed

    Weafer, P P; Reynolds, N H; Jarvis, S P; McGarry, J P

    2015-11-01

    A novel series of experiments are performed on single cells using a bespoke AFM system where the response of cells to dynamic loading at physiologically relevant frequencies is uncovered. Measured forces for the untreated cells are dramatically different to cytochalasin-D (cyto-D) treated cells, indicating that the contractile actin cytoskeleton plays a critical role in the response of cells to dynamic loading. Following a change in applied strain magnitude, while maintaining a constant applied strain rate, the compression force for contractile cells recovers to 88.9±7.8% of the steady state force. In contrast, cyto-D cell compression forces recover to only 38.0±6.7% of the steady state force. Additionally, untreated cells exhibit strongly negative (pulling) forces during unloading half-cycles when the probe is retracted. In comparison, negligible pulling forces are measured for cyto-D cells during probe retraction. The current study demonstrates that active contractile forces, generated by actin-myosin cross-bridge cycling, dominate the response of single cells to dynamic loading. Such active force generation is shown to be independent of applied strain magnitude. Passive forces generated by the applied deformation are shown to be of secondary importance, exhibiting a high dependence on applied strain magnitude, in contrast to the active forces in untreated cells. A novel series of experiments are performed on single cells using a bespoke AFM system where the response of cells to dynamic loading at physiologically relevant frequencies is uncovered. Contractile cells, which contain the active force generation machinery of the actin cytoskeleton, are shown to be insensitive to applied strain magnitude, exhibiting high resistance to dynamic compression and stretching. Such trends are not observed for cells in which the actin cytoskeleton has been chemically disrupted. These biomechanical insights have not been previously reported. This detailed characterisation of

  13. 3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations

    NASA Astrophysics Data System (ADS)

    Page, Alister J.; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A.; Warr, Gregory G.; Voïtchovsky, Kislon; Atkin, Rob

    2014-06-01

    In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level

  14. Raman spectrum reveals the cell cycle arrest of Triptolide-induced leukemic T-lymphocytes apoptosis

    NASA Astrophysics Data System (ADS)

    Zhang, Daosen; Feng, Yanyan; Zhang, Qinnan; Su, Xin; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

    2015-04-01

    Triptolide (TPL), a traditional Chinese medicine extract, possesses anti-inflammatory and anti-tumor properties. Though some research results have implicated that Triptolide (TPL) can be utilized in the treatment of leukemia, it remains controversial about the mechanism of TPL-induced leukemic T-lymphocytes apoptosis. In this study, combining Raman spectroscopic data, principal component analysis (PCA) and atomic force microscopy (AFM) imaging, both the biochemical changes and morphological changes during TPL-induced cell apoptosis were presented. In contrast, the corresponding data during Daunorubicin (DNR)-induced cell apoptosis was also exhibited. The obtained results showed that Raman spectral changes during TPL-induced cell apoptosis were greatly different from DNR-induced cell apoptosis in the early stage of apoptosis but revealed the high similarity in the late stage of apoptosis. Moreover, above Raman spectral changes were respectively consistent with the morphological changes of different stages during TPL-induced apoptosis or DNR-induced apoptosis, including membrane shrinkage and blebbing, chromatin condensation and the formation of apoptotic bodies. Importantly, it was found that Raman spectral changes with TPL-induced apoptosis or DNR-induced apoptosis were respectively related with the cell cycle G1 phase arrest or G1 and S phase arrest.

  15. Nanomechanical characterization of nanostructured bainitic steel: Peak Force Microscopy and Nanoindentation with AFM

    PubMed Central

    Morales-Rivas, Lucia; González-Orive, Alejandro; Garcia-Mateo, Carlos; Hernández-Creus, Alberto; Caballero, Francisca G.; Vázquez, Luis

    2015-01-01

    The full understanding of the deformation mechanisms in nanostructured bainite requires the local characterization of its mechanical properties, which are expected to change from one phase, bainitic ferrite, to another, austenite. This study becomes a challenging process due to the bainitic nanostructured nature and high Young’s modulus. In this work, we have carried out such study by means of the combination of AFM-based techniques, such as nanoindentation and Peak Force Quantitative Nanomechanical Mapping (PF-QNM) measurements. We have addressed critically the limits and advantages of these techniques and been able to measure some elastoplastic parameters of both phases. Specifically, we have analyzed by PF-QNM two nanostructured bainitic steels, with a finer and a coarser structure, and found that both phases have a similar Young’s modulus. PMID:26602631

  16. AFM study of the morphologic change of HDPE surface photografted with glycidyl methacrylate.

    PubMed

    Wang, Huiliang; Han, Jianmei

    2009-05-01

    The UV-induced grafting of glycidyl methacrylate (GMA) onto high-density polyethylene (HDPE) and the atomic force microscopy (AFM) study of the morphologic change of the grafted surface are reported. The grafting was carried out in GMA acetone solutions with different monomer concentrations. Grafting was much faster in a solution with a higher monomer concentration. FTIR analyses proved that GMA had been successfully grafted onto HDPE. The morphologies of grafted HDPE surfaces changed with UV irradiation time. The monomer concentration had a significant effect on the morphologies of the grafted HDPE surfaces. The HDPE surface grafted in a solution with a higher monomer concentration was much rougher than that grafted in a solution with a lower monomer concentration. The growth models of the grafted granules or clusters are also proposed.

  17. Simultaneous AFM topography and recognition imaging at the plasma membrane of mammalian cells.

    PubMed

    Chtcheglova, Lilia A; Hinterdorfer, Peter

    2018-01-01

    Elucidation the nano-organization of membrane proteins at/within the plasma membrane is probably the most demanding and still challenging task in cell biology since requires experimental approaches with nanoscale resolution. During last decade, atomic force microscopy (AFM)-based simultaneous topography and recognition imaging (TREC) has become a powerful tool to quickly obtain local receptor nano-maps on complex heterogeneous biosurfaces such as cells and membranes. Here we emphasize the TREC technique and explain how to unravel the nano-landscape of mammalian cells. We describe the procedures for all steps of the experiment including tip functionalization with ligand molecules, sample preparation, and localization of key molecules on the cell surface. We also discuss the current limitations and future perspectives of this technique. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Integrative Analysis Reveals Regulatory Programs in Endometriosis

    PubMed Central

    Yang, Huan; Kang, Kai; Cheng, Chao; Mamillapalli, Ramanaiah; Taylor, Hugh S.

    2015-01-01

    Endometriosis is a common gynecological disease found in approximately 10% of reproductive-age women. Gene expression analysis has been performed to explore alterations in gene expression associated with endometriosis; however, the underlying transcription factors (TFs) governing such expression changes have not been investigated in a systematic way. In this study, we propose a method to integrate gene expression with TF binding data and protein–protein interactions to construct an integrated regulatory network (IRN) for endometriosis. The IRN has shown that the most regulated gene in endometriosis is RUNX1, which is targeted by 14 of 26 TFs also involved in endometriosis. Using 2 published cohorts, GSE7305 (Hover, n = 20) and GSE7307 (Roth, n = 36) from the Gene Expression Omnibus database, we identified a network of TFs, which bind to target genes that are differentially expressed in endometriosis. Enrichment analysis based on the hypergeometric distribution allowed us to predict the TFs involved in endometriosis (n = 40). This included known TFs such as androgen receptor (AR) and critical factors in the pathology of endometriosis, estrogen receptor α, and estrogen receptor β. We also identified several new ones from which we selected FOXA2 and TFAP2C, and their regulation was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry (IHC). Further, our analysis revealed that the function of AR and p53 in endometriosis is regulated by posttranscriptional changes and not by differential gene expression. Our integrative analysis provides new insights into the regulatory programs involved in endometriosis. PMID:26134036

  19. 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.

  20. 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.

  1. Simultaneous topographic and amperometric membrane mapping using an AFM probe integrated biosensor.

    PubMed

    Stanca, Sarmiza Elena; Csaki, Andrea; Urban, Matthias; Nietzsche, Sandor; Biskup, Christoph; Fritzsche, Wolfgang

    2011-02-15

    The investigation of the plasma membrane with intercorrelated multiparameter techniques is a prerequisite for understanding its function. Presented here, is a simultaneous electrochemical and topographic study of the cell membrane using a miniaturized amperometric enzymatic biosensor. The fabrication of this biosensor is also reported. The biosensor combines a scanning force microscopy (AFM) gold-coated cantilever and an enzymatic transducer layer of peroxidases (PODs). When these enzymes are brought in contact with the substrate, the specific redox reaction produces an electric current. The intensity of this current is detected simultaneously with the surface imaging. For sensor characterization, hydroquinone-2-carboxylic acid (HQ) is selected as an intrinsic source of H(2)O(2). HQ has been electrochemically regenerated by the reduction of antraquinone-2-carboxylic acid (AQ). The biosensor reaches the steady state value of the current intensity in 1 ± 0.2s. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

    PubMed

    Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

    2015-01-01

    Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

  3. Mapping mechanical force propagation through biomolecular complexes

    DOE PAGES

    Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; ...

    2015-08-11

    In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

  4. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    PubMed

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  5. Rapid and automated analysis of aflatoxin M1 in milk and dairy products by online solid phase extraction coupled to ultra-high-pressure-liquid-chromatography tandem mass spectrometry.

    PubMed

    Campone, Luca; Piccinelli, Anna Lisa; Celano, Rita; Pagano, Imma; Russo, Mariateresa; Rastrelli, Luca

    2016-01-08

    This study reports a fast and automated analytical procedure for the analysis of aflatoxin M1 (AFM1) in milk and dairy products. The method is based on the simultaneous protein precipitation and AFM1 extraction, by salt-induced liquid-liquid extraction (SI-LLE), followed by an online solid-phase extraction (online SPE) coupled to ultra-high-pressure-liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis to the automatic pre-concentration, clean up and sensitive and selective determination of AFM1. The main parameters affecting the extraction efficiency and accuracy of the analytical method were studied in detail. In the optimal conditions, acetonitrile and NaCl were used as extraction/denaturant solvent and salting-out agent in SI-LLE, respectively. After centrifugation, the organic phase (acetonitrile) was diluted with water (1:9 v/v) and purified (1mL) by online C18 cartridge coupled with an UHPLC column. Finally, selected reaction monitoring (SRM) acquisition mode was applied to the detection of AFM1. Validation studies were carried out on different dairy products (whole and skimmed cow milk, yogurt, goat milk, and powder infant formula), providing method quantification limits about 25 times lower than AFM1 maximum levels permitted by EU regulation 1881/2006 in milk and dairy products for direct human consumption. Recoveries (86-102%) and repeatability (RSD<3, n=6) meet the performance criteria required by EU regulation N. 401/2006 for the determination of the levels of mycotoxins in foodstuffs. Moreover, no matrix effects were observed in the different milk and dairy products studied. The proposed method improves the performance of AFM1 analysis in milk samples as AFM1 determination is performed with a degree of accuracy higher than the conventional methods. Other advantages are the reduction of sample preparation procedure, time and cost of the analysis, enabling high sample throughput that meet the current concerns of food safety and the public

  6. AFM Colloidal Probe Measurements Implicate Capillary Condensation in Punch-Particle Surface Interactions during Tableting.

    PubMed

    Badal Tejedor, Maria; Nordgren, Niklas; Schuleit, Michael; Millqvist-Fureby, Anna; Rutland, Mark W

    2017-11-21

    Adhesion of the powders to the punches is a common issue during tableting. This phenomenon is known as sticking and affects the quality of the manufactured tablets. Defective tablets increase the cost of the manufacturing process. Thus, the ability to predict the tableting performance of the formulation blend before the process is scaled-up is important. The adhesive propensity of the powder to the tableting tools is mostly governed by the surface-surface adhesive interactions. Atomic force microscopy (AFM) colloidal probe is a surface characterization technique that allows the measurement of the adhesive interactions between two materials of interest. In this study, AFM steel colloidal probe measurements were performed on ibuprofen, MCC (microcrystalline cellulose), α-lactose monohydrate, and spray-dried lactose particles as an approach to modeling the punch-particle surface interactions during tableting. The excipients (lactose and MCC) showed constant, small, attractive, and adhesive forces toward the steel surface after a repeated number of contacts. In comparison, ibuprofen displayed a much larger attractive and adhesive interaction increasing over time both in magnitude and in jump-in/jump-out separation distance. The type of interaction acting on the excipient-steel interface can be related to a van der Waals force, which is relatively weak and short-ranged. By contrast, the ibuprofen-steel interaction is described by a capillary force profile. Even though ibuprofen is not highly hydrophilic, the relatively smooth surfaces of the crystals allow "contact flooding" upon contact with the steel probe. Capillary forces increase because of the "harvesting" of moisture-due to the fast condensation kinetics-leaving a residual condensate that contributes to increase the interaction force after each consecutive contact. Local asperity contacts on the more hydrophilic surface of the excipients prevent the flooding of the contact zone, and there is no such adhesive

  7. Nanoscale deformation and fracture mechanics of polycrystalline silicon and diamond-like carbon for MEMS by the AFM/DIC method

    NASA Astrophysics Data System (ADS)

    Cho, Sung Woo

    A method for nanoscale experimental mechanics was developed to address problems in deformation and fracture of micron-scale components in Microelectromechanical Systems (MEMS). Specifically, the effective and local, elastic and fracture behavior of polycrystalline silicon (polysilicon) and tetrahedral amorphous diamond-like carbon (ta-C) were studied using freestanding thin films subject to uniaxial tension. In this method, direct measurements of local deformations were derived from Atomic Force Microscopy (AFM) images in specimen areas varying between 1x2 mum2 and 15x15 mum2 using Digital Image Correlation (DIC) to extract displacements and strains with spatial resolution of 1-2 nm. The effective elastic modulus and Poisson's ratio of polysilicon and ta-C from the Sandia National Laboratories (SUMMiT) were 155 +/- 6 GPa and 0.22 +/- 0.02, and 759 +/- 22 GPa and 0.17 +/- 0.03, respectively. Similarly, the elastic modulus and Poisson's ratio of polysilicon fabricated at MCNC via the Multi-User MEMS Processes (MUMPs) with <110> texture were 164 +/- 7 GPa and 0.22 +/- 0.02, respectively. A second problem studied using the AFM/DIC method was the fracture of polysilicon in the presence of atomically sharp cracks. The effective (macroscopic) Mode-I critical stress intensity factor for polysilicon from different MUMPs runs was 1.00 +/- 0.1 MPa√m, where 0.1 MPa√m was the standard deviation, attributed to local cleavage anisotropy and grain boundary toughening. The variation in the effective critical stress intensity factor and the subcritical crack growth of polysilicon that was spatially recorded and quantified for the first time were the result of the spatial variation of the 4 local stress intensity factor at the crack tip that controlled crack initiation and thus, the overall fracture process. The AFM/DIC method was also applied to determine the minimum size of a polysilicon domain whose effective mechanical behavior could be described by the isotropic elastic

  8. 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).

  9. Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

    PubMed

    Sturgis, James N; Niederman, Robert A

    2008-01-01

    Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

  10. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    PubMed

    Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

    2014-01-01

    Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  11. Characterization of Cr/6H-SiC(0 0 0 1) nano-contacts by current-sensing AFM

    NASA Astrophysics Data System (ADS)

    Grodzicki, Miłosz; Smolarek, Szymon; Mazur, Piotr; Zuber, Stefan; Ciszewski, Antoni

    2009-11-01

    The electrical properties and interface chemistry of Cr/6H-SiC(0 0 0 1) contacts have been studied by current-sensing atomic force microscopy (CS-AFM) and X-ray photoelectron spectroscopy (XPS). Cr layers were vapor deposited under ultrahigh vacuum onto both ex situ etched in H 2 and in situ Ar + ion-bombarded samples. The Cr/SiC contacts are electrically non-uniform. Both the measured I- V characteristics and the modeling calculations enabled to estimate changes of the Schottky barrier height caused by Ar + bombardment. Formation of ohmic nano-contacts on Ar +-bombarded surfaces was observed.

  12. Formation of surface relief grating in polymers with pendant azobenzene chromophores as studied by AFM/UFM

    NASA Astrophysics Data System (ADS)

    Kulikovska, Olga; Gharagozloo-Hubmann, Kati; Stumpe, Joachim; Huey, Bryan D.; Bliznyuk, Valery N.

    2012-12-01

    We studied peculiarities of the structural reconstruction within holographically recorded gratings on the surface of several different amorphous azobenzene-containing polymers. Under illumination with a light interference pattern, two processes take place in this type of polymer. The first process is the light-induced orientation of azobenzene units perpendicular to the polarization plane of the incident light. The second one is a transfer of macromolecules along the grating vector (i.e. perpendicular to the grating lines). These two processes result in the creation of a volume orientation grating (alternating regions of different direction or degree of molecular orientation) and a surface relief grating (SRG)—i.e. modulation of film thickness. One can assume that both orientation of molecules and their movement might change the local mechanical properties of the material. Therefore, formation of the SRG is expected to result also in modulation of the local stiffness of the polymer film. To reveal and investigate these stiffness changes within the grating, spin-coated polymer films were prepared and the gratings were recorded on them in two different ways: with an orthogonal circular or orthogonal linear polarization of two recording light beams. A combination of atomic force microscopy (AFM) and ultrasonic force microscopy (UFM) techniques was applied for SRG development monitoring. We demonstrate that formation of the phase gratings depends on the chemical structure of polymers being used, polymer film thickness, and recording parameters, with the height of grating structures (depth of modulation) increasing with both the exposure time and the film thickness. UFM images suggest that the slopes of the topographic peaks in the phase gratings exhibit an increased stiffness with respect to the grating depressions.

  13. Scanning electron and atomic force microscopy, and raman and x-ray photoelectron spectroscopy characterization of near-isogenic soft and hard wheat kernels and corresponding flours

    USDA-ARS?s Scientific Manuscript database

    Atomic force microscopy (AFM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) are used to investigate vitreous (hard) and non-vitreous (soft) wheat kernels and their corresponding wheat flours. AFM data reveal two different microstructures. The vitreous kernel reveals a granular text...

  14. Fourier Transform Infrared (FTIR) Spectroscopy, Ultraviolet Resonance Raman (UVRR) Spectroscopy, and Atomic Force Microscopy (AFM) for Study of the Kinetics of Formation and Structural Characterization of Tau Fibrils.

    PubMed

    Ramachandran, Gayathri

    2017-01-01

    Kinetic studies of tau fibril formation in vitro most commonly employ spectroscopic probes such as thioflavinT fluorescence and laser light scattering or negative stain transmission electron microscopy. Here, I describe the use of Fourier transform infrared (FTIR) spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and atomic force microscopy (AFM) as complementary probes for studies of tau aggregation. The sensitivity of vibrational spectroscopic techniques (FTIR and UVRR) to secondary structure content allows for measurement of conformational changes that occur when the intrinsically disordered protein tau transforms into cross-β-core containing fibrils. AFM imaging serves as a gentle probe of structures populated over the time course of tau fibrillization. Together, these assays help further elucidate the structural and mechanistic complexity inherent in tau fibril formation.

  15. Tuning the Pairing Interaction in a d -Wave Superconductor by Paramagnons Injected through Interfaces

    DOE PAGES

    Naritsuka, M.; Rosa, P. F. S.; Luo, Yongkang; ...

    2018-05-04

    Unconventional superconductivity and magnetism are intertwined on a microscopic level in a wide class of materials. A new approach to this most fundamental and hotly debated issue focuses on the role of interactions between superconducting electrons and bosonic fluctuations at the interface between adjacent layers in heterostructures. In this paper, we fabricate hybrid superlattices consisting of alternating atomic layers of the heavy-fermion superconductormore » $${\\mathrm{CeCoIn}}_{5}$$ and antiferromagnetic (AFM) metal $${\\mathrm{CeRhIn}}_{5}$$, in which the AFM order can be suppressed by applying pressure. We find that the superconducting and AFM states coexist in spatially separated layers, but their mutual coupling via the interface significantly modifies the superconducting properties. An analysis of upper critical fields reveals that, upon suppressing the AFM order by applied pressure, the force binding superconducting electron pairs acquires an extreme strong-coupling nature. Finally, this demonstrates that superconducting pairing can be tuned nontrivially by magnetic fluctuations (paramagnons) injected through the interface.« less

  16. Tuning the Pairing Interaction in a d -Wave Superconductor by Paramagnons Injected through Interfaces

    NASA Astrophysics Data System (ADS)

    Naritsuka, M.; Rosa, P. F. S.; Luo, Yongkang; Kasahara, Y.; Tokiwa, Y.; Ishii, T.; Miyake, S.; Terashima, T.; Shibauchi, T.; Ronning, F.; Thompson, J. D.; Matsuda, Y.

    2018-05-01

    Unconventional superconductivity and magnetism are intertwined on a microscopic level in a wide class of materials. A new approach to this most fundamental and hotly debated issue focuses on the role of interactions between superconducting electrons and bosonic fluctuations at the interface between adjacent layers in heterostructures. Here we fabricate hybrid superlattices consisting of alternating atomic layers of the heavy-fermion superconductor CeCoIn5 and antiferromagnetic (AFM) metal CeRhIn5 , in which the AFM order can be suppressed by applying pressure. We find that the superconducting and AFM states coexist in spatially separated layers, but their mutual coupling via the interface significantly modifies the superconducting properties. An analysis of upper critical fields reveals that, upon suppressing the AFM order by applied pressure, the force binding superconducting electron pairs acquires an extreme strong-coupling nature. This demonstrates that superconducting pairing can be tuned nontrivially by magnetic fluctuations (paramagnons) injected through the interface.

  17. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Naritsuka, M.; Rosa, P. F. S.; Luo, Yongkang

    Unconventional superconductivity and magnetism are intertwined on a microscopic level in a wide class of materials. A new approach to this most fundamental and hotly debated issue focuses on the role of interactions between superconducting electrons and bosonic fluctuations at the interface between adjacent layers in heterostructures. In this paper, we fabricate hybrid superlattices consisting of alternating atomic layers of the heavy-fermion superconductormore » $${\\mathrm{CeCoIn}}_{5}$$ and antiferromagnetic (AFM) metal $${\\mathrm{CeRhIn}}_{5}$$, in which the AFM order can be suppressed by applying pressure. We find that the superconducting and AFM states coexist in spatially separated layers, but their mutual coupling via the interface significantly modifies the superconducting properties. An analysis of upper critical fields reveals that, upon suppressing the AFM order by applied pressure, the force binding superconducting electron pairs acquires an extreme strong-coupling nature. Finally, this demonstrates that superconducting pairing can be tuned nontrivially by magnetic fluctuations (paramagnons) injected through the interface.« less

  18. Local coexistence of VO 2 phases revealed by deep data analysis

    DOE PAGES

    Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; ...

    2016-07-07

    We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO 2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffermore » from information misinterpretation due to low resolving power.« less

  19. BOREAS AFM-2 King Air 1994 Aircraft Flux and Moving Window Data

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

    The BOREAS AFM-2 team collected pass-by-pass fluxes (and many other statistics) for a large number of level (constant altitude), straight-line passes used in a variety of flight patterns. The data were collected by the University of Wyoming King Air in 1994 BOREAS IFCs 1-3. Most of these data were collected at 60-70 m above ground level, but a significant number of passes were also flown at various levels in the planetary boundary layer, up to about the inversion height. This documentation concerns only the data from the straight and level passes that are presented as original (over the NSA and SSA) and moving window values (over the Transect). Another archive of King Air data is also available, containing data from all the soundings flown by the King Air 1994 IFCs 1-3. The 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).

  20. Analysis of Nanodomain Composition in High-Impact Polypropylene by Atomic Force Microscopy-Infrared.

    PubMed

    Tang, Fuguang; Bao, Peite; Su, Zhaohui

    2016-05-03

    In this paper, compositions of nanodomains in a commercial high-impact polypropylene (HIPP) were investigated by an atomic force microscopy-infrared (AFM-IR) technique. An AFM-IR quantitative analysis method was established for the first time, which was then employed to analyze the polyethylene content in the nanoscopic domains of the rubber particles dispersed in the polypropylene matrix. It was found that the polyethylene content in the matrix was close to zero and was high in the rubbery intermediate layers, both as expected. However, the major component of the rigid cores of the rubber particles was found to be polypropylene rather than polyethylene, contrary to what was previously believed. The finding provides new insight into the complicated structure of HIPPs, and the AFM-IR quantitative method reported here offers a useful tool for assessing compositions of nanoscopic domains in complex polymeric systems.

  1. Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

    PubMed

    Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

    2014-02-01

    While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  2. Optimal sensitivity for molecular recognition MAC-mode AFM

    PubMed

    Schindler; Badt; Hinterdorfer; Kienberger; Raab; Wielert-Badt; Pastushenko

    2000-02-01

    Molecular recognition force microscopy (MRFM) using the magnetic AC mode (MAC mode) atomic force microscope (AFM) was recently investigated to locate and probe recognition sites. A flexible crosslinker carrying a ligand is bound to the tip for the molecular recognition of receptors on the surface of a sample. In this report, the driving frequency is calculated which optimizes the sensitivity (S). The sensitivity of MRFM is defined as the relative change of the magnetically excited cantilever deflection amplitude arising from a crosslinker/antibody/antigen connection that is characterized by a very small force constant. The sensitivity is calculated in a damped oscillator model with a certain value of quality factor Q, which, together with load, defines the frequency response (unloaded oscillator shows resonance at Q > 0.707). If Q < 1, the greatest value of S corresponds to zero driving frequency omega (measured in units of eigenfrequency). Therefore, for Q < 1, MAC-mode has no advantage in comparison with DC-mode. Two additional extremes are found at omegaL = (1 - 1/Q)(1/2) and omegaR = (1 + 1/Q)(1/2), with corresponding sensitivities S(L) = Q2/(2Q - 1), S(R) = Q2/(2Q + 1). The L-extreme exists only for Q > 1, and then S(L) > S(R), i.e. the L-extreme is the main one. For Q > 1, S(L) > 1, and for Q > 2.41, S(R) > 1. These are the critical Q-values, above which selecting driving frequency equal to sigmaL or sigmaR brings advantage to MAC mode vs. DC mode. Satisfactory quality of the oscillator model is demonstrated by comparison of some results with those calculated within the classical description of cantilevers.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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 × 109 cm-2) sensitivity to impacts at grazing angle incidence; and better definition of the lateral interaction volume in target materials.

  5. Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

    PubMed

    Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

    2015-04-17

    Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

  6. Mechanical properties of complex biological systems using AFM-based force spectroscopy

    NASA Astrophysics Data System (ADS)

    Graham, John Stephen

    An atomic force microscope (AFM) was designed and built to study the mechanical properties of small collagen fibrils and the plasma membrane of living cells. Collagen is a major component of bone, skin and connective tissues, and is abundant in the extracellular matrix (ECM). Because of its abundance, an understanding of how disease affects collagen mechanics is crucial in disease prevention efforts. Two levels of type I collagen structure were investigated, subfibrils (on the order of 1 mum in length) and longer fibrils. Comparisons were made between measurements of wild-type (wt) collagen and collagen from the mouse model of osteogenesis imperfecta (OI). Significant differences between OI and wt collagen were observed, primarily that intermolecular bonds in OI collagen fibrils are weaker than in wt, or not ruptured, as in the case of OI subfibrils. As cells interact with collagen in the ECM, the mechanical properties of the plasma membrane are also of great interest. Membrane tethers were extracted from living cells under varied conditions in order to assess the contributions of membrane-associated macromolecules such as the actin cytoskeleton and the glycocalyx, and intracellular signaling. Tether extraction force was found to be sensitive to all of these altered conditions, suggesting that tether extraction may be used to monitor various cellular processes.

  7. Molecular-level insights of early-stage prion protein aggregation on mica and gold surface determined by AFM imaging and molecular simulation.

    PubMed

    Lou, Zhichao; Wang, Bin; Guo, Cunlan; Wang, Kun; Zhang, Haiqian; Xu, Bingqian

    2015-11-01

    By in situ time-lapse AFM, we investigated early-stage aggregates of PrP formed at low concentration (100 ng/mL) on mica and Au(111) surfaces in acetate buffer (pH 4.5). Remarkably different PrP assemblies were observed. Oligomeric structures of PrP aggregates were observed on mica surface, which was in sharp contrast to the multi-layer PrP aggregates yielding parallel linear patterns observed Au(111) surface. Combining molecular dynamics and docking simulations, PrP monomers, dimers and trimers were revealed as the basic units of the observed aggregates. Besides, the mechanisms of the observed PrP aggregations and the corresponding molecular-substrate and intermolecular interactions were suggested. These interactions involved gold-sulfur interaction, electrostatic interaction, hydrophobic interaction, and hydrogen binding interaction. In contrast, the PrP aggregates observed in pH 7.2 PBS buffer demonstrated similar large ball-like structures on both mica and Au(111) surfaces. The results indicate that the pH of a solution and the surface of the system can have strong effects on supramolecular assemblies of prion proteins. This study provides in-depth understanding on the structural and mechanistic nature of PrP aggregation, and can be used to study the aggregation mechanisms of other proteins with similar misfolding properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Crystallographic order and decomposition of [MnIII 6CrIII]3+ single-molecule magnets deposited in submonolayers and monolayers on HOPG studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin probe force microscopy in UHV

    NASA Astrophysics Data System (ADS)

    Gryzia, Aaron; Volkmann, Timm; Brechling, Armin; Hoeke, Veronika; Schneider, Lilli; Kuepper, Karsten; Glaser, Thorsten; Heinzmann, Ulrich

    2014-02-01

    Monolayers and submonolayers of [Mn III 6 Cr III ] 3+ single-molecule magnets (SMMs) adsorbed on highly oriented pyrolytic graphite (HOPG) using the droplet technique characterized by non-contact atomic force microscopy (nc-AFM) as well as by Kelvin probe force microscopy (KPFM) show island-like structures with heights resembling the height of the molecule. Furthermore, islands were found which revealed ordered 1D as well as 2D structures with periods close to the width of the SMMs. Along this, islands which show half the heights of intact SMMs were observed which are evidences for a decomposing process of the molecules during the preparation. Finally, models for the structure of the ordered SMM adsorbates are proposed to explain the observations.

  9. Analysis of hysteresis effect on the vibration motion of a bimodal non-uniform micro-cantilever using MCS theory

    NASA Astrophysics Data System (ADS)

    Korayem, M. H.; Korayem, A. H.; Hosseini Hashemi, Sh.

    2016-02-01

    Nowadays, to enhance the performance of atomic force microscopy (AFM) micro-cantilevers (MCs) during imaging, reduce costs and increase the surface topography precision, advanced MCs equipped with piezoelectric layers are utilized. Using the modified couple stress (MCS) theory not only makes the modeling more exhaustive, but also increases the accuracy of prediction of the vibration behavior of the system. In this paper, Hamilton's principle by consideration of the MCS theory has been used to extract the equations. In addition, to discretize the equations, differential quadrature method has been adopted. Analysis of the hysteresis effect on the vibration behavior of the AFM MC is of significant importance. Thus, to model the hysteresis effect, Bouc-Wen method, which is solved simultaneously with the vibration equations of non-uniform Timoshenko beam, has been utilized. Furthermore, a bimodal excitation of the MC has been considered. The results reveal that the hysteresis effect appears as a phase difference in the time response. Finally, the effect of the geometric parameters on the vibration frequency of the system which is excited by combination of the first two vibration modes of the non-uniform piezoelectric MC has been examined. The results indicate the considerable effect of the MC length in comparison with other geometric parameters such as the MC width and thickness.

  10. STM, SECPM, AFM and Electrochemistry on Single Crystalline Surfaces

    PubMed Central

    Wolfschmidt, Holger; Baier, Claudia; Gsell, Stefan; Fischer, Martin; Schreck, Matthias; Stimming, Ulrich

    2010-01-01

    Scanning probe microscopy (SPM) techniques have had a great impact on research fields of surface science and nanotechnology during the last decades. They are used to investigate surfaces with scanning ranges between several 100 μm down to atomic resolution. Depending on experimental conditions, and the interaction forces between probe and sample, different SPM techniques allow mapping of different surface properties. In this work, scanning tunneling microscopy (STM) in air and under electrochemical conditions (EC-STM), atomic force microscopy (AFM) in air and scanning electrochemical potential microscopy (SECPM) under electrochemical conditions, were used to study different single crystalline surfaces in electrochemistry. Especially SECPM offers potentially new insights into the solid-liquid interface by providing the possibility to image the potential distribution of the surface, with a resolution that is comparable to STM. In electrocatalysis, nanostructured catalysts supported on different electrode materials often show behavior different from their bulk electrodes. This was experimentally and theoretically shown for several combinations and recently on Pt on Au(111) towards fuel cell relevant reactions. For these investigations single crystals often provide accurate and well defined reference and support systems. We will show heteroepitaxially grown Ru, Ir and Rh single crystalline surface films and bulk Au single crystals with different orientations under electrochemical conditions. Image studies from all three different SPM methods will be presented and compared to electrochemical data obtained by cyclic voltammetry in acidic media. The quality of the single crystalline supports will be verified by the SPM images and the cyclic voltammograms. Furthermore, an outlook will be presented on how such supports can be used in electrocatalytic studies. PMID:28883327

  11. Advances in research on structural characterisation of agricultural products using atomic force microscopy.

    PubMed

    Liu, Dongli; Cheng, Fang

    2011-03-30

    Atomic force microscopy (AFM) has many unique features compared with other conventional microscopies, such as high magnification with high resolution, minimal sample preparation, acquiring 2D and 3D images at the same time, observing ongoing processes directly, the possibility of manipulating macromolecules, etc. As a nanotechnology tool, AFM has been used to investigate the nanostructure of materials in many fields. This mini-review focuses mainly on its latest application to characterise the macromolecular nanostructure and surface topography of agricultural products. First the fundamentals of AFM are briefly explained. Then the macromolecular nanostructure information on agricultural products from AFM images is introduced by exploring the structure-function relationship in three aspects: agricultural product processing, agricultural product ripening and storage, and genetic and environmental factors. The surface topography characterisation of agricultural products using AFM is also discussed. The results reveal that AFM could be a powerful nanotechnology tool to acquire a deeper understanding of the mechanisms of structure and quality variations of agricultural products, which could be instructive in improving processing and storage technologies, and AFM is also helpful to reveal the essential nature of a product at nanoscale. Copyright © 2011 Society of Chemical Industry.

  12. AFM-based micro/nanoscale lithography of poly(dimethylsiloxane): stick-slip on a softpolymer

    NASA Astrophysics Data System (ADS)

    Watson, Jolanta A.; Myhra, Sverre; Brown, Christopher L.; Watson, Gregory S.

    2005-02-01

    Silicone rubbers have steadily gained importance in industry since their introduction in the 1960"s. Poly(dimethylsiloxane) (PDMS) is a relatively soft and optically clear, two-part elastomer with interesting and, more importantly, useful physical and electrical properties. Some of its common applications include protective coatings (e.g., against moisture, environmental attack, mechanical and thermal shock and vibrations), and encapsulation (e.g., amplifiers, inductive coils, connectors and circuit boards). The polymer has attracted recent interest for applications in soft lithography. The polymer is now routinely used as a patterned micro-stamp for chemical modification of surfaces, in particular Au substrates. Prominent stick-slip effects, surface relaxation and elastic recovery were found to be associated with micro/nano manipulation of the polymer by an AFM-based contact mode methodology. Those effects provide the means to explore in detail the meso-scale tip-to-surface interactions between a tip and a soft surface. The dependence of scan speed, loading force, attack angle and number of scan lines have been investigated.

  13. AFM Study of Surface Nanobubbles on Binary Self-Assembled Monolayers on Ultraflat Gold with Identical Macroscopic Static Water Contact Angles and Different Terminal Functional Groups.

    PubMed

    Song, Bo; Chen, Kun; Schmittel, Michael; Schönherr, Holger

    2016-11-01

    All experimental findings related to surface nanobubbles, such as their pronounced stability and the striking differences of macroscopic and apparent nanoscopic contact angles, need to be addressed in any theory or model of surface nanobubbles. In this work we critically test a recent explanation of surface nanobubble stability and their consequences and contrast this with previously proposed models. In particular, we elucidated the effect of surface chemical composition of well-controlled solid-aqueous interfaces of identical roughness and defect density on the apparent nanoscopic contact angles. Expanding on a previous atomic force microscopy (AFM) study on the systematic variation of the macroscopic wettability using binary self-assembled monolayers (SAMs) on ultraflat template stripped gold (TSG), we assessed here the effect of different surface chemical composition for macroscopically identical static water contact angles. SAMs on TSG with a constant macroscopic water contact angle of 81 ± 2° were obtained by coadsorption of a methyl-terminated thiol and a second thiol with different terminal functional groups, including hydroxy, amino, and carboxylic acid groups. In addition, surface nanobubbles formed by entrainment of air on SAMs of a bromoisobutyrate-terminated thiol were analyzed by AFM. Despite the widely differing surface potentials and different functionality, such as hydrogen bond acceptor or donor, and different dipole moments and polarizability, the nanoscopic contact angles (measured through the condensed phase and corrected for AFM tip broadening effects) were found to be 145 ± 10° for all surfaces. Hence, different chemical functionalities at identical macroscopic static water contact angle do not noticeably influence the apparent nanoscopic contact angle of surface nanobubbles. This universal contact angle is in agreement with recent models that rely on contact line pinning and the equilibrium of gas outflux due to the Laplace pressure and

  14. AFM Imaging of Hybridization Chain Reaction Mediated Signal Transmission between Two DNA Origami Structures.

    PubMed

    Helmig, Sarah; Gothelf, Kurt Vesterager

    2017-10-23

    Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-range signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for the signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins, one of which is immobilized at specific points along tracks on DNA origami structures, are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred more than 200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another and, therefore, has the potential to be applied to larger multi-component DNA assemblies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  16. Nanostructure and force spectroscopy analysis of human peripheral blood CD4+ T cells using atomic force microscopy.

    PubMed

    Hu, Mingqian; Wang, Jiongkun; Cai, Jiye; Wu, Yangzhe; Wang, Xiaoping

    2008-09-12

    To date, nanoscale imaging of the morphological changes and adhesion force of CD4(+) T cells during in vitro activation remains largely unreported. In this study, we used atomic force microscopy (AFM) to study the morphological changes and specific binding forces in resting and activated human peripheral blood CD4(+) T cells. The AFM images revealed that the volume of activated CD4(+) T cells increased and the ultrastructure of these cells also became complex. Using a functionalized AFM tip, the strength of the specific binding force of the CD4 antigen-antibody interaction was found to be approximately three times that of the unspecific force. The adhesion forces were not randomly distributed over the surface of a single activated CD4(+) T cell, indicated that the CD4 molecules concentrated into nanodomains. The magnitude of the adhesion force of the CD4 antigen-antibody interaction did not change markedly with the activation time. Multiple bonds involved in the CD4 antigen-antibody interaction were measured at different activation times. These results suggest that the adhesion force involved in the CD4 antigen-antibody interaction is highly selective and of high affinity.

  17. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    PubMed

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Optical and AFM study of electrostatically assembled films of CdS and ZnS colloid nanoparticles

    NASA Astrophysics Data System (ADS)

    Suryajaya; Nabok, A.; Davis, F.; Hassan, A.; Higson, S. P. J.; Evans-Freeman, J.

    2008-05-01

    CdS and ZnS semiconducting colloid nanoparticles coated with the organic shell, containing either SO 3- or NH 2+ groups, were prepared using the aqueous phase synthesis. The multilayer films of CdS (or ZnS) were deposited onto glass, quartz and silicon substrates using the technique of electrostatic self-assembly. The films produced were characterized with UV-vis spectroscopy, spectroscopic ellipsometry and atomic force microscopy. A substantial blue shift of the main absorption band with respect to the bulk materials was found for both CdS and ZnS films. The Efros equation in the effective mass approximation (EMA) theoretical model allowed the evaluation of the nanoparticle radius of 1.8 nm, which corresponds well to the ellipsometry results. AFM shows the formation of larger aggregates of nanoparticles on solid surfaces.

  19. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

    PubMed Central

    Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

    2016-01-01

    Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

  20. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    PubMed

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. On physical changes on surface of human cervical epithelial cells during cancer transformations

    NASA Astrophysics Data System (ADS)

    Sokolov, Igor; Dokukin, Maxim; Guz, Nataliia; Woodworth, Craig

    2013-03-01

    Physical changes of the cell surface of cells during transformation from normal to cancerous state are rather poorly studied. Here we describe our recent studies of such changes done on human cervical epithelial cells during their transformation from normal through infected with human papillomavirus type-16 (HPV-16), immortalized (precancerous), to cancerous cells. The changes were studied with the help of atomic force microscopy (AFM) and through the measurement of physical adhesion of fluorescent silica beads to the cell surface. Based on the adhesion experiments, we clearly see the difference in nonspecific adhesion which occurs at the stage of immortalization of cells, precancerous cells. The analysis done with the help of AFM shows that the difference observed comes presumably from the alteration of the cellular ``brush,'' a layer that surrounds cells and which consists of mostly microvilli, microridges, and glycocalyx. Further AFM analysis reveals the emergence of fractal scaling behavior on the surface of cells when normal cells turn into cancerous. The possible causes and potential significance of these observations will be discussed.

  2. Biomechanical Properties of Murine Meniscus Surface via AFM-based Nanoindentation

    PubMed Central

    Li, Qing; Doyran, Basak; Gamer, Laura W.; Lu, X. Lucas; Qin, Ling; Ortiz, Christine; Grodzinsky, Alan J.; Rosen, Vicki; Han, Lin

    2015-01-01

    This study aimed to quantify the biomechanical properties of murine meniscus surface. Atomic force microscopy (AFM)-based nanoindentation was performed on the central region, proximal side of menisci from 6- to 24-week old male C57BL/6 mice using microspherical tips (Rtip ≈ 5 μm) in PBS. A unique, linear correlation between indentation depth, D, and response force, F, was found on menisci from all age groups. This non-Hertzian behavior is likely due to the dominance of tensile resistance by the collagen fibril bundles on meniscus surface that are mostly aligned along the circumferential direction observed on 12-week old menisci. The indentation resistance was calculated as both the effective stiffness, Sind = dF/dD, and the effective modulus, Eind, via the isotropic Hertz model. Values of Sind and Eind were found to depend on indentation rate, suggesting the existence of poro-viscoelasticity. These values do not significantly vary with anatomical sites, lateral versus medial compartments, or mouse age. In addition, Eind of meniscus surface (e.g., 6.1 ± 0.8 MPa for 12 weeks of age, mean ± SEM, n = 13) was found to be significantly higher than those of meniscus surfaces in other species, and of murine articular cartilage surface (1.4 ± 0.1 MPa, n = 6). In summary, these results provided the first direct mechanical knowledge of murine knee meniscus tissues. We expect this understanding to serve as a mechanics-based benchmark for further probing the developmental biology and osteoarthritis symptoms of meniscus in various murine models. PMID:25817332

  3. Fabrication of Nanoscale Pits with High Throughput on Polymer Thin Film Using AFM Tip-Based Dynamic Plowing Lithography

    NASA Astrophysics Data System (ADS)

    He, Yang; Geng, Yanquan; Yan, Yongda; Luo, Xichun

    2017-09-01

    We show that an atomic force microscope (AFM) tip-based dynamic plowing lithography (DPL) approach can be used to fabricate nanoscale pits with high throughput. The method relies on scratching with a relatively large speed over a sample surface in tapping mode, which is responsible for the separation distance of adjacent pits. Scratching tests are carried out on a poly(methyl methacrylate) (PMMA) thin film using a diamond-like carbon coating tip. Results show that 100 μm/s is the critical value of the scratching speed. When the scratching speed is greater than 100 μm/s, pit structures can be generated. In contrast, nanogrooves can be formed with speeds less than the critical value. Because of the difficulty of breaking the molecular chain of glass-state polymer with an applied high-frequency load and low-energy dissipation in one interaction of the tip and the sample, one pit requires 65-80 penetrations to be achieved. Subsequently, the forming process of the pit is analyzed in detail, including three phases: elastic deformation, plastic deformation, and climbing over the pile-up. In particular, 4800-5800 pits can be obtained in 1 s using this proposed method. Both experiments and theoretical analysis are presented that fully determine the potential of this proposed method to fabricate pits efficiently.

  4. Fabrication of Nanoscale Pits with High Throughput on Polymer Thin Film Using AFM Tip-Based Dynamic Plowing Lithography.

    PubMed

    He, Yang; Geng, Yanquan; Yan, Yongda; Luo, Xichun

    2017-09-22

    We show that an atomic force microscope (AFM) tip-based dynamic plowing lithography (DPL) approach can be used to fabricate nanoscale pits with high throughput. The method relies on scratching with a relatively large speed over a sample surface in tapping mode, which is responsible for the separation distance of adjacent pits. Scratching tests are carried out on a poly(methyl methacrylate) (PMMA) thin film using a diamond-like carbon coating tip. Results show that 100 μm/s is the critical value of the scratching speed. When the scratching speed is greater than 100 μm/s, pit structures can be generated. In contrast, nanogrooves can be formed with speeds less than the critical value. Because of the difficulty of breaking the molecular chain of glass-state polymer with an applied high-frequency load and low-energy dissipation in one interaction of the tip and the sample, one pit requires 65-80 penetrations to be achieved. Subsequently, the forming process of the pit is analyzed in detail, including three phases: elastic deformation, plastic deformation, and climbing over the pile-up. In particular, 4800-5800 pits can be obtained in 1 s using this proposed method. Both experiments and theoretical analysis are presented that fully determine the potential of this proposed method to fabricate pits efficiently.

  5. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

    PubMed Central

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

    2016-01-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

  6. Fractal analysis as a potential tool for surface morphology of thin films

    NASA Astrophysics Data System (ADS)

    Soumya, S.; Swapna, M. S.; Raj, Vimal; Mahadevan Pillai, V. P.; Sankararaman, S.

    2017-12-01

    Fractal geometry developed by Mandelbrot has emerged as a potential tool for analyzing complex systems in the diversified fields of science, social science, and technology. Self-similar objects having the same details in different scales are referred to as fractals and are analyzed using the mathematics of non-Euclidean geometry. The present work is an attempt to correlate fractal dimension for surface characterization by Atomic Force Microscopy (AFM). Taking the AFM images of zinc sulphide (ZnS) thin films prepared by pulsed laser deposition (PLD) technique, under different annealing temperatures, the effect of annealing temperature and surface roughness on fractal dimension is studied. The annealing temperature and surface roughness show a strong correlation with fractal dimension. From the regression equation set, the surface roughness at a given annealing temperature can be calculated from the fractal dimension. The AFM images are processed using Photoshop and fractal dimension is calculated by box-counting method. The fractal dimension decreases from 1.986 to 1.633 while the surface roughness increases from 1.110 to 3.427, for a change of annealing temperature 30 ° C to 600 ° C. The images are also analyzed by power spectrum method to find the fractal dimension. The study reveals that the box-counting method gives better results compared to the power spectrum method.

  7. Hybrid Metrology and 3D-AFM Enhancement for CD Metrology Dedicated to 28 nm Node and Below Requirements

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Foucher, J.; Faurie, P.; Dourthe, L.

    2011-11-10

    The measurement accuracy is becoming one of the major components that have to be controlled in order to guarantee sufficient production yield. Already at the R and D level, we have to come up with the accurate measurements of sub-40 nm dense trenches and contact holes coming from 193 immersion lithography or E-Beam lithography. Current production CD (Critical Dimension) metrology techniques such as CD-SEM (CD-Scanning Electron Microscope) and OCD (Optical Critical Dimension) are limited in relative accuracy for various reasons (i.e electron proximity effect, outputs parameters correlation, stack influence, electron interaction with materials...). Therefore, time for R and D ismore » increasing, process windows degrade and finally production yield can decrease because you cannot manufactured correctly if you are unable to measure correctly. A new high volume manufacturing (HVM) CD metrology solution has to be found in order to improve the relative accuracy of production environment otherwise current CD Metrology solution will very soon get out of steam.In this paper, we will present a potential Hybrid CD metrology solution that smartly tuned 3D-AFM (3D-Atomic Force Microscope) and CD-SEM data in order to add accuracy both in R and D and production. The final goal for 'chip makers' is to improve yield and save R and D and production costs through real-time feedback loop implement on CD metrology routines. Such solution can be implemented and extended to any kind of CD metrology solution. In a 2{sup nd} part we will discuss and present results regarding a new AFM3D probes breakthrough with the introduction of full carbon tips made will E-Beam Deposition process. The goal is to overcome the current limitations of conventional flared silicon tips which are definitely not suitable for sub-32 nm nodes production.« less

  8. Microscopy based studies on the interaction of bio-based silver nanoparticles with Bombyx mori Nuclear Polyhedrosis virus.

    PubMed

    Tamilselvan, Selvaraj; Ashokkumar, Thirunavukkarasu; Govindaraju, Kasivelu

    2017-04-01

    In the present investigation, silver nanoparticles (AgNPs) interactions with Bombyx mori Nuclear Polyhedrosis virus (BmNPV) were characterized using High-Resolution Scanning Electron Microscopy (HR-SEM), Energy Dispersive X-ray Analysis (EDAX), Transmission Electron Microscopy (TEM), Atomic Force Microcopy (AFM) and Confocal Microscope (CM). HR-SEM study reveals that the biosynthesized AgNPs have interacted with BmNPV and were found on the surface. TEM micrographs of normal and viral polyhedra treated with AgNPs showed that the nanoparticles were accumulated in the membrane and it was noted that some of the AgNPs successfully penetrated the membrane by reaching the capsid of BmNPV. AFM and confocal microscopy studies reveal that the disruption in the shell membrane tends to lose its stability due to exposure of AgNPs to BmNPV. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Application of atomic force microscopy as a nanotechnology tool in food science.

    PubMed

    Yang, Hongshun; Wang, Yifen; Lai, Shaojuan; An, Hongjie; Li, Yunfei; Chen, Fusheng

    2007-05-01

    Atomic force microscopy (AFM) provides a method for detecting nanoscale structural information. First, this review explains the fundamentals of AFM, including principle, manipulation, and analysis. Applications of AFM are then reported in food science and technology research, including qualitative macromolecule and polymer imaging, complicated or quantitative structure analysis, molecular interaction, molecular manipulation, surface topography, and nanofood characterization. The results suggested that AFM could bring insightful knowledge on food properties, and the AFM analysis could be used to illustrate some mechanisms of property changes during processing and storage. However, the current difficulty in applying AFM to food research is lacking appropriate methodology for different food systems. Better understanding of AFM technology and developing corresponding methodology for complicated food systems would lead to a more in-depth understanding of food properties at macromolecular levels and enlarge their applications. The AFM results could greatly improve the food processing and storage technologies.

  10. Genomewide DNA methylation analysis in combat veterans reveals a novel locus for PTSD.

    PubMed

    Mehta, D; Bruenig, D; Carrillo-Roa, T; Lawford, B; Harvey, W; Morris, C P; Smith, A K; Binder, E B; Young, R McD; Voisey, J

    2017-11-01

    Epigenetic modifications such as DNA methylation may play a key role in the aetiology and serve as biomarkers for post-traumatic stress disorder (PTSD). We performed a genomewide analysis to identify genes whose DNA methylation levels are associated with PTSD. A total of 211 individuals comprising Australian male Vietnam War veterans (n = 96) and males from a general population belonging to the Grady Trauma Project (n = 115) were included. Genomewide DNA methylation was performed from peripheral blood using the Illumina arrays. Data analysis was performed using generalized linear regression models. Differential DNA methylation of 17 previously reported PTSD candidate genes was associated with PTSD symptom severity. Genomewide analyses revealed CpG sites spanning BRSK1, LCN8, NFG and DOCK2 genes were associated with PTSD symptom severity. We replicated the findings of DOCK2 in an independent cohort. Pathway analysis revealed that among the associated genes, genes within actin cytoskeleton and focal adhesion molecular pathways were enriched. These data highlight the role of DNA methylation as biomarkers of PTSD. The results support the role of previous candidates and uncover novel genes associated with PTSD, such as DOCK2. This study contributes to our understanding of the biological underpinnings of PTSD. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Atomic Force Microscopy Reveals a Morphological Differentiation of Chromobacterium violaceum Cells Associated with Biofilm Development and Directed by N-Hexanoyl-L-Homoserine Lactone

    PubMed Central

    Kamaeva, Anara A.; Vasilchenko, Alexey S.; Deryabin, Dmitry G.

    2014-01-01

    Chromobacterium violaceum abounds in soil and water ecosystems in tropical and subtropical regions and occasionally causes severe and often fatal human and animal infections. The quorum sensing (QS) system and biofilm formation are essential for C. violaceum's adaptability and pathogenicity, however, their interrelation is still unknown. C. violaceum's cell and biofilm morphology were examined by atomic force microscopy (AFM) in comparison with growth rates, QS-dependent violacein biosynthesis and biofilm biomass quantification. To evaluate QS regulation of these processes, the wild-type strain C. violaceum ATCC 31532 and its mini-Tn5 mutant C. violaceum NCTC 13274, cultivated with and without the QS autoinducer N-hexanoyl-L-homoserine lactone (C6-HSL), were used. We report for the first time the unusual morphological differentiation of C. violaceum cells, associated with biofilm development and directed by the QS autoinducer. AFM revealed numerous invaginations of the external cytoplasmic membrane of wild-type cells, which were repressed in the mutant strain and restored by exogenous C6-HSL. With increasing bacterial growth, polymer matrix extrusions formed in place of invaginations, whereas mutant cells were covered with a diffusely distributed extracellular substance. Thus, quorum sensing in C. violaceum involves a morphological differentiation that organises biofilm formation and leads to a highly differentiated matrix structure. PMID:25111599

  12. Atomic force microscopy reveals a morphological differentiation of chromobacterium violaceum cells associated with biofilm development and directed by N-hexanoyl-L-homoserine lactone.

    PubMed

    Kamaeva, Anara A; Vasilchenko, Alexey S; Deryabin, Dmitry G

    2014-01-01

    Chromobacterium violaceum abounds in soil and water ecosystems in tropical and subtropical regions and occasionally causes severe and often fatal human and animal infections. The quorum sensing (QS) system and biofilm formation are essential for C. violaceum's adaptability and pathogenicity, however, their interrelation is still unknown. C. violaceum's cell and biofilm morphology were examined by atomic force microscopy (AFM) in comparison with growth rates, QS-dependent violacein biosynthesis and biofilm biomass quantification. To evaluate QS regulation of these processes, the wild-type strain C. violaceum ATCC 31532 and its mini-Tn5 mutant C. violaceum NCTC 13274, cultivated with and without the QS autoinducer N-hexanoyl-L-homoserine lactone (C6-HSL), were used. We report for the first time the unusual morphological differentiation of C. violaceum cells, associated with biofilm development and directed by the QS autoinducer. AFM revealed numerous invaginations of the external cytoplasmic membrane of wild-type cells, which were repressed in the mutant strain and restored by exogenous C6-HSL. With increasing bacterial growth, polymer matrix extrusions formed in place of invaginations, whereas mutant cells were covered with a diffusely distributed extracellular substance. Thus, quorum sensing in C. violaceum involves a morphological differentiation that organises biofilm formation and leads to a highly differentiated matrix structure.

  13. BOREAS AFM-1 NOAA/ATDD Long-EZ Aircraft Flux data Over the SSA

    NASA Technical Reports Server (NTRS)

    Crawford, Timothy L.; Baldocchi, Dennis; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Gunter, Laureen; Dumas, Ed; Smith, David E. (Technical Monitor)

    2000-01-01

    This data set contains measurements from the Airborne Flux and Meteorology (AFM)-1 National Oceanographic and Atmospheric Administration/Atmospheric Turbulence and Diffusion Division (NOAA/ATDD) Long-EZ Aircraft collected during the 1994 Intensive Field Campaigns (IFCs) at the southern study area (SSA). These measurements were made from various instruments mounted on the aircraft. The data that were collected include aircraft altitude, wind direction, wind speed, air temperature, potential temperature, water mixing ratio, U and V components of wind velocity, static pressure, surface radiative temperature, downwelling and upwelling total radiation, downwelling and upwelling longwave radiation, net radiation, downwelling and upwelling photosynthectically active radiation (PAR), greenness index, CO2 concentration, O3 concentration, and CH4 concentration. There are also various columns that indicate the standard deviation, skewness, kurtosis, and trend of some of these data. The data are stored in tabular ASCII files. The NOAA/ATDD Long-EZ aircraft flux 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. Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas.

    PubMed

    Phi, Ji Hoon; Park, Ae Kyung; Lee, Semin; Choi, Seung Ah; Baek, In-Pyo; Kim, Pora; Kim, Eun-Hye; Park, Hee Chul; Kim, Byung Chul; Bhak, Jong; Park, Sung-Hye; Lee, Ji Yeoun; Wang, Kyu-Chang; Kim, Dong-Seok; Shim, Kyu Won; Kim, Se Hoon; Kim, Chae-Yong; Kim, Seung-Ki

    2018-06-01

    Despite great advances in understanding of molecular pathogenesis and achievement of a high cure rate in medulloblastoma, recurrent medulloblastomas are still dismal. Additionally, misidentification of secondary malignancies due to histological ambiguity leads to misdiagnosis and eventually to inappropriate treatment. Nevertheless, the genomic characteristics of recurrent medulloblastomas are poorly understood, largely due to a lack of matched primary and recurrent tumor tissues. We performed a genomic analysis of recurrent tumors from 17 pediatric medulloblastoma patients. Whole transcriptome sequencing revealed that a subset of recurrent tumors initially diagnosed as locally recurrent medulloblastomas are secondary glioblastomas after radiotherapy, showing high similarity to the non-G-CIMP proneural subtype of glioblastoma. Further analysis, including whole exome sequencing, revealed missense mutations or complex gene fusion events in PDGFRA with augmented expression in the secondary glioblastomas after radiotherapy, implicating PDGFRA as a putative driver in the development of secondary glioblastomas after treatment exposure. This result provides insight into the possible application of PDGFRA-targeted therapy in these second malignancies. Furthermore, genomic alterations of TP53 including 17p loss or germline/somatic mutations were also found in most of the secondary glioblastomas after radiotherapy, indicating a crucial role of TP53 alteration in the process. On the other hand, analysis of recurrent medulloblastomas revealed that the most prevalent alterations are the loss of 17p region including TP53 and gain of 7q region containing EZH2 which already exist in primary tumors. The 7q gain events are frequently accompanied by high expression levels of EZH2 in both primary and recurrent medulloblastomas, which provides a clue to a new therapeutic target to prevent recurrence. Considering the fact that it is often challenging to differentiate between recurrent

  15. AFM visualization at a single-molecule level of denaturated states of proteins on graphite.

    PubMed

    Barinov, Nikolay A; Prokhorov, Valery V; Dubrovin, Evgeniy V; Klinov, Dmitry V

    2016-10-01

    Different graphitic materials are either already used or believed to be advantageous in biomedical and biotechnological applications, e.g., as biomaterials or substrates for sensors. Most of these applications or associated important issues, such as biocompatibility, address the problem of adsorption of protein molecules and, in particular the conformational state of the adsorbed protein molecule on graphite. High-resolution AFM demonstrates highly oriented pyrolytic graphite (HOPG) induced denaturation of four proteins of blood plasma, such as ferritin, fibrinogen, human serum albumin (HSA) and immunoglobulin G (IgG), at a single molecule level. Protein denaturation is accompanied by the decrease of the heights of protein globules and spreading of the denatured protein fraction on the surface. In contrast, the modification of HOPG with the amphiphilic oligoglycine-hydrocarbon derivative monolayer preserves the native-like conformation and provides even more mild conditions for the protein adsorption than typically used mica. Protein unfolding on HOPG may have universal character for "soft" globular proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Micromorphological characterization of zinc/silver particle composite coatings.

    PubMed

    Méndez, Alia; Reyes, Yolanda; Trejo, Gabriel; StĘpień, Krzysztof; Ţălu, Ştefan

    2015-12-01

    The aim of this study was to evaluate the three-dimensional (3D) surface micromorphology of zinc/silver particles (Zn/AgPs) composite coatings with antibacterial activity prepared using an electrodeposition technique. These 3D nanostructures were investigated over square areas of 5 μm × 5 μm by atomic force microscopy (AFM), fractal, and wavelet analysis. The fractal analysis of 3D surface roughness revealed that (Zn/AgPs) composite coatings have fractal geometry. Triangulation method, based on the linear interpolation type, applied for AFM data was employed in order to characterise the surfaces topographically (in amplitude, spatial distribution and pattern of surface characteristics). The surface fractal dimension Df , as well as height values distribution have been determined for the 3D nanostructure surfaces. © 2015 The Authors published by Wiley Periodicals, Inc.

  17. Genomic analysis of primordial dwarfism reveals novel disease genes.

    PubMed

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  18. Genomic analysis of primordial dwarfism reveals novel disease genes

    PubMed Central

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N.; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S.

    2014-01-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis. PMID:24389050

  19. Microscale analysis of in vitro anaerobic degradation of lignocellulosic wastes by rumen microorganisms.

    PubMed

    Hu, Zhen-Hu; Liu, Shao-Yang; Yue, Zheng-Bo; Yan, Li-Feng; Yang, Ming-Tao; Yu, Han-Qing

    2008-01-01

    Anaerobic degradation of lignin in waste straw by ruminal microbes was directly observed using atomic force microscope (AFM). A series of high-resolution AFM images of the straw surface in the biodegradation show that the wax flakelets and lignin granules covering the straw surface were removed by the rumen microorganisms. Such degradation resulted in an exposure of cellulose fibers located inside the straw. The appearance of holes and microfibers in fermentation reveals that tunneling might be one of the ways for rumen microorganisms to attack the straw. Increases in the atomic ratio of oxygen to carbon (O/C) and the ratio C2/C3 in C1s spectra of X-ray photoelectron spectroscopy confirm that more cellulose was exposed on the surface after the anaerobic fermentation of straw. Gas chromatography/mass spectrometry analytical results demonstrate the decomposition of lignin by rumen microorganisms. Fourier transform infrared spectroscopy spectra and the measurement of degradation efficiency of the main straw components further verify these microscaled observations.

  20. Systematic analysis of the gerontome reveals links between aging and age-related diseases

    PubMed Central

    Fernandes, Maria; Wan, Cen; Tacutu, Robi; Barardo, Diogo; Rajput, Ashish; Wang, Jingwei; Thoppil, Harikrishnan; Thornton, Daniel; Yang, Chenhao; Freitas, Alex

    2016-01-01

    Abstract In model organisms, over 2,000 genes have been shown to modulate aging, the collection of which we call the ‘gerontome’. Although some individual aging-related genes have been the subject of intense scrutiny, their analysis as a whole has been limited. In particular, the genetic interaction of aging and age-related pathologies remain a subject of debate. In this work, we perform a systematic analysis of the gerontome across species, including human aging-related genes. First, by classifying aging-related genes as pro- or anti-longevity, we define distinct pathways and genes that modulate aging in different ways. Our subsequent comparison of aging-related genes with age-related disease genes reveals species-specific effects with strong overlaps between aging and age-related diseases in mice, yet surprisingly few overlaps in lower model organisms. We discover that genetic links between aging and age-related diseases are due to a small fraction of aging-related genes which also tend to have a high network connectivity. Other insights from our systematic analysis include assessing how using datasets with genes more or less studied than average may result in biases, showing that age-related disease genes have faster molecular evolution rates and predicting new aging-related drugs based on drug-gene interaction data. Overall, this is the largest systems-level analysis of the genetics of aging to date and the first to discriminate anti- and pro-longevity genes, revealing new insights on aging-related genes as a whole and their interactions with age-related diseases. PMID:28175300

  1. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders

    PubMed Central

    Li, Jingjing; Shi, Minyi; Ma, Zhihai; Zhao, Shuchun; Euskirchen, Ghia; Ziskin, Jennifer; Urban, Alexander; Hallmayer, Joachim; Snyder, Michael

    2014-01-01

    Autism is a complex disease whose etiology remains elusive. We integrated previously and newly generated data and developed a systems framework involving the interactome, gene expression and genome sequencing to identify a protein interaction module with members strongly enriched for autism candidate genes. Sequencing of 25 patients confirmed the involvement of this module in autism, which was subsequently validated using an independent cohort of over 500 patients. Expression of this module was dichotomized with a ubiquitously expressed subcomponent and another subcomponent preferentially expressed in the corpus callosum, which was significantly affected by our identified mutations in the network center. RNA-sequencing of the corpus callosum from patients with autism exhibited extensive gene mis-expression in this module, and our immunochemical analysis showed that the human corpus callosum is predominantly populated by oligodendrocyte cells. Analysis of functional genomic data further revealed a significant involvement of this module in the development of oligodendrocyte cells in mouse brain. Our analysis delineates a natural network involved in autism, helps uncover novel candidate genes for this disease and improves our understanding of its molecular pathology. PMID:25549968

  2. Quantitative analysis of the flexibility effect of cisplatin on circular DNA

    NASA Astrophysics Data System (ADS)

    Ji, Chao; Zhang, Lingyun; Wang, Peng-Ye

    2013-10-01

    We study the effects of cisplatin on the circular configuration of DNA using atomic force microscopy (AFM) and observe that the DNA gradually transforms to a complex configuration with an intersection and interwound structures from a circlelike structure. An algorithm is developed to extract the configuration profiles of circular DNA from AFM images and the radius of gyration is used to describe the flexibility of circular DNA. The quantitative analysis of the circular DNA demonstrates that the radius of gyration gradually decreases and two processes on the change of flexibility of circular DNA are found as the cisplatin concentration increases. Furthermore, a model is proposed and discussed to explain the mechanism for understanding the complicated interaction between DNA and cisplatin.

  3. Correlating microscopy techniques and ToF-SIMS analysis of fully grown mammalian oocytes.

    PubMed

    Gulin, Alexander; Nadtochenko, Victor; Astafiev, Artyom; Pogorelova, Valentina; Rtimi, Sami; Pogorelov, Alexander

    2016-06-20

    The 2D-molecular thin film analysis protocol for fully grown mice oocytes is described using an innovative approach. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), scanning electron microscopy (SEM), atomic force microscopy (AFM) and optical microscopy imaging were applied to the same mice oocyte section on the same sample holder. A freeze-dried mice oocyte was infiltrated into embedding media, e.g. Epon, and then was cut with a microtome and 2 μm thick sections were transferred onto an ITO coated conductive glass. Mammalian oocytes can contain "nucleolus-like body" (NLB) units and ToF-SIMS analysis was used to investigate the NLB composition. The ion-spatial distribution in the cell components was identified and compared with the images acquired by SEM, AFM and optical microscopy. This study presents a significant advancement in cell embryology, cell physiology and cancer-cell biochemistry.

  4. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia.

    PubMed

    Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

    2014-01-01

    Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group

  5. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

    PubMed Central

    Damaraju, E.; Allen, E.A.; Belger, A.; Ford, J.M.; McEwen, S.; Mathalon, D.H.; Mueller, B.A.; Pearlson, G.D.; Potkin, S.G.; Preda, A.; Turner, J.A.; Vaidya, J.G.; van Erp, T.G.; Calhoun, V.D.

    2014-01-01

    Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group

  6. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    PubMed

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

    PubMed

    Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

    2018-03-27

    Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

  8. Nanostructure and force spectroscopy analysis of human peripheral blood CD4{sup +} T cells using atomic force microscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hu Mingqian; Wang Jiongkun; Cai Jiye

    2008-09-12

    To date, nanoscale imaging of the morphological changes and adhesion force of CD4{sup +} T cells during in vitro activation remains largely unreported. In this study, we used atomic force microscopy (AFM) to study the morphological changes and specific binding forces in resting and activated human peripheral blood CD4{sup +} T cells. The AFM images revealed that the volume of activated CD4{sup +} T cells increased and the ultrastructure of these cells also became complex. Using a functionalized AFM tip, the strength of the specific binding force of the CD4 antigen-antibody interaction was found to be approximately three times thatmore » of the unspecific force. The adhesion forces were not randomly distributed over the surface of a single activated CD4{sup +} T cell, indicated that the CD4 molecules concentrated into nanodomains. The magnitude of the adhesion force of the CD4 antigen-antibody interaction did not change markedly with the activation time. Multiple bonds involved in the CD4 antigen-antibody interaction were measured at different activation times. These results suggest that the adhesion force involved in the CD4 antigen-antibody interaction is highly selective and of high affinity.« less

  9. Strain relaxation induced surface morphology of heterogeneous GaInNAs layers grown on GaAs substrate

    NASA Astrophysics Data System (ADS)

    Gelczuk, Ł.; Jóźwiak, G.; Moczała, M.; Dłużewski, P.; Dąbrowska-Szata, M.; Gotszalk, T. P.

    2017-07-01

    The partially-relaxed heterogeneous GaInNAs layers grown on GaAs substrate by atmospheric pressure vapor phase epitaxy (AP-MOVPE) were investigated by transmission electron microscopy (TEM) and atomic force microscopy (AFM). The planar-view TEM image shows a regular 2D network of misfit dislocations oriented in two orthogonal 〈1 1 0〉 crystallographic directions at the (0 0 1) layer interface. Moreover, the cross-sectional view TEM image reveals InAs-rich and V-shaped precipitates in the near surface region of the GaInNAs epitaxial layer. The resultant undulating surface morphology, known as a cross-hatch pattern, is formed as observed by AFM. The numerical analysis of the AFM image of the GaInNAs layer surface with the well-defined cross-hatch morphology enabled us to determine a lower bound of actual density of misfit dislocations. However, a close correspondence between the asymmetric distribution of interfacial misfit dislocations and undulating surface morphology is observed.

  10. Inverting dynamic force microscopy: From signals to time-resolved interaction forces

    PubMed Central

    Stark, Martin; Stark, Robert W.; Heckl, Wolfgang M.; Guckenberger, Reinhard

    2002-01-01

    Transient forces between nanoscale objects on surfaces govern friction, viscous flow, and plastic deformation, occur during manipulation of matter, or mediate the local wetting behavior of thin films. To resolve transient forces on the (sub) microsecond time and nanometer length scale, dynamic atomic force microscopy (AFM) offers largely unexploited potential. Full spectral analysis of the AFM signal completes dynamic AFM. Inverting the signal formation process, we measure the time course of the force effective at the sensing tip. This approach yields rich insight into processes at the tip and dispenses with a priori assumptions about the interaction, as it relies solely on measured data. Force measurements on silicon under ambient conditions demonstrate the distinct signature of the interaction and reveal that peak forces exceeding 200 nN are applied to the sample in a typical imaging situation. These forces are 2 orders of magnitude higher than those in covalent bonds. PMID:12070341

  11. The relation of apple texture with cell wall nanostructure studied using an atomic force microscope.

    PubMed

    Cybulska, Justyna; Zdunek, Artur; Psonka-Antonczyk, Katarzyna M; Stokke, Bjørn T

    2013-01-30

    In this study, the relation of the nanostructure of cell walls with their texture was investigated for six different apple cultivars. Cell wall material (CWM) and cellulose microfibrils were imaged by atomic force microscope (AFM). The mean diameter of cellulose microfibrils for each cultivar was estimated based on the AFM height topographs obtained using the tapping mode of dried specimens. Additionally, crystallinity of cellulose microfibrils and pectin content was determined. Texture of apple cultivars was evaluated by sensory and instrumental analysis. Differences in cellulose diameter as determined from the AFM height topographs of the nanostructure of cell walls of the apple cultivars are found to relate to the degree of crystallinity and pectin content. Cultivars with thicker cellulose microfibrils also revealed crisper, harder and juicier texture, and greater acoustic emission. The data suggest that microfibril thickness affects the mechanical strength of cell walls which has consequences for sensory and instrumental texture. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Exchange bias in multiferroic Ca3Mn2O7 effected by Dzyaloshinskii-Moriya interaction

    NASA Astrophysics Data System (ADS)

    Sahlot, Pooja; Jana, Anupam; Awasthi, A. M.

    2018-04-01

    Ruddlesden-Popper manganite Ca3Mn2O7 has been synthesized in single phase orthorhombic structure with Cmcm space group. Temperature dependent magnetization M(T) shows that Ca3Mn2O7 undergoes long range antiferromagnetic (AFM) transition below 123 K, with weak ferromagnetism (WFM) at lower temperatures. Field dependent magnetization M(H) confirms WFM character below ˜110 K in the AFM-base magnetic structure. Detailed analysis of the zero field cooled magnetic hysteresis loops reveals a measurable exchange bias (EB) effect in the sample. EB is attributed to the high anisotropy in the sample and the presence of Dzyaloshinskii-Moriya (D-M) interaction, responsible for the canted interfacial-spins that couple "FM-clusters" with the "AFM-matrix". Temperature dependence of horizontal shifts of the M(H) loops in terms of the coercive fields (Hc±) and vertical shifts in terms of the remnant magnetizations (Mr±) is presented.

  13. An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics.

    PubMed

    Tan, Shangjin; Zhou, Jin; Zhu, Xiaoshan; Yu, Shichen; Zhan, Wugen; Wang, Bo; Cai, Zhonghua

    2015-02-01

    Algal blooms are a worldwide phenomenon and the biological interactions that underlie their regulation are only just beginning to be understood. It is established that algal microorganisms associate with many other ubiquitous, oceanic organisms, but the interactions that lead to the dynamics of bloom formation are currently unknown. To address this gap, we used network approaches to investigate the association patterns among microeukaryotes and bacterioplankton in response to a natural Scrippsiella trochoidea bloom. This is the first study to apply network approaches to bloom dynamics. To this end, terminal restriction fragment (T-RF) length polymorphism analysis showed dramatic changes in community compositions of microeukaryotes and bacterioplankton over the blooming period. A variance ratio test revealed significant positive overall associations both within and between microeukaryotic and bacterioplankton communities. An association network generated from significant correlations between T-RFs revealed that S. trochoidea had few connections to other microeukaryotes and bacterioplankton and was placed on the edge. This lack of connectivity allowed for the S. trochoidea sub-network to break off from the overall network. These results allowed us to propose a conceptual model for explaining how changes in microbial associations regulate the dynamics of an algal bloom. In addition, key T-RFs were screened by principal components analysis, correlation coefficients, and network analysis. Dominant T-RFs were then identified through 18S and 16S rRNA gene clone libraries. Results showed that microeukaryotes clustered predominantly with Dinophyceae and Perkinsea while the majority of bacterioplankton identified were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The ecologi-cal roles of both were discussed in the context of these findings. © 2014 Phycological Society of America.

  14. Atomic force microscopy and scanning electron microscopy analysis of daily disposable limbal ring contact lenses.

    PubMed

    Lorenz, Kathrine Osborn; Kakkassery, Joseph; Boree, Danielle; Pinto, David

    2014-09-01

    Limbal ring (also known as 'circle') contact lenses are becoming increasingly popular, especially in Asian markets because of their eye-enhancing effects. The pigment particles that give the eye-enhancing effects of these lenses can be found on the front or back surface of the contact lens or 'enclosed' within the lens matrix. The purpose of this research was to evaluate the pigment location and surface roughness of seven types of 'circle' contact lenses. Scanning electron microscopic (SEM) analysis was performed using a variable pressure Hitachi S3400N instrument to discern the placement of lens pigments. Atomic force microscopy (Dimension Icon AFM from Bruker Nano) was used to determine the surface roughness of the pigmented regions of the contact lenses. Atomic force microscopic analysis was performed in fluid phase under contact mode using a Sharp Nitride Lever probe (SNL-10) with a spring constant of 0.06 N/m. Root mean square (RMS) roughness values were analysed using a generalised linear mixed model with a log-normal distribution. Least square means and their corresponding 95% confidence intervals were estimated for each brand, location and pigment combination. SEM cross-sectional images at 500× and 2,000× magnification showed pigment on the surface of six of the seven lens types tested. The mean depth of pigment for 1-DAY ACUVUE DEFINE (1DAD) lenses was 8.1 μm below the surface of the lens, while the remaining lens types tested had pigment particles on the front or back surface. Results of the atomic force microscopic analysis indicated that 1DAD lenses had significantly lower root mean square roughness values in the pigmented area of the lens than the other lens types tested. SEM and AFM analysis revealed pigment on the surface of the lens for all types tested with the exception of 1DAD. Further research is required to determine if the difference in pigment location influences on-eye performance. © 2014 The Authors. Clinical and Experimental

  15. Atomic force microscopy and scanning electron microscopy analysis of daily disposable limbal ring contact lenses

    PubMed Central

    Lorenz, Kathrine Osborn; Kakkassery, Joseph; Boree, Danielle; Pinto, David

    2014-01-01

    Background Limbal ring (also known as ‘circle’) contact lenses are becoming increasingly popular, especially in Asian markets because of their eye-enhancing effects. The pigment particles that give the eye-enhancing effects of these lenses can be found on the front or back surface of the contact lens or ‘enclosed’ within the lens matrix. The purpose of this research was to evaluate the pigment location and surface roughness of seven types of ‘circle’ contact lenses. Methods Scanning electron microscopic (SEM) analysis was performed using a variable pressure Hitachi S3400N instrument to discern the placement of lens pigments. Atomic force microscopy (Dimension Icon AFM from Bruker Nano) was used to determine the surface roughness of the pigmented regions of the contact lenses. Atomic force microscopic analysis was performed in fluid phase under contact mode using a Sharp Nitride Lever probe (SNL-10) with a spring constant of 0.06 N/m. Root mean square (RMS) roughness values were analysed using a generalised linear mixed model with a log-normal distribution. Least square means and their corresponding 95% confidence intervals were estimated for each brand, location and pigment combination. Results SEM cross-sectional images at 500× and 2,000× magnification showed pigment on the surface of six of the seven lens types tested. The mean depth of pigment for 1-DAY ACUVUE DEFINE (1DAD) lenses was 8.1 μm below the surface of the lens, while the remaining lens types tested had pigment particles on the front or back surface. Results of the atomic force microscopic analysis indicated that 1DAD lenses had significantly lower root mean square roughness values in the pigmented area of the lens than the other lens types tested. Conclusions SEM and AFM analysis revealed pigment on the surface of the lens for all types tested with the exception of 1DAD. Further research is required to determine if the difference in pigment location influences on-eye performance. PMID

  16. Spectroellipsometric, AFM and XPS probing of stainless steel surfaces subjected to biological influences

    NASA Astrophysics Data System (ADS)

    Vinnichenko, M.; Chevolleau, Th; Pham, M. T.; Poperenko, L.; Maitz, M. F.

    2002-11-01

    Surface modification of austenitic stainless steel (SS) 316L after incubation in growing cell cultures and cell-free media as control has been studied. The following treatments were applied: mouse fibrosarcoma cells L929 for 3 and 7 days, polymorphonuclear neutrophils for 3 and 7 days and human osteosarcoma cells SAOS-2 for 7 and 14 days. Cells were enzymatically removed in all cases. The modified surfaces were probed in comparison with untreated ones by means of spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). XPS shows the appearance of the peak of bonded nitrogen at 400.5 eV characteristic for adsorbed proteins on the surface for each type of cells and for the cell-free medium. Migration of Ni in the adsorbed layer is observed in all cases for samples after the cell cultures. The protein layer thickness is ellipsometrically determined to be within 2.5-6.0 nm for all treated samples with parameterization of its optical constants in Cauchy approach. The study showed that for such biological treatments of the SS the protein layer adsorption is the dominating process in the first 2 weeks, which could play a role in the process of corrosion by complex forming properties with metal ions.

  17. Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

    NASA Astrophysics Data System (ADS)

    Yen, Chi-Fu; Sivasankar, Sanjeevi

    2018-03-01

    Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

  18. Noncontact viscoelastic measurement of polymer thin films in a liquid medium using a long-needle AFM

    NASA Astrophysics Data System (ADS)

    Guan, Dongshi; Barraud, Chloe; Charlaix, Elisabeth; Tong, Penger

    We report noncontact measurement of the viscoelastic property of polymer thin films in a liquid medium using frequency-modulation atomic force microscopy (FM-AFM) with a newly developed long-needle probe. The probe contains a long vertical glass fiber with one end adhered to a cantilever beam and the other end with a sharp tip placed near the liquid-film interface. The nanoscale flow generated by the resonant oscillation of the needle tip provides a precise hydrodynamic force acting on the soft surface of the thin film. By accurately measuring the mechanical response of the thin film, we obtain the elastic and loss moduli of the thin film using the linear response theory of elasto-hydrodynamics. The experiment verifies the theory and demonstrates its applications. The technique can be used to accurately measure the viscoelastic property of soft surfaces, such as those made of polymers, nano-bubbles, live cells and tissues. This work was supported by the Research Grants Council of Hong Kong SAR.

  19. Morphological Properties of Siloxane-Hydrogel Contact Lens Surfaces.

    PubMed

    Stach, Sebastian; Ţălu, Ştefan; Trabattoni, Silvia; Tavazzi, Silvia; Głuchaczka, Alicja; Siek, Patrycja; Zając, Joanna; Giovanzana, Stefano

    2017-04-01

    The aim of this study was to quantitatively characterize the micromorphology of contact lens (CL) surfaces using atomic force microscopy (AFM) and multifractal analysis. AFM and multifractal analysis were used to characterize the topography of new and worn siloxane-hydrogel CLs made of Filcon V (I FDA group). CL surface roughness was studied by AFM in intermittent-contact mode, in air, on square areas of 25 and 100 μm 2 , by using a Nanoscope V MultiMode (Bruker). Detailed surface characterization of the surface topography was obtained using statistical parameters of 3-D (three-dimensional) surface roughness, in accordance with ISO 25178-2: 2012. Before wear, the surface was found to be characterized by out-of-plane and sharp structures, whilst after a wear of 8 h, two typical morphologies were observed. One morphology (sharp type) has a similar aspect as the unworn CLs and the other morphology (smooth type) is characterized by troughs and bumpy structures. The analysis of the AFM images revealed a multifractal geometry. The generalized dimension D q and the singularity spectrum f(α) provided quantitative values that characterize the local scale properties of CL surface geometry at nanometer scale. Surface statistical parameters deduced by multifractal analysis can be used to assess the CL micromorphology and can be used by manufacturers in developing CLs with improved surface characteristics. These parameters can also be used in understanding the tribological interactions of the back surface of the CL with the corneal surface and the front surface of the CL with the under-surface of the eyelid (friction, wear, and micro-elastohydrodynamic lubrication at a nanometer scale).

  20. Nanoscale evaluation of lubricity on well-defined polymer brush surfaces using QCM-D and AFM.

    PubMed

    Kitano, Kazuhiko; Inoue, Yuuki; Matsuno, Ryosuke; Takai, Madoka; Ishihara, Kazuhiko

    2009-11-01

    For preparing a "highly lubricated biointerface", which has both excellent lubricity and biocompatibility, we investigated the factors responsible for resistance to friction during polymer grafting. We prepared poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(methyl methacrylate) (PMMA) brush layers with high graft density and well-controlled thickness using atom transfer radical polymerization (ATRP). We measured the water absorptivity in the polymer brush layers and the viscoelasticity of the polymer-hydrated layers using a quartz crystal microbalance with dissipation monitoring (QCM-D) measurements. The PMPC brush layer had the highest water absorptivity, while the PMPC-hydrated layer had the highest fluidity. The friction properties of the polymer brush layers were determined in air, water, and toluene by atomic force microscopy (AFM). The friction on each polymer brush decreased only when a good solvent was chosen for each polymer. In conclusion, the brush layer possessing high water absorptivity and fluidity in water contributes to reduce friction. PMPC grafting is an effective and promising method for obtaining highly lubricated biointerfaces.

  1. The growth and characterization of alkylphosphonic acid self-assembled nanofibers

    NASA Astrophysics Data System (ADS)

    Salmon, Michael Edward

    The focus of this research was to investigate the formation and properties of novel Self-Assembled Nanofibers (SANs) created by the treatment of aluminum with solutions of short chain-length alkylphosphonic acids (APAs) in ethanol. A special emphasis was placed on the creation of APA SANs isolated from the immersed aluminum source and development of analysis techniques for artifact reduced characterization of as-grown individual SANs. Novel immersion growth techniques were devised for the reproducible creation of supported and unsupported isolated methylphosphonic acid (C1), propylphosphonic acid (C3), and pentylphosphonic acid (C5) SANs on Si3N4 and aluminum coated ProtoChips(TM) DuraSiN(TM) Si3N 4 meshes respectively. Additionally, a novel biased immersion growth technique was developed, increasing growth rates as well as allowing for APA SAN deposition onto a variety of substrates including Au microelectrodes. A combination of complementary analysis techniques including: Atomic force microscopy (AFM), Scanning Transmission Electron Microscopy (STEM), Energy Dispersive Spectrometry (EDS), X-Ray Photoelectron Spectroscopy (XPS), and Electron Energy Loss Spectroscopy (EELS) were utilized to characterize the morphology, composition and chemistry of isolated individual APA SANs. STEM and AFM revealed individual APA SANs are actually composed of layered fibril bundles. Qualitative compositional analysis showed APA SANs were primarily composed of oxygen, carbon, phosphorus, and aluminum with phosphorus:aluminum ratios determined to be between 1.5 and 4.2. Quantitative XPS and EELS analysis provided further evidence that the detected aluminum was non-metallic and likely oxidized. STEM with EELS was utilized to definitively correlate the presence of aluminum, phosphorus, oxygen, and carbon to a 5 nm region of several overlapping unsupported C1 SANs. Thermal analysis of APA SANs on Al as well as isolated on Si3N 4 revealed a nearly 5X increase in thermal stability as

  2. Using risk analysis to reveal opportunities for the management of unplanned ignitions in wilderness

    Treesearch

    Kevin Barnett; Carol Miller; Tyron J. Venn

    2016-01-01

    A goal of fire management in wilderness is to allow fire to play its natural ecological role without intervention. Unfortunately, most unplanned ignitions in wilderness are suppressed, in part because of the risk they might pose to values outside of the wilderness. We capitalize on recent advances in fire risk analysis to demonstrate a risk-based approach for revealing...

  3. Surface pressure and elasticity of hydrophobin HFBII layers on the air-water interface: rheology versus structure detected by AFM imaging.

    PubMed

    Stanimirova, Rumyana D; Gurkov, Theodor D; Kralchevsky, Peter A; Balashev, Konstantin T; Stoyanov, Simeon D; Pelan, Eddie G

    2013-05-21

    Here, we combine experiments with Langmuir trough and atomic force microscopy (AFM) to investigate the reasons for the special properties of layers from the protein HFBII hydrophobin spread on the air-water interface. The hydrophobin interfacial layers possess the highest surface dilatational and shear elastic moduli among all investigated proteins. The AFM images show that the spread HFBII layers are rather inhomogeneous, (i.e., they contain voids, monolayer and multilayer domains). A continuous compression of the layer leads to filling the voids and transformation of a part of the monolayer into a trilayer. The trilayer appears in the form of large surface domains, which can be formed by folding and subduction of parts from the initial monolayer. The trilayer appears also in the form of numerous submicrometer spots, which can be obtained by forcing protein molecules out of the monolayer and their self-assembly into adjacent pimples. Such structures are formed because not only the hydrophobic parts, but also the hydrophilic parts of the HFBII molecules can adhere to each other in the water medium. If a hydrophobin layer is subjected to oscillations, its elasticity considerably increases, up to 500 mN/m, which can be explained with compaction. The relaxation of the layer's tension after expansion or compression follows the same relatively simple law, which refers to two-dimensional diffusion of protein aggregates within the layer. The characteristic diffusion time after compression is longer than after expansion, which can be explained with the impedence of diffusion in the more compact interfacial layer. The results shed light on the relation between the mesoscopic structure of hydrophobin interfacial layers and their unique mechanical properties that find applications for the production of foams and emulsions of extraordinary stability; for the immobilization of functional molecules at surfaces, and as coating agents for surface modification.

  4. AFM, CLSM and EIS characterization of the immobilization of antibodies on indium-tin oxide electrode and their capture of Legionella pneumophila.

    PubMed

    Souiri, Mina; Blel, Nesrine; Sboui, Dejla; Mhamdi, Lotfi; Epalle, Thibaut; Mzoughi, Ridha; Riffard, Serge; Othmane, Ali

    2014-01-01

    The microscopic surface molecular structures and properties of monoclonal anti-Legionella pneumophila antibodies on an indium-tin oxide (ITO) electrode surface were studied to elaborate an electrochemical immunosensor for Legionella pneumophila detection. A monoclonal anti-Legionella pneumophila antibody (MAb) has been immobilized onto an ITO electrode via covalent chemical bonds between antibodies amino-group and the ring of (3-Glycidoxypropyl) trimethoxysilane (GPTMS). The functionalization of the immunosensor was characterized by atomic force microscopy (AFM), water contact angle measurement, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) in the presence of [Fe(CN)₆](3-/4-) as a redox probe. Specific binding of Legionella pneumophila sgp 1 cells onto the antibody-modified ITO electrode was shown by confocal laser scanning microscopy (CLSM) imaging and EIS. AFM images evidenced the dense and relatively homogeneous morphology on the ITO surface. The formation of the complex epoxysilane-antibodies acting as barriers for the electron transfer between the electrode surface and the redox species in the solution induced a significant increase in the charge transfer resistance (Rct) compared to all the electric elements. A linear relationship between the change in charge transfer resistance (ΔRct=Rct after immunoreactions - Rct control) and the logarithmic concentration value of L. pneumophila was observed in the range of 5 × 10(1)-5 × 10(4) CFU mL(-1) with a limit of detection 5 × 10(1)CFU mL(-1). The present study has demonstrated the successful deposition of an anti-L. pneumophila antibodies on an indium-tin oxide surface, opening its subsequent use as immuno-captor for the specific detection of L. pneumophila in environmental samples. © 2013 Elsevier B.V. All rights reserved.

  5. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    PubMed Central

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  6. Analysis of dynamic cantilever behavior in tapping mode atomic force microscopy.

    PubMed

    Deng, Wenqi; Zhang, Guang-Ming; Murphy, Mark F; Lilley, Francis; Harvey, David M; Burton, David R

    2015-10-01

    Tapping mode atomic force microscopy (AFM) provides phase images in addition to height and amplitude images. Although the behavior of tapping mode AFM has been investigated using mathematical modeling, comprehensive understanding of the behavior of tapping mode AFM still poses a significant challenge to the AFM community, involving issues such as the correct interpretation of the phase images. In this paper, the cantilever's dynamic behavior in tapping mode AFM is studied through a three dimensional finite element method. The cantilever's dynamic displacement responses are firstly obtained via simulation under different tip-sample separations, and for different tip-sample interaction forces, such as elastic force, adhesion force, viscosity force, and the van der Waals force, which correspond to the cantilever's action upon various different representative computer-generated test samples. Simulated results show that the dynamic cantilever displacement response can be divided into three zones: a free vibration zone, a transition zone, and a contact vibration zone. Phase trajectory, phase shift, transition time, pseudo stable amplitude, and frequency changes are then analyzed from the dynamic displacement responses that are obtained. Finally, experiments are carried out on a real AFM system to support the findings of the simulations. © 2015 Wiley Periodicals, Inc.

  7. Decision Makers Use Norms, Not Cost-Benefit Analysis, When Choosing to Conceal or Reveal Unfair Rewards

    PubMed Central

    Heimann, Marco; Girotto, Vittorio; Legrenzi, Paolo; Bonnefon, Jean-François

    2013-01-01

    We introduce the Conceal or Reveal Dilemma, in which individuals receive unfair benefits, and must decide whether to conceal or to reveal this unfair advantage. This dilemma has two important characteristics: it does not lend itself easily to cost-benefit analysis, neither to the application of any strong universal norm. As a consequence, it is ideally suited to the study of interindividual and intercultural variations in moral-economic norms. In this paper we focus on interindividual variations, and we report four studies showing that individuals cannot be swayed by financial incentives to conceal or to reveal, and follow instead fixed, idiosyncratic strategies. We discuss how this result can be extended to individual and cultural variations in the tendency to display or to hide unfair rewards. PMID:24066040

  8. Decision makers use norms, not cost-benefit analysis, when choosing to conceal or reveal unfair rewards.

    PubMed

    Heimann, Marco; Girotto, Vittorio; Legrenzi, Paolo; Bonnefon, Jean-François

    2013-01-01

    We introduce the Conceal or Reveal Dilemma, in which individuals receive unfair benefits, and must decide whether to conceal or to reveal this unfair advantage. This dilemma has two important characteristics: it does not lend itself easily to cost-benefit analysis, neither to the application of any strong universal norm. As a consequence, it is ideally suited to the study of interindividual and intercultural variations in moral-economic norms. In this paper we focus on interindividual variations, and we report four studies showing that individuals cannot be swayed by financial incentives to conceal or to reveal, and follow instead fixed, idiosyncratic strategies. We discuss how this result can be extended to individual and cultural variations in the tendency to display or to hide unfair rewards.

  9. Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

    PubMed

    Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

    2017-05-12

    Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

  10. Passive microrheology of soft materials with atomic force microscopy: A wavelet-based spectral analysis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martinez-Torres, C.; Streppa, L.; Arneodo, A.

    2016-01-18

    Compared to active microrheology where a known force or modulation is periodically imposed to a soft material, passive microrheology relies on the spectral analysis of the spontaneous motion of tracers inherent or external to the material. Passive microrheology studies of soft or living materials with atomic force microscopy (AFM) cantilever tips are rather rare because, in the spectral densities, the rheological response of the materials is hardly distinguishable from other sources of random or periodic perturbations. To circumvent this difficulty, we propose here a wavelet-based decomposition of AFM cantilever tip fluctuations and we show that when applying this multi-scale methodmore » to soft polymer layers and to living myoblasts, the structural damping exponents of these soft materials can be retrieved.« less

  11. In situ AFM investigation of slow crack propagation mechanisms in a glassy polymer

    NASA Astrophysics Data System (ADS)

    George, M.; Nziakou, Y.; Goerke, S.; Genix, A.-C.; Bresson, B.; Roux, S.; Delacroix, H.; Halary, J.-L.; Ciccotti, M.

    2018-03-01

    A novel experimental technique based on in situ AFM monitoring of the mechanisms of damage and the strain fields associated to the slow steady-state propagation of a fracture in glassy polymers is presented. This micron-scale investigation is complemented by optical measurements of the sample deformation up to the millimetric macroscopic scale of the sample in order to assess the proper crack driving conditions. These multi-scale observations provide important insights towards the modeling of the fracture toughness of glassy polymers and its relationship with the macromolecular structure and non-linear rheological properties. This novel technique is first tested on a standard PMMA thermoplastic in order to both evaluate its performance and the richness of this new kind of observations. Although the fracture propagation in PMMA is well known to proceed through crazing in the bulk of the samples, our observations provide a clear description and quantitative evaluation of a change of fracture mechanism towards shear yielding fracture accompanied by local necking close to the free surface of the sample, which can be explained by the local change of stress triaxiality. Moreover, this primary surface necking mechanism is shown to be accompanied by a network of secondary grooves that can be related to surface crazes propagating towards the interior of the sample. This overall scenario is validated by post-mortem fractographic investigations by scanning electron microscopy.

  12. Survival analysis of timing of first marriage among women of reproductive age in Nigeria: regional differences.

    PubMed

    Adebowale, Stephen A; Fagbamigbe, Francis A; Okareh, Titus O; Lawal, Ganiyu O

    2012-12-01

    Early marriage is common among women in developing countries. Age at first marriage (AFM) has health implication on women and their under-five children. In Nigeria, few studies have explored AFM; the current study was designed to fill the gap. Nigeria Demographic and Health Survey, 2008 dataset on married women aged 15-49 (N = 24,986) was used. Chi-square, OLS regression and Cox proportional hazard models were used in the analysis. The mean AFM was 17.8 +/- 4.8 years and significant difference existed between the mean AFM of women in the North (16.0 +/- 3.6) and South (20.4 +/- 5.0) (p < 0.001). Region, education, religion, residence, nutritional status, age at first sexual intercourse and children ever born were significantly associated with timing of first marriage (p < 0.001). Majority of the women married between ages 15-19 years (43.1%), while very few married late (2.3%) and about 27.0% married too early (less than 15 years). Early marriage was more common in all the regions in the North than the South and the hazard was highest in the North West and North East. Women who reside in rural area (H.R = 1.15; C.I = 1.11-1.18) married early than their counterparts in the urban area. Age at first marriage was directly related to levels of education (p < 0.001). Muslim women married early (H.R = 1.34; C.I = 1.29-1.39) than Christians. Three models were generated from the data. Women married too early in Nigeria with Teenage marriage more common in the North than the South. Education has influence on AFM; therefore, women should have at least secondary education before marriage in Nigeria.

  13. Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

    PubMed Central

    Bianco, Giuseppe; Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia; Pigolotti, Simone

    2014-01-01

    Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs. PMID:24789560

  14. Stripe Antiferromagnetic Spin Fluctuations in SrCo 2As 2

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jayasekara, Wageesha; Lee, Young-Jin; Pandey, Abhishek

    Inelastic neutron scattering measurements of paramagnetic SrCo 2As 2 at T = 5 K reveal antiferromagnetic (AFM) spin fluctuations that are peaked at a wave vector of Q AFM = (1/2, 1/2, 1) and possess a large energy scale. These stripe spin fluctuations are similar to those found in AFe 2As 2 compounds, where spin-density wave AFM is driven by Fermi surface nesting between electron and hole pockets separated by Q AFM. SrCo 2As 2 has a more complex Fermi surface and band-structure calculations indicate a potential instability toward either a ferromagnetic or stripe AFM ground state. The results suggestmore » that stripe AFM magnetism is a general feature of both iron and cobalt-based arsenides and the search for spin fluctuation-induced unconventional superconductivity should be expanded to include cobalt-based compounds.« less

  15. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    PubMed Central

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  16. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    PubMed

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  17. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    PubMed

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Analyzing the vibrational response of an AFM cantilever in liquid with the consideration of tip mass by comparing the hydrodynamic and contact repulsive force models in higher modes

    NASA Astrophysics Data System (ADS)

    Korayem, Moharam Habibnejad; Nahavandi, Amir

    2017-04-01

    This paper investigates the vibration of a tapping-mode Atomic Force Microscope (AFM) cantilever covered with two whole piezoelectric layers in a liquid medium. The authors of this article have already modeled the vibration of a cantilever immersed in liquid over rough surfaces. Five new ideas have been considered for improving the results of the previous work. Mass and damping of a cantilever probe tip have been considered. Since the probe tip of an AFM cantilever has a mass, which can itself affect the natural frequency of vibration, the significance of this mass has been explored. Also, two hydrodynamic force models for analyzing the mass and damping added to a cantilever in liquid medium have been evaluated. In modeling the vibration of a cantilever in liquid, simplifications are made to the theoretical equations used in the modeling, which may make the obtained results different from those in the real case. So, two hydrodynamic force models are introduced and compared with each other. In addition to the already introduced DMT model, the JKR model has been proposed. The forces acting on a probe tip have attractive and repulsive effects. The attractive Van der Waals force can vary depending on the surface smoothness or roughness, and the repulsive contact force, which is independent of the type of surface roughness and usually varies with the hardness or softness of a surface. When the first mode is used in the vibration of an AFM cantilever, the changes of the existing physical parameters in the simulation do not usually produce a significant difference in the response. Thus, three cantilever vibration modes have been investigated. Finally, an analytical approach for obtaining the response of equations is presented which solves the resulting motion equation by the Laplace method and, thus, a time function is obtained for cantilever deflection is determined. Also, using the COMSOL software to model a cantilever in a liquid medium, the computed natural

  19. Micromorphological characterization of zinc/silver particle composite coatings

    PubMed Central

    Méndez, Alia; Reyes, Yolanda; Trejo, Gabriel; StĘpień, Krzysztof

    2015-01-01

    ABSTRACT The aim of this study was to evaluate the three‐dimensional (3D) surface micromorphology of zinc/silver particles (Zn/AgPs) composite coatings with antibacterial activity prepared using an electrodeposition technique. These 3D nanostructures were investigated over square areas of 5 μm × 5 μm by atomic force microscopy (AFM), fractal, and wavelet analysis. The fractal analysis of 3D surface roughness revealed that (Zn/AgPs) composite coatings have fractal geometry. Triangulation method, based on the linear interpolation type, applied for AFM data was employed in order to characterise the surfaces topographically (in amplitude, spatial distribution and pattern of surface characteristics). The surface fractal dimension D f, as well as height values distribution have been determined for the 3D nanostructure surfaces. Microsc. Res. Tech. 78:1082–1089, 2015. © 2015 The Authors published by Wiley Periodicals, Inc. PMID:26500164

  20. Selective depression of titanaugite in the ilmenite flotation with carboxymethyl starch

    NASA Astrophysics Data System (ADS)

    Meng, Qingyou; Yuan, Zhitao; Yu, Li; Xu, Yuankai; Du, Yusheng; Zhang, Chen

    2018-05-01

    In order to intensify the flotation separation of ilmenite from titanaugite, surface modification of mineral particles was carried out using carboxymethyl starch (CMS) by microflotation experiments, zeta potential measurements, Fourier transform infrared (FTIR) and atomic force microscopy (AFM) analysis. Microflotation results showed that CMS was a selective depressant, and it effectively enhanced the floatability difference between ilmenite and titanaugite in the pH range from 6.0 to 10.0. As it was revealed by the zeta potential, FTIR and AFM analysis, the CMS adsorption occurred onto mineral surfaces through chemisorption and hydrogen bonding, while CMS exhibited a stronger interaction with titanaugite than ilmenite. After that, the CMS adsorption impeded the adsorption of sodium oleate collector on titanaugite surfaces, giving rise to a concomitant decrease in the floatability of titanaugite. These findings exhibit great potential for CMS application in the selective flotation of ilmenite.

  1. High resolution imaging of latent fingerprints by localized corrosion on brass surfaces.

    PubMed

    Goddard, Alex J; Hillman, A Robert; Bond, John W

    2010-01-01

    The Atomic Force Microscope (AFM) is capable of imaging fingerprint ridges on polished brass substrates at an unprecedented level of detail. While exposure to elevated humidity at ambient or slightly raised temperatures does not change the image appreciably, subsequent brief heating in a flame results in complete loss of the sweat deposit and the appearance of pits and trenches. Localized elemental analysis (using EDAX, coupled with SEM imaging) shows the presence of the constituents of salt in the initial deposits. Together with water and atmospheric oxygen--and with thermal enhancement--these are capable of driving a surface corrosion process. This process is sufficiently localized that it has the potential to generate a durable negative topographical image of the fingerprint. AFM examination of surface regions between ridges revealed small deposits (probably microscopic "spatter" of sweat components or transferred particulates) that may ultimately limit the level of ridge detail analysis.

  2. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    PubMed

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  3. BOREAS AFM-08 ECMWF Hourly Surface and Upper Air Data for the SSA and NSA

    NASA Technical Reports Server (NTRS)

    Viterbo, Pedro; Betts, Alan; Hall, Forrest G. (Editor); Newcomer, Jeffrey A.; Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-8 team focused on modeling efforts to improve the understanding of the diurnal evolution of the convective boundary layer over the boreal forest. This data set contains hourly data from the European Center for for Medium-Range Weather Forecasts (ECMWF) operational model from below the surface to the top of the atmosphere, including the model fluxes at the surface. Spatially, the data cover a pair of the points that enclose the rawinsonde sites at Candle Lake, Saskatchewan, in the Southern Study Area (SSA) and Thompson, Manitoba, in the Northern Study Area (NSA). Temporally, the data include the two time periods of 13 May 1994 to 30 Sept 1994 and 01 Mar 1996 to 31 Mar 1997. The data are stored in tabular ASCII files. The number of records in the upper air data files may exceed 20,000, causing a problem for some software packages. The ECMWF hourly surface and upper air 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).

  4. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells

    PubMed Central

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-01-01

    The ‘neural plate border’ of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure. DOI: http://dx.doi.org/10.7554/eLife.21620.001 PMID:28355135

  5. A Unique Self-Sensing, Self-Actuating AFM Probe at Higher Eigenmodes

    PubMed Central

    Wu, Zhichao; Guo, Tong; Tao, Ran; Liu, Leihua; Chen, Jinping; Fu, Xing; Hu, Xiaotang

    2015-01-01

    With its unique structure, the Akiyama probe is a type of tuning fork atomic force microscope probe. The long, soft cantilever makes it possible to measure soft samples in tapping mode. In this article, some characteristics of the probe at its second eigenmode are revealed by use of finite element analysis (FEA) and experiments in a standard atmosphere. Although the signal-to-noise ratio in this environment is not good enough, the 2 nm resolution and 0.09 Hz/nm sensitivity prove that the Akiyama probe can be used at its second eigenmode under FM non-contact mode or low amplitude FM tapping mode, which means that it is easy to change the measuring method from normal tapping to small amplitude tapping or non-contact mode with the same probe and equipment. PMID:26580619

  6. Observation of molecular level behavior in molecular electronic junction device

    NASA Astrophysics Data System (ADS)

    Maitani, Masato

    In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs

  7. Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus.

    PubMed

    Guan, Tian-Pei; Teng, Jade L L; Yeong, Kai-Yan; You, Zhang-Qiang; Liu, Hao; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

    2018-06-07

    The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Analysis of correlations between the placental expression of glucose transporters GLUT-1, GLUT-4 and GLUT-9 and selected maternal and fetal parameters in pregnancies complicated by diabetes mellitus.

    PubMed

    Stanirowski, Paweł Jan; Szukiewicz, Dariusz; Pyzlak, Michał; Abdalla, Nabil; Sawicki, Włodzimierz; Cendrowski, Krzysztof

    2017-10-16

    The aim of the study was to analyze the correlations between the expression of glucose transporters GLUT-1, GLUT-4, and GLUT-9 in human term placenta and selected maternal and fetal parameters in pregnancies complicated by diabetes mellitus (DM). Placental samples were obtained from healthy control (n = 25) and diabetic pregnancies, including diet-controlled gestational diabetes mellitus (GDMG1) (n = 16), insulin-controlled gestational diabetes mellitus (GDMG2) (n = 6), and pregestational DM (PGDM) (n = 6). Computer-assisted quantitative morphometry of stained placental sections was performed to determine the expression of selected glucose transporter proteins. For the purposes of correlation analysis, the following parameters were selected: type of diabetes, gestational age, maternal prepregnancy body mass index (BMI), gestational weight gain, third trimester glycated hemoglobin concentration, placental weight, fetal birth weight (FBW) as well as ultrasonographic indicators of fetal adiposity, including subscapular (SSFM), abdominal (AFM), and midthigh (MTFM) fat mass measurements. In the PGDM group, the analysis demonstrated positive correlations between the placental expression of GLUT-1, GLUT-4, and GLUT-9 and FBW, AFM, and SSFM measurements (p < .05). Similarly in the GDMG2 patients positive correlations between GLUT-4 expression, FBW and SSFM were observed (p < .05). In the multivariate regression analysis, only the type of diabetes and FBW were significantly associated with GLUTs expression (p < .001). In addition, maternal prepregnancy BMI significantly contributed to GLUT-1 expression (p < .001). The study results revealed that placental expression of GLUT-1, GLUT-4, and GLUT-9 may be involved in the intensification of the fetal growth in pregnancies complicated by GDM/PGDM.

  9. Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus.

    PubMed

    Vecsey, Christopher G; Peixoto, Lucia; Choi, Jennifer H K; Wimmer, Mathieu; Jaganath, Devan; Hernandez, Pepe J; Blackwell, Jennifer; Meda, Karuna; Park, Alan J; Hannenhalli, Sridhar; Abel, Ted

    2012-10-17

    Sleep deprivation is a common problem of considerable health and economic impact in today's society. Sleep loss is associated with deleterious effects on cognitive functions such as memory and has a high comorbidity with many neurodegenerative and neuropsychiatric disorders. Therefore, it is crucial to understand the molecular basis of the effect of sleep deprivation in the brain. In this study, we combined genome-wide and traditional molecular biological approaches to determine the cellular and molecular impacts of sleep deprivation in the mouse hippocampus, a brain area crucial for many forms of memory. Microarray analysis examining the effects of 5 h of sleep deprivation on gene expression in the mouse hippocampus found 533 genes with altered expression. Bioinformatic analysis revealed that a prominent effect of sleep deprivation was to downregulate translation, potentially mediated through components of the insulin signaling pathway such as the mammalian target of rapamycin (mTOR), a key regulator of protein synthesis. Consistent with this analysis, sleep deprivation reduced levels of total and phosphorylated mTOR, and levels returned to baseline after 2.5 h of recovery sleep. Our findings represent the first genome-wide analysis of the effects of sleep deprivation on the mouse hippocampus, and they suggest that the detrimental effects of sleep deprivation may be mediated by reductions in protein synthesis via downregulation of mTOR. Because protein synthesis and mTOR activation are required for long-term memory formation, our study improves our understanding of the molecular mechanisms underlying the memory impairments induced by sleep deprivation.

  10. A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology

    PubMed Central

    2015-01-01

    Background Recently, a wide range of diseases have been associated with changes in DNA methylation levels, which play a vital role in gene expression regulation. With ongoing developments in technology, attempts to understand disease mechanism have benefited greatly from epigenetics and transcriptomics studies. In this work, we have used expression and methylation data of thyroid carcinoma as a case study and explored how to optimally incorporate expression and methylation information into the disease study when both data are available. Moreover, we have also investigated whether there are important post-translational modifiers which could drive critical insights on thyroid cancer genetics. Results In this study, we have conducted a threshold analysis for varying methylation levels to identify whether setting a methylation level threshold increases the performance of functional enrichment. Moreover, in order to decide on best-performing analysis strategy, we have performed data integration analysis including comparison of 10 different analysis strategies. As a result, combining methylation with expression and using genes with more than 15% methylation change led to optimal detection rate of thyroid-cancer associated pathways in top 20 functional enrichment results. Furthermore, pooling the data from different experiments increased analysis confidence by improving the data range. Consequently, we have identified 207 transcription factors and 245 post-translational modifiers with more than 15% methylation change which may be important in understanding underlying mechanisms of thyroid cancer. Conclusion While only expression or only methylation information would not reveal both primary and secondary mechanisms involved in disease state, combining expression and methylation led to a better detection of thyroid cancer-related genes and pathways that are found in the recent literature. Moreover, focusing on genes that have certain level of methylation change improved the

  11. Impact of helical organization on the photovoltaic properties of oligothiophene supramolecular polymers† †Electronic supplementary information (ESI) available: Synthesis and characterization of 3 and 4, UV-vis spectra, solar cell device properties and AFM images. See DOI: 10.1039/c7sc05093c

    PubMed Central

    Ouchi, Hayato; Kizaki, Takahiro; Yamato, Masaki; Lin, Xu; Hoshi, Nagahiro; Silly, Fabien; Kajitani, Takashi; Fukushima, Takanori

    2018-01-01

    Helical self-assembly of functional π-conjugated molecules offers unique photochemical and electronic properties in the spectroscopic level, but there are only a few examples that demonstrate their positive impact on the optoelectronic device level. Here, we demonstrate that hydrogen-bonded tapelike supramolecular polymers of a barbiturated oligo(alkylthiophene) show notable improvement in their photovoltaic properties upon organizing into helical nanofibers. A tapelike hydrogen-bonded supramolecular array of barbiturated oligo(butylthiophene) molecules was directly visualized by STM at a liquid–solid interface. TEM, AFM and XRD revealed that the tapelike supramolecular polymers further organize into helical nanofibers in solution and bulk states. Bulk heterojunction solar cells of the helical nanofibers and soluble fullerene showed a power conversion efficiency of 4.5%, which is markedly high compared to that of the regioisomer of butyl chains organizing into 3D lamellar agglomerates. PMID:29780493

  12. Combined Analysis of the Fruit Metabolome and Transcriptome Reveals Candidate Genes Involved in Flavonoid Biosynthesis in Actinidia arguta.

    PubMed

    Li, Yukuo; Fang, Jinbao; Qi, Xiujuan; Lin, Miaomiao; Zhong, Yunpeng; Sun, Leiming; Cui, Wen

    2018-05-15

    To assess the interrelation between the change of metabolites and the change of fruit color, we performed a combined metabolome and transcriptome analysis of the flesh in two different Actinidia arguta cultivars: "HB" ("Hongbaoshixing") and "YF" ("Yongfengyihao") at two different fruit developmental stages: 70d (days after full bloom) and 100d (days after full bloom). Metabolite and transcript profiling was obtained by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. The identification and quantification results of metabolites showed that a total of 28,837 metabolites had been obtained, of which 13,715 were annotated. In comparison of HB100 vs. HB70, 41 metabolites were identified as being flavonoids, 7 of which, with significant difference, were identified as bracteatin, luteolin, dihydromyricetin, cyanidin, pelargonidin, delphinidin and (-)-epigallocatechin. Association analysis between metabolome and transcriptome revealed that there were two metabolic pathways presenting significant differences during fruit development, one of which was flavonoid biosynthesis, in which 14 structural genes were selected to conduct expression analysis, as well as 5 transcription factor genes obtained by transcriptome analysis. RT-qPCR results and cluster analysis revealed that AaF3H , AaLDOX , AaUFGT , AaMYB , AabHLH , and AaHB2 showed the best possibility of being candidate genes. A regulatory network of flavonoid biosynthesis was established to illustrate differentially expressed candidate genes involved in accumulation of metabolites with significant differences, inducing red coloring during fruit development. Such a regulatory network linking genes and flavonoids revealed a system involved in the pigmentation of all-red-fleshed and all-green-fleshed A. arguta , suggesting this conjunct analysis approach is not only useful in understanding the relationship between genotype and phenotype

  13. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

    PubMed Central

    Förster, Frank; Beisser, Daniela; Grohme, Markus A.; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C.; Shkumatov, Alexander V.; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. PMID:22563243

  14. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.

    PubMed

    Förster, Frank; Beisser, Daniela; Grohme, Markus A; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C; Shkumatov, Alexander V; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.

  15. Dependency Network Analysis (DEPNA) Reveals Context Related Influence of Brain Network Nodes

    PubMed Central

    Jacob, Yael; Winetraub, Yonatan; Raz, Gal; Ben-Simon, Eti; Okon-Singer, Hadas; Rosenberg-Katz, Keren; Hendler, Talma; Ben-Jacob, Eshel

    2016-01-01

    Communication between and within brain regions is essential for information processing within functional networks. The current methods to determine the influence of one region on another are either based on temporal resolution, or require a predefined model for the connectivity direction. However these requirements are not always achieved, especially in fMRI studies, which have poor temporal resolution. We thus propose a new graph theory approach that focuses on the correlation influence between selected brain regions, entitled Dependency Network Analysis (DEPNA). Partial correlations are used to quantify the level of influence of each node during task performance. As a proof of concept, we conducted the DEPNA on simulated datasets and on two empirical motor and working memory fMRI tasks. The simulations revealed that the DEPNA correctly captures the network’s hierarchy of influence. Applying DEPNA to the functional tasks reveals the dynamics between specific nodes as would be expected from prior knowledge. To conclude, we demonstrate that DEPNA can capture the most influencing nodes in the network, as they emerge during specific cognitive processes. This ability opens a new horizon for example in delineating critical nodes for specific clinical interventions. PMID:27271458

  16. Phenotypic analysis of prostate-infiltrating lymphocytes reveals TH17 and Treg skewing.

    PubMed

    Sfanos, Karen Sandell; Bruno, Tullia C; Maris, Charles H; Xu, Lauren; Thoburn, Christopher J; DeMarzo, Angelo M; Meeker, Alan K; Isaacs, William B; Drake, Charles G

    2008-06-01

    Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. CD4+ PIL showed a paucity of TH2 (interleukin-4-secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating T(reg) revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer.

  17. Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.

    PubMed

    Nakashima, Yu; Egami, Yoko; Kimura, Miki; Wakimoto, Toshiyuki; Abe, Ikuro

    2016-01-01

    Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.

  18. Applying AFM-based nanofabrication for measuring the thickness of nanopatterns: the role of head groups in the vertical self-assembly of omega-functionalized n-alkanethiols.

    PubMed

    Kelley, Algernon T; Ngunjiri, Johnpeter N; Serem, Wilson K; Lawrence, Steve O; Yu, Jing-Jiang; Crowe, William E; Garno, Jayne C

    2010-03-02

    Molecules of n-alkanethiols with methyl head groups typically form well-ordered monolayers during solution self-assembly for a wide range of experimental conditions. However, we have consistently observed that, for either carboxylic acid or thiol-terminated n-alkanethiols, under certain conditions nanografted patterns are generated with a thickness corresponding precisely to a double layer. To investigate the role of head groups for solution self-assembly, designed patterns of omega-functionalized n-alkanethiols were nanografted with systematic changes in concentration. Nanografting is an in situ approach for writing patterns of thiolated molecules on gold surfaces by scanning with an AFM tip under high force, accomplished in dilute solutions of desired ink molecules. As the tip is scanned across the surface of a self-assembled monolayer under force, the matrix molecules are displaced from the surface and are immediately replaced with fresh molecules from solution to generate nanopatterns. In this report, side-by-side comparison of nanografted patterns is achieved for different matrix molecules using AFM images. The chain length and head groups (i.e., carboxyl, hydroxyl, methyl, thiol) were varied for the nanopatterns and matrix monolayers. Interactions such as head-to-head dimerization affect the vertical self-assembly of omega-functionalized n-alkanethiol molecules within nanografted patterns. At certain threshold concentrations, double layers were observed to form when nanografting with head groups of carboxylic acid and dithiols, whereas single layers were generated exclusively for nanografted patterns with methyl and hydroxyl groups, regardless of changes in concentration.

  19. Needs and workflow assessment prior to implementation of a digital pathology infrastructure for the US Air Force Medical Service

    PubMed Central

    Ho, Jonhan; Aridor, Orly; Glinski, David W.; Saylor, Christopher D.; Pelletier, Joseph P.; Selby, Dale M.; Davis, Steven W.; Lancia, Nicholas; Gerlach, Christopher B.; Newberry, Jonathan; Anthony, Leslie; Pantanowitz, Liron; Parwani, Anil V.

    2013-01-01

    inquiry method helped reveal similarities and key differences with civilian pathologists. Such an analysis helped identify specific instances that would benefit from implementing digital pathology in a military environment. Employing digital pathology to facilitate workload distribution, secondary consultations, and quality assurance (over-reads) could help the AFMS deliver more accurate, efficient, and timely AP services at a global level. PMID:24392246

  20. 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

  1. The structure of [MnIII6 CrIII]3+ single-molecule magnets deposited in submono-layers and monolayers on surfaces studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin Probe Force Microscopy in UHV

    NASA Astrophysics Data System (ADS)

    Heinzmann, U.; Gryzia, A.; Volkmann, T.; Brechling, A.; Hoeke, V.; Glaser, T.

    2014-04-01

    Single molecule magnets (SMM) deposited in submonolayers and monolayers have been analyzed with respect to their structures by means of non-contact AFM (topographic as well as damping mode) and Kelvin Probe Force Microscopy with molecular resolution.

  2. Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.

    PubMed

    Lygirou, Vasiliki; Latosinska, Agnieszka; Makridakis, Manousos; Mullen, William; Delles, Christian; Schanstra, Joost P; Zoidakis, Jerome; Pieske, Burkert; Mischak, Harald; Vlahou, Antonia

    2018-04-17

    Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related

  3. Analysis of the Transcriptional Differences between Indigenous and Invasive Whiteflies Reveals Possible Mechanisms of Whitefly Invasion

    PubMed Central

    Wang, Yong-Liang; Wang, Yu-Jun; Luan, Jun-Bo; Yan, Gen-Hong; Liu, Shu-Sheng; Wang, Xiao-Wei

    2013-01-01

    Background The whitefly Bemisa tabaci is a species complex of more than 31 cryptic species which include some of the most destructive invasive pests of crops worldwide. Among them, Middle East-Asia Minor 1 (MEAM1) and Mediterranean have invaded many countries and displaced the native whitefly species. The successful invasion of the two species is largely due to their wide range of host plants, high resistance to insecticides and remarkable tolerance to environmental stresses. However, the molecular differences between invasive and indigenous whiteflies remain largely unknown. Methodology/Principal Findings Here the global transcriptional difference between the two invasive whitefly species (MEAM1, MED) and one indigenous whitefly species (Asia II 3) were analyzed using the Illumina sequencing. Our analysis indicated that 2,422 genes between MEAM1 and MED; 3,073 genes between MEAM1 and Asia II 3; and 3,644 genes between MED and Asia II 3 were differentially expressed. Gene Ontology enrichment analysis revealed that the differently expressed genes between the invasive and indigenous whiteflies were significantly enriched in the term of ‘oxidoreductase activity’. Pathway enrichment analysis showed that carbohydrate, amino acid and glycerolipid metabolisms were more active in MEAM1 and MED than in Asia II 3, which may contribute to their differences in biological characteristics. Our analysis also illustrated that the majority of genes involved in ‘drug metabolic pathway’ were expressed at a higher level in MEAM1 and MED than in Asia II 3. Taken together, these results revealed that the genes related to basic metabolism and detoxification were expressed at an elevated level in the invasive whiteflies, which might be responsible for their higher resistance to insecticides and environmental stresses. Conclusions/Significance The extensive comparison of MEAM1, MED and Asia II 3 gene expression may serve as an invaluable resource for revealing the molecular

  4. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    PubMed

    Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

    2016-10-07

    Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

  5. Fundamental aspects of electric double layer force-distance measurements at liquid-solid interfaces using atomic force microscopy

    PubMed Central

    Black, Jennifer M.; Zhu, Mengyang; Zhang, Pengfei; Unocic, Raymond R.; Guo, Daqiang; Okatan, M. Baris; Dai, Sheng; Cummings, Peter T.; Kalinin, Sergei V.; Feng, Guang; Balke, Nina

    2016-01-01

    Atomic force microscopy (AFM) force-distance measurements are used to investigate the layered ion structure of Ionic Liquids (ILs) at the mica surface. The effects of various tip properties on the measured force profiles are examined and reveal that the measured ion position is independent of tip properties, while the tip radius affects the forces required to break through the ion layers as well as the adhesion force. Force data is collected for different ILs and directly compared with interfacial ion density profiles predicted by molecular dynamics. Through this comparison it is concluded that AFM force measurements are sensitive to the position of the ion with the larger volume and mass, suggesting that ion selectivity in force-distance measurements are related to excluded volume effects and not to electrostatic or chemical interactions between ions and AFM tip. The comparison also revealed that at distances greater than 1 nm the system maintains overall electroneutrality between the AFM tip and sample, while at smaller distances other forces (e.g., van der waals interactions) dominate and electroneutrality is no longer maintained. PMID:27587276

  6. Colloid-probe AFM studies of the interaction forces of proteins adsorbed on colloidal crystals.

    PubMed

    Singh, Gurvinder; Bremmell, Kristen E; Griesser, Hans J; Kingshott, Peter

    2015-04-28

    In recent years, colloid-probe AFM has been used to measure the direct interaction forces between colloidal particles of different size or surface functionality in aqueous media, as one can study different forces in symmerical systems (i.e., sphere-sphere geometry). The present study investigates the interaction between protein coatings on colloid probes and hydrophilic surfaces decorated with hexagonally close packed single particle layers that are either uncoated or coated with proteins. Controlled solvent evaporation from aqueous suspensions of colloidal particles (coated with or without lysozyme and albumin) produces single layers of close-packed colloidal crystals over large areas on a solid support. The measurements have been carried out in an aqueous medium at different salt concentrations and pH values. The results show changes in the interaction forces as the surface charge of the unmodified or modified particles, and ionic strength or pH of the solution is altered. At high ionic strength or pH, electrostatic interactions are screened, and a strong repulsive force at short separation below 5 nm dominates, suggesting structural changes in the absorbed protein layer on the particles. We also study the force of adhesion, which decreases with an increment in the salt concentration, and the interaction between two different proteins indicating a repulsive interaction on approach and adhesion on retraction.

  7. A Rasch analysis of the Brief Pain Inventory Interference subscale reveals three dimensions and an age bias.

    PubMed

    Walton, David M; Beattie, Tyler; Putos, Joseph; MacDermid, Joy C

    2016-06-01

    The Brief Pain Inventory is composed of two quantifiable scales: pain severity and pain interference. The reported factor structure of the interference subscale is not consistent in the extant literature, with no clear choice between a single- or two-factor structure. Here, we report on the results of Rasch-based analysis of the interference subscale using a large population-based ambulatory patient database (the Quebec Pain Registry). Observational cohort. A total of 1,000 responses were randomly drawn from a total database of 5,654 for this analysis. Both the original 7-item and an expanded 10-item version (Tyler 2002) of the interference subscale were evaluated. Rasch analysis revealed significant misfit of both versions of the scale, with the original 7-item version outperforming the expanded 10-item version. Analysis of dimensionality revealed that both versions showed improved model fit when considered two subscales (affective and physical interference) with the item on sleep interference removed or considered separately. Additionally, significant uniform differential item functioning was identified for 6 of the 7 original items when the sample was stratified by age above or below 55 years. The interference subscale achieved adequate model fit when considered as two separate subscales with age as a mediator of response, while interpreting the sleep interference item separately. A transformation matrix revealed that in all cases, ordinal-level change at the extreme ends of the scale appears to be more meaningful than does a similar change at the midpoints. The Interference subscale of the BPI should be interpreted as two separate subscales (Affective Interference, Physical Interference) with the sleep item removed or interpreted separately for optimal fit to the Rasch model. Implications for research and clinical use are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Multiple heavy metal removal using an entomopathogenic fungi Beauveria bassiana.

    PubMed

    Gola, Deepak; Dey, Priyadarshini; Bhattacharya, Arghya; Mishra, Abhishek; Malik, Anushree; Namburath, Maneesh; Ahammad, Shaikh Ziauddin

    2016-10-01

    Towards the development of a potential remediation technology for multiple heavy metals [Zn(II), Cu(II), Cd(II), Cr(VI) and Ni(II)] from contaminated water, present study examined the growth kinetics and heavy metal removal ability of Beauveria bassiana in individual and multi metals. The specific growth rate of B. bassiana varied from 0.025h(-1) to 0.039h(-1) in presence of individual/multi heavy metals. FTIR analysis indicated the involvement of different surface functional groups in biosorption of different metals, while cellular changes in fungus was reflected by various microscopic (SEM, AFM and TEM) analysis. TEM studies proved removal of heavy metals via sorption and accumulation processes, whereas AFM studies revealed increase in cell surface roughness in fungal cells exposed to heavy metals. Present study delivers first report on the mechanism of bioremediation of heavy metals when present individually as well as multi metal mixture by entomopathogenic fungi. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yin, L. H., E-mail: lhyin@issp.ac.cn, E-mail: ypsun@issp.ac.cn; Yang, J.; Dai, J. M.

    We have investigated the detailed magnetic, magnetoelectric (ME), magnetodielectric (MD) and thermal expansion properties in Co{sub 4}Nb{sub 2}O{sub 9} crystal. A magnetic-field-induced spin flop was observed below antiferromagnetic (AFM) transition temperature T{sub N}. Dielectric constant at applied magnetic field nearly diverges around the AFM transition, giving rise to a colossal MD effect as high as ∼138% around T{sub N}. Theoretical analysis of the ME and MD data revealed a major contribution of critical spin fluctuation to the colossal MD effect in Co{sub 4}Nb{sub 2}O{sub 9}. These results suggest that linear ME materials with large ME coupling might be potentially usedmore » to realize large MD effect for future application.« less

  10. Ferri-magnetic order in Mn induced spinel Co3-xMnxO4 (0.1≤x≤1.0) ceramic compositions

    NASA Astrophysics Data System (ADS)

    Meena, P. L.; Sreenivas, K.; Singh, M. R.; Kumar, Ashok; Singh, S. P.; Kumar, Ravi

    2016-04-01

    We report structural and magnetic properties of spinel Co3-xMnxO4 (x=0.1-1.0) synthesized by solid state reaction technique. Rietveld refinement analysis of X-ray diffraction (XRD) data, revealed the formation of polycrystalline single phase Co3-xMnxO4 without any significant structural change in cubic crystal symmetry with Mn substitution, except change in lattice parameter. Temperature dependent magnetization data show changes in magnetic ordering temperature, indicating formation of antiferromagnetic (AFM) and ferrimagnetic (FM) phase at low Mn concentration (x≤0.3) and well-defined FM phase at high Mn concentration (x≥0.5). The isothermal magnetization records established an AFM/FM mixed phase for composition ranging 0.10.5.

  11. Phenotypic Analysis of Prostate-Infiltrating Lymphocytes Reveals TH17 and Treg Skewing

    PubMed Central

    Sfanos, Karen Sandell; Bruno, Tullia C.; Maris, Charles H.; Xu, Lauren; Thoburn, Christopher J.; DeMarzo, Angelo M.; Meeker, Alan K.; Isaacs, William B.; Drake, Charles G.

    2011-01-01

    Purpose Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. Experimental Design We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. Results CD4+ PIL showed a paucity of TH2 (interleukin-4– secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating Treg revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Conclusion Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer. PMID:18519750

  12. Latent class analysis reveals clinically relevant atopy phenotypes in 2 birth cohorts.

    PubMed

    Hose, Alexander J; Depner, Martin; Illi, Sabina; Lau, Susanne; Keil, Thomas; Wahn, Ulrich; Fuchs, Oliver; Pfefferle, Petra Ina; Schmaußer-Hechfellner, Elisabeth; Genuneit, Jon; Lauener, Roger; Karvonen, Anne M; Roduit, Caroline; Dalphin, Jean-Charles; Riedler, Josef; Pekkanen, Juha; von Mutius, Erika; Ege, Markus J

    2017-06-01

    Phenotypes of childhood-onset asthma are characterized by distinct trajectories and functional features. For atopy, definition of phenotypes during childhood is less clear. We sought to define phenotypes of atopic sensitization over the first 6 years of life using a latent class analysis (LCA) integrating 3 dimensions of atopy: allergen specificity, time course, and levels of specific IgE (sIgE). Phenotypes were defined by means of LCA in 680 children of the Multizentrische Allergiestudie (MAS) and 766 children of the Protection against allergy: Study in Rural Environments (PASTURE) birth cohorts and compared with classical nondisjunctive definitions of seasonal, perennial, and food sensitization with respect to atopic diseases and lung function. Cytokine levels were measured in the PASTURE cohort. The LCA classified predominantly by type and multiplicity of sensitization (food vs inhalant), allergen combinations, and sIgE levels. Latent classes were related to atopic disease manifestations with higher sensitivity and specificity than the classical definitions. LCA detected consistently in both cohorts a distinct group of children with severe atopy characterized by high seasonal sIgE levels and a strong propensity for asthma; hay fever; eczema; and impaired lung function, also in children without an established asthma diagnosis. Severe atopy was associated with an increased IL-5/IFN-γ ratio. A path analysis among sensitized children revealed that among all features of severe atopy, only excessive sIgE production early in life affected asthma risk. LCA revealed a set of benign, symptomatic, and severe atopy phenotypes. The severe phenotype emerged as a latent condition with signs of a dysbalanced immune response. It determined high asthma risk through excessive sIgE production and directly affected impaired lung function. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  13. Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

    PubMed

    Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

    2013-07-01

    Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Comparative transcriptome analysis of pepper (Capsicum annuum) revealed common regulons in multiple stress conditions and hormone treatments.

    PubMed

    Lee, Sanghyeob; Choi, Doil

    2013-09-01

    Global transcriptome analysis revealed common regulons for biotic/abiotic stresses, and some of these regulons encoding signaling components in both stresses were newly identified in this study. In this study, we aimed to identify plant responses to multiple stress conditions and discover the common regulons activated under a variety of stress conditions. Global transcriptome analysis revealed that salicylic acid (SA) may affect the activation of abiotic stress-responsive genes in pepper. Our data indicate that methyl jasmonate (MeJA) and ethylene (ET)-responsive genes were primarily activated by biotic stress, while abscisic acid (ABA)-responsive genes were activated under both types of stresses. We also identified differentially expressed gene (DEG) responses to specific stress conditions. Biotic stress induces more DEGs than those induced by abiotic and hormone applications. The clustering analysis using DEGs indicates that there are common regulons for biotic or abiotic stress conditions. Although SA and MeJA have an antagonistic effect on gene expression levels, SA and MeJA show a largely common regulation as compared to the regulation at the DEG expression level induced by other hormones. We also monitored the expression profiles of DEG encoding signaling components. Twenty-two percent of these were commonly expressed in both stress conditions. The importance of this study is that several genes commonly regulated by both stress conditions may have future applications for creating broadly stress-tolerant pepper plants. This study revealed that there are complex regulons in pepper plant to both biotic and abiotic stress conditions.

  15. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    PubMed Central

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  16. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2014-01-01

    Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

  17. A versatile atomic force microscope integrated with a scanning electron microscope.

    PubMed

    Kreith, J; Strunz, T; Fantner, E J; Fantner, G E; Cordill, M J

    2017-05-01

    A versatile atomic force microscope (AFM), which can be installed in a scanning electron microscope (SEM), is introduced. The flexible design of the instrument enables correlated analysis for different experimental configurations, such as AFM imaging directly after nanoindentation in vacuum. In order to demonstrate the capabilities of the specially designed AFM installed inside a SEM, slip steps emanating around nanoindents in single crystalline brass were examined. This example showcases how the combination of AFM and SEM imaging can be utilized for quantitative dislocation analysis through the measurement of the slip step heights without the hindrance of oxide formation. Finally, an in situ nanoindentation technique is introduced, illustrating the use of AFM imaging during indentation experiments to examine plastic deformation occurring under the indenter tip. The mechanical indentation data are correlated to the SEM and AFM images to estimate the number of dislocations emitted to the surface.

  18. Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis.

    PubMed

    Ulfah, Maria; Perwitasari, Dyah; Jakaria, Jakaria; Muladno, Muhammad; Farajallah, Achmad

    2017-03-01

    The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.

  19. Proteomics Analysis of Tissue Samples Reveals Changes in Mitochondrial Protein Levels in Parathyroid Hyperplasia over Adenoma

    PubMed Central

    AKPINAR, GURLER; KASAP, MURAT; CANTURK, NUH ZAFER; ZULFIGAROVA, MEHIN; ISLEK, EYLÜL ECE; GULER, SERTAC ATA; SIMSEK, TURGAY; CANTURK, ZEYNEP

    2017-01-01

    Background/Aim: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. Materials and Methods: Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. Results: The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. Conclusion: Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma. PMID:28446534

  20. Genomic analysis of Meckel–Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes

    PubMed Central

    Shaheen, Ranad; Faqeih, Eissa; Alshammari, Muneera J; Swaid, Abdulrahman; Al-Gazali, Lihadh; Mardawi, Elham; Ansari, Shinu; Sogaty, Sameera; Seidahmed, Mohammed Z; AlMotairi, Muhammed I; Farra, Chantal; Kurdi, Wesam; Al-Rasheed, Shatha; Alkuraya, Fowzan S

    2013-01-01

    Meckel–Gruber syndrome (MKS, OMIM #249000) is a multiple congenital malformation syndrome that represents the severe end of the ciliopathy phenotypic spectrum. Despite the relatively common occurrence of this syndrome among Arabs, little is known about its genetic architecture in this population. This is a series of 18 Arab families with MKS, who were evaluated clinically and studied using autozygome-guided mutation analysis and exome sequencing. We show that autozygome-guided candidate gene analysis identified the underlying mutation in the majority (n=12, 71%). Exome sequencing revealed a likely pathogenic mutation in three novel candidate MKS disease genes. These include C5orf42, Ellis–van-Creveld disease gene EVC2 and SEC8 (also known as EXOC4), which encodes an exocyst protein with an established role in ciliogenesis. This is the largest and most comprehensive genomic study on MKS in Arabs and the results, in addition to revealing genetic and allelic heterogeneity, suggest that previously reported disease genes and the novel candidates uncovered by this study account for the overwhelming majority of MKS patients in our population. PMID:23169490

  1. Determination of precursor sites for pitting corrosion of polycrystalline titanium by using different techniques

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Garfias-Mesias, L.F.; Alodan, M.; James, P.I.

    1998-06-01

    Scanning electrochemical microscopy (SECM) in ferrocyanide and bromide solutions was used to locate active sites (pitting precursors) on polycrystalline Ti where oxidation of Br{sup {minus}} and Fe(CN){sub 6}{sup 4{minus}} was possible. Analysis of the electrochemically active sites was done by using electron microscopy (SEM), energy dispersive X-ray analysis (EDX), atomic force microscopy (AFM), and in situ confocal laser scanning microscopy (CLSM). In most cases, the active sites were found to be associated with particles (inclusions) which contained mainly Al and Si; however, some other areas not associated with particles were also found to be active. Although the size of themore » inclusions was normally smaller than 20 {micro}m, as revealed by SEM and AFM imaging, in some cases larger particles were also found. Pitting corrosion tests in bromide solution at potentials above 1.5 V{sub SCE} followed by EDX analysis inside the pits and in situ CLSM observation, confirmed that most of the localized attack started in the areas where particles had been located.« less

  2. Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

    PubMed

    An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

    2017-08-01

    Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis.

    PubMed

    Kurth, Daniel; Amadio, Ariel; Ordoñez, Omar F; Albarracín, Virginia H; Gärtner, Wolfgang; Farías, María E

    2017-04-21

    Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

  4. Revealed preferences towards the appraisal of orphan drugs in Poland - multi criteria decision analysis.

    PubMed

    Kolasa, Katarzyna; Zwolinski, Krzysztof Miroslaw; Zah, Vladimir; Kaló, Zoltán; Lewandowski, Tadeusz

    2018-04-27

    A Multi Criteria Decision Analysis (MCDA) technique was adopted to reveal the preferences of the Appraisal Body of the Polish HTA agency towards orphan drugs (OMPs). There were 34 positive and 23 negative HTA recommendations out of 54 distinctive drug-indication pairs. The MCDA matrix consisted of 13 criteria, seven of which made the most impact on the HTA process. Appraisal of clinical evidence, cost of therapy, and safety considerations were the main contributors to the HTA guidance, whilst advancement of technology and manufacturing costs made the least impact. MCDA can be regarded as a valuable tool for revealing decision makers' preferences in the healthcare sector. Given that only roughly half of all criteria included in the MCDA matrix were deemed to make an impact on the HTA process, there is certainly some room for improvement with respect to the adaptation of a new approach towards the value assessment of OMPs in Poland.

  5. Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.

    PubMed

    Winata, Cecilia L; Kondrychyn, Igor; Kumar, Vibhor; Srinivasan, Kandhadayar G; Orlov, Yuriy; Ravishankar, Ashwini; Prabhakar, Shyam; Stanton, Lawrence W; Korzh, Vladimir; Mathavan, Sinnakaruppan

    2013-10-01

    Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches--ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.

  6. 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'.

  7. Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

    NASA Astrophysics Data System (ADS)

    Li, Yue; Zhang, Zhaolei

    2014-11-01

    Carcinogenesis consists of oncogenesis and metastasis, and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.

  8. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    PubMed

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  9. Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.

    PubMed

    Lamy, Philippe; Nordentoft, Iver; Birkenkamp-Demtröder, Karin; Thomsen, Mathilde Borg Houlberg; Villesen, Palle; Vang, Søren; Hedegaard, Jakob; Borre, Michael; Jensen, Jørgen Bjerggaard; Høyer, Søren; Pedersen, Jakob Skou; Ørntoft, Torben F; Dyrskjøt, Lars

    2016-10-01

    Greater knowledge concerning tumor heterogeneity and clonality is needed to determine the impact of targeted treatment in the setting of bladder cancer. In this study, we performed whole-exome, transcriptome, and deep-focused sequencing of metachronous tumors from 29 patients initially diagnosed with early-stage bladder tumors (14 with nonprogressive disease and 15 with progressive disease). Tumors from patients with progressive disease showed a higher variance of the intrapatient mutational spectrum and a higher frequency of APOBEC-related mutations. Allele-specific expression was also higher in these patients, particularly in tumor suppressor genes. Phylogenetic analysis revealed a common origin of the metachronous tumors, with a higher proportion of clonal mutations in the ancestral branch; however, 19 potential therapeutic targets were identified as both ancestral and tumor-specific alterations. Few subclones were present based on PyClone analysis. Our results illuminate tumor evolution and identify candidate therapeutic targets in bladder cancer. Cancer Res; 76(19); 5894-906. ©2016 AACR. ©2016 American Association for Cancer Research.

  10. Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum

    PubMed Central

    Cuypers, Bart; Van den Broeck, Frederik; Van Reet, Nick; Meehan, Conor J.; Cauchard, Julien; Wilkes, Jonathan M.; Claes, Filip; Goddeeris, Bruno; Birhanu, Hadush; Dujardin, Jean-Claude; Laukens, Kris; Büscher, Philippe

    2017-01-01

    Abstract Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes. In this study, we have conducted a phylogenetic analysis based on genome-wide SNP analysis comprising 56 genomes from the Trypanozoon subgenus. Our data reveal that T. equiperdum has emerged at least once in Eastern Africa and T. evansi at two independent occasions in Western Africa. The genomes within the T. equiperdum and T. evansi monophyletic clusters show extremely little variation, probably due to the clonal spread linked to the independence from tsetse flies for their transmission. PMID:28541535

  11. Gene array analysis reveals a common Runx transcriptional program controlling cell adhesion and survival

    PubMed Central

    Wotton, Sandy; Terry, Anne; Kilbey, Anna; Jenkins, Alma; Herzyk, Pawel; Cameron, Ewan; Neil, James C.

    2008-01-01

    The Runx genes play divergent roles in development and cancer, where they can act either as oncogenes or tumour suppressors. We compared the effects of ectopic Runx expression in established fibroblasts, where all three genes produce an indistinguishable phenotype entailing epithelioid morphology and increased cell survival under stress conditions. Gene array analysis revealed a strongly overlapping transcriptional signature, with no examples of opposing regulation of the same target gene. A common set of 50 highly regulated genes was identified after further filtering on regulation by inducible RUNX1-ER. This set revealed a strong bias towards genes with annotated roles in cancer and development, and a preponderance of targets encoding extracellular or surface proteins, reflecting the marked effects of Runx on cell adhesion. Furthermore, in silico prediction of resistance to glucocorticoid growth inhibition was confirmed in fibroblasts and lymphoid cells expressing ectopic Runx. The effects of fibroblast expression of common RUNX1 fusion oncoproteins (RUNX1-ETO, TEL-RUNX1, CBFB-MYH11) were also tested. While two direct Runx activation target genes were repressed (Ncam1, Rgc32), the fusion proteins appeared to disrupt regulation of down-regulated targets (Cebpd, Id2, Rgs2) rather than impose constitutive repression. These results elucidate the oncogenic potential of the Runx family and reveal novel targets for therapeutic inhibition. PMID:18560354

  12. Fibrotic-like changes in degenerate human intervertebral discs revealed by quantitative proteomic analysis.

    PubMed

    Yee, A; Lam, M P Y; Tam, V; Chan, W C W; Chu, I K; Cheah, K S E; Cheung, K M C; Chan, D

    2016-03-01

    Intervertebral disc degeneration (IDD) can lead to symptomatic conditions including sciatica and back pain. The purpose of this study is to understand the extracellular matrix (ECM) changes in disc biology through comparative proteomic analysis of degenerated and non-degenerated human intervertebral disc (IVD) tissues of different ages. Seven non-degenerated (11-46 years of age) and seven degenerated (16-53 years of age) annulus fibrosus (AF) and nucleus pulposus (NP) samples were used. Proteins were extracted using guanidine hydrochloride, separated from large proteoglycans (PGs) by caesium chloride (CsCl) density gradient ultracentrifugation, and identified using liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). For quantitative comparison, proteins were labeled with iTRAQ reagents. Collagen fibrils in the NP were assessed using scanning electron microscopy (SEM). In the AF, quantitative analysis revealed increased levels of HTRA1, COMP and CILP in degeneration when compared with samples from older individuals. Fibronectin showed increment with age and degeneration. In the NP, more CILP and CILP2 were present in degenerated samples of younger individuals. Reduced protein solubility was observed in degenerated and older non-degenerated samples correlated with an accumulation of type I collagen in the insoluble fibers. Characterization of collagen fibrils in the NP revealed smaller mean fibril diameters and decreased porosity in the degenerated samples. Our study identified distinct matrix changes associated with aging and degeneration in the intervertebral discs (IVDs). The nature of the ECM changes, together with observed decreased in solubility and changes in fibril diameter is consistent with a fibrotic-like environment. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  13. Network analysis reveals disrupted functional brain circuitry in drug-naive social anxiety disorder.

    PubMed

    Yang, Xun; Liu, Jin; Meng, Yajing; Xia, Mingrui; Cui, Zaixu; Wu, Xi; Hu, Xinyu; Zhang, Wei; Gong, Gaolang; Gong, Qiyong; Sweeney, John A; He, Yong

    2017-12-07

    Social anxiety disorder (SAD) is a common and disabling condition characterized by excessive fear and avoidance of public scrutiny. Psychoradiology studies have suggested that the emotional and behavior deficits in SAD are associated with abnormalities in regional brain function and functional connectivity. However, little is known about whether intrinsic functional brain networks in patients with SAD are topologically disrupted. Here, we collected resting-state fMRI data from 33 drug-naive patients with SAD and 32 healthy controls (HC), constructed functional networks with 34 predefined regions based on previous meta-analytic research with task-based fMRI in SAD, and performed network-based statistic and graph-theory analyses. The network-based statistic analysis revealed a single connected abnormal circuitry including the frontolimbic circuit (termed the "fear circuit", including the dorsolateral prefrontal cortex, ventral medial prefrontal cortex and insula) and posterior cingulate/occipital areas supporting perceptual processing. In this single altered network, patients with SAD had higher functional connectivity than HC. At the global level, graph-theory analysis revealed that the patients exhibited a lower normalized characteristic path length than HC, which suggests a disorder-related shift of network topology toward randomized configurations. SAD-related deficits in nodal degree, efficiency and participation coefficient were detected in the parahippocampal gyrus, posterior cingulate cortex, dorsolateral prefrontal cortex, insula and the calcarine sulcus. Aspects of abnormal connectivity were associated with anxiety symptoms. These findings highlight the aberrant topological organization of functional brain network organization in SAD, which provides insights into the neural mechanisms underlying excessive fear and avoidance of social interactions in patients with debilitating social anxiety. Copyright © 2017. Published by Elsevier Inc.

  14. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas.

    PubMed

    Beltrami, Caroline Moraes; Dos Reis, Mariana Bisarro; Barros-Filho, Mateus Camargo; Marchi, Fabio Albuquerque; Kuasne, Hellen; Pinto, Clóvis Antônio Lopes; Ambatipudi, Srikant; Herceg, Zdenko; Kowalski, Luiz Paulo; Rogatto, Silvia Regina

    2017-01-01

    Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAF V600E-positive tumors. The methylation and expression pattern of six selected genes ( ERBB3 , FGF1 , FGFR2 , GABRB2 , HMGA2 , and RDH5 ) were confirmed as altered by pyrosequencing and RT-qPCR. DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC

  15. Non-classic multiscale modeling of manipulation based on AFM, in aqueous and humid ambient

    NASA Astrophysics Data System (ADS)

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

    2018-05-01

    To achieve a precise manipulation, it is important that an accurate model consisting the size effect and environmental conditions be employed. In this paper, the non-classical multiscale modeling is developed to investigate the manipulation in a vacuum, aqueous and humid ambient. The manipulation structure is considered into two parts as a macro-field (MF) and a nano-field (NF). The governing equations of the AFM components (consist of the cantilever and tip) in the MF are derived based on the modified couple stress theory. The material length scale parameter is used to study the size effect. The fluid flow in the MF is assumed as the Couette and Creeping flows. Moreover, the NF is modeled using the molecular dynamics. The Electro-Based (ELBA) model is considered to model the ambient condition in the NF. The nanoparticle in the different conditions is taken into account to study the manipulation. The results of the manipulation indicate that the predicted deflection of the non-classical model is less than the classical one. Comparison of the nanoparticle travelled distance on substrate shows that the manipulation in the submerged condition is close to the ideal manipulation. The results of humid condition illustrate that by increasing the relative humidity (RH) the manipulation force decreases. Furthermore, Root Mean Square (RMS) as a criterion of damage demonstrates that the submerged nanoparticle has the minimum damage, however, the minimum manipulation force occurs in superlative humid ambient.

  16. Sexual dimorphic floral development in dioecious plants revealed by transcriptome, phytohormone, and DNA methylation analysis in Populus tomentosa.

    PubMed

    Song, Yuepeng; Ma, Kaifeng; Ci, Dong; Chen, Qingqing; Tian, Jiaxing; Zhang, Deqiang

    2013-12-01

    Dioecious plants have evolved sex-specific floral development mechanisms. However, the precise gene expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. Comparative transcriptome and physiological analysis allowed us to characterize sex-specific development of female and male flowers. Transcriptome analysis identified genes significantly differentially expressed between the sexes, including genes related to floral development, phytohormone synthesis and metabolism, and DNA methylation. Correlation analysis revealed a significant correlation between phytohormone signaling and gene expression, identifying specific phytohormone-responsive genes and their cis-regulatory elements. Two genes related to DNA methylation, METHYLTRANSFERASE1 (MET1) and DECREASED DNA METHYLATION 1 (DDM1), which are located in the sex determination region of Chromosome XIX, have differential expression between female and male flowers. A time-course analysis revealed that MET1 and DDM1 expression may produce different DNA methylation levels in female and male flowers. Understanding the interactions of phytohormone signaling, DNA methylation and target gene expression should lead to a better understanding of sexual differences in floral development. Thus, this study identifies a set of candidate genes for further studies of poplar sexual dimorphism and relates sex-specific floral development to physiological and epigenetic changes.

  17. Time-Resolved Study of Nanomorphology and Nanomechanic Change of Early-Stage Mineralized Electrospun Poly(lactic acid) Fiber by Scanning Electron Microscopy, Raman Spectroscopy and Atomic Force Microscopy

    PubMed Central

    Wang, Mengmeng; Cai, Yin; Zhao, Bo; Zhu, Peizhi

    2017-01-01

    In this study, scanning electron microscopy (SEM), Raman spectroscopy and high-resolution atomic force microscopy (AFM) were used to reveal the early-stage change of nanomorphology and nanomechanical properties of poly(lactic acid) (PLA) fibers in a time-resolved manner during the mineralization process. Electrospun PLA nanofibers were soaked in simulated body fluid (SBF) for different periods of time (0, 1, 3, 5, 7 and 21 days) at 10 °C, much lower than the conventional 37 °C, to simulate the slow biomineralization process. Time-resolved Raman spectroscopy analysis can confirm that apatites were deposited on PLA nanofibers after 21 days of mineralization. However, there is no significant signal change among several Raman spectra before 21 days. SEM images can reveal the mineral deposit on PLA nanofibers during the process of mineralization. In this work, for the first time, time-resolved AFM was used to monitor early-stage nanomorphology and nanomechanical changes of PLA nanofibers. The Surface Roughness and Young’s Modulus of the PLA nanofiber quantitatively increased with the time of mineralization. The electrospun PLA nanofibers with delicate porous structure could mimic the extracellular matrix (ECM) and serve as a model to study the early-stage mineralization. Tested by the mode of PLA nanofibers, we demonstrated that AFM technique could be developed as a potential diagnostic tool to monitor the early onset of pathologic mineralization of soft tissues. PMID:28817096

  18. AFM study of morphology and mechanical properties of a chimeric spider silk and bone sialoprotein protein for bone regeneration

    PubMed Central

    Gomes, Sílvia; Numata, Keiji; Leonor, Isabel B.; Mano, João F.; Reis, Rui L.; Kaplan, David L.

    2011-01-01

    Atomic force microscopy (AFM) was used to assess a new chimeric protein consisting of a fusion protein of the consensus repeat for Nephila clavipes spider dragline protein and bone sialoprotein (6mer+BSP). The elastic modulus of this protein in film form was assessed through force curves, and film surface roughness was also determined. The results showed a significant difference between the elastic modulus of the chimeric silk protein, 6mer+BSP, and control films consisting of only the silk component (6mer). The behaviour of the 6mer+BSP and 6mer proteins in aqueous solution in the presence of calcium (Ca) ions was also assessed to determine interactions between the inorganic and organic components related to bone interactions, anchoring and biomaterial network formation. The results demonstrated the formation of protein networks in the presence of Ca2+ ions, characteristics that may be important in the context of controlling materials assembly and properties related to bone-formation with this new chimeric silk-BSP protein. PMID:21370930

  19. AFM study of morphology and mechanical properties of a chimeric spider silk and bone sialoprotein protein for bone regeneration.

    PubMed

    Gomes, Sílvia; Numata, Keiji; Leonor, Isabel B; Mano, João F; Reis, Rui L; Kaplan, David L

    2011-05-09

    Atomic force microscopy (AFM) was used to assess a new chimeric protein consisting of a fusion protein of the consensus repeat for Nephila clavipes spider dragline protein and bone sialoprotein (6mer+BSP). The elastic modulus of this protein in film form was assessed through force curves, and film surface roughness was also determined. The results showed a significant difference among the elastic modulus of the chimeric silk protein, 6mer+BSP, and control films consisting of only the silk component (6mer). The behavior of the 6mer+BSP and 6mer proteins in aqueous solution in the presence of calcium (Ca) ions was also assessed to determine interactions between the inorganic and organic components related to bone interactions, anchoring, and biomaterial network formation. The results demonstrated the formation of protein networks in the presence of Ca(2+) ions, characteristics that may be important in the context of controlling materials assembly and properties related to bone formation with this new chimeric silk-BSP protein.

  20. Comparative abrasive wear resistance and surface analysis of dental resin-based materials

    PubMed Central

    Nayyer, Maleeha; Zahid, Shahreen; Hassan, Syed Hammad; Mian, Salman Aziz; Mehmood, Sana; Khan, Haroon Ahmed; Kaleem, Muhammad; Zafar, Muhammad Sohail; Khan, Abdul Samad

    2018-01-01

    Objective: The objective of this study was to assess the surface properties (microhardness and wear resistance) of various composites and compomer materials. In addition, the methodologies used for assessing wear resistance were compared. Materials and Methods: This study was conducted using restorative material (Filtek Z250, Filtek Z350, QuiXfil, SureFil SDR, and Dyract XP) to assess wear resistance. A custom-made toothbrush simulator was employed for wear testing. Before and after wear resistance, structural, surface, and physical properties were assessed using various techniques. Results: Structural changes and mass loss were observed after treatment, whereas no significant difference in terms of microhardness was observed. The correlation between atomic force microscopy (AFM) and profilometer and between wear resistance and filler volume was highly significant. The correlation between wear resistance and microhardness were insignificant. Conclusions: The AFM presented higher precision compared to optical profilometers at a nanoscale level, but both methods can be used in tandem for a more detailed and precise roughness analysis. PMID:29657526