High-sensitivity noncontact atomic force microscope/scanning tunneling microscope (nc AFM/STM) operating at subangstrom oscillation amplitudes for atomic resolution imaging and force spectroscopy

Cataloged from PDF version of article.We describe a new, highly sensitive noncontact atomic force microscope/scanning tunneling microscope (STM) operating in ultrahigh vacuum (UHV) with subangstrom oscillation amplitudes for atomic resolution imaging and force-distance spectroscopy. A novel fiber interferometer with similar to4x10(-4) A/rootHz noise level is employed to detect cantilever displacements. Subangstrom oscillation amplitude is applied to the lever at a frequency well below the resonance and changes in the oscillation amplitude due to tip-sample force interactions are measured with a lock-in amplifier. Quantitative force gradient images can be obtained simultaneously with the STM topography. Employment of subangstrom oscillation amplitudes lets us perform force-distance measurements, which reveal very short-range force interactions, consistent with the theory. Performance of the microscope is demonstrated with quantitative atomic resolution images of Si(111)(7x7) and force-distance curves showing short interaction range, all obtained with <0.25 Angstrom lever oscillation amplitude. Our technique is not limited to UHV only and operation under liquids and air is feasible. (C) 2003 American Institute of Physics

Conceptual aspects of line tensions

We analyze two representative systems containing a three-phase-contact line: a liquid lens at a fluid--fluid interface and a liquid drop in contact with a gas phase residing on a solid substrate. We discuss to which extent the decomposition of the grand canonical free energy of such systems into volume, surface, and line contributions is unique in spite of the freedom one has in positioning the Gibbs dividing interfaces. In the case of a lens it is found that the line tension is independent of arbitrary choices of the Gibbs dividing interfaces. In the case of a drop, however, one arrives at two different possible definitions of the line tension. One of them corresponds seamlessly to that applicable to the lens. The line tension defined this way turns out to be independent of choices of the Gibbs dividing interfaces. In the case of the second definition,however, the line tension does depend on the choice of the Gibbs dividing interfaces. We provide equations for the equilibrium contact angles which are form-invariant with respect to notional shifts of dividing interfaces which only change the description of the system. Conceptual consistency requires to introduce additional stiffness constants attributed to the line. We show how these constants transform as a function of the relative displacements of the dividing interfaces. The dependences of the contact angles on lens or drop volumes do not render the line tension alone but a combination of the line tension, the Tolman length, and the stiffness constants of the line.Comment: 34 pages, 9 figure

Nanoscratch Characterization of GaN Epilayers on c- and a-Axis Sapphire Substrates

In this study, we used metal organic chemical vapor deposition to form gallium nitride (GaN) epilayers on c- and a-axis sapphire substrates and then used the nanoscratch technique and atomic force microscopy (AFM) to determine the nanotribological behavior and deformation characteristics of the GaN epilayers, respectively. The AFM morphological studies revealed that pile-up phenomena occurred on both sides of the scratches formed on the GaN epilayers. It is suggested that cracking dominates in the case of GaN epilayers while ploughing during the process of scratching; the appearances of the scratched surfaces were significantly different for the GaN epilayers on the c- and a-axis sapphire substrates. In addition, compared to the c-axis substrate, we obtained higher values of the coefficient of friction (μ) and deeper penetration of the scratches on the GaN a-axis sapphire sample when we set the ramped force at 4,000 μN. This discrepancy suggests that GaN epilayers grown on c-axis sapphire have higher shear resistances than those formed on a-axis sapphire. The occurrence of pile-up events indicates that the generation and motion of individual dislocation, which we measured under the sites of critical brittle transitions of the scratch track, resulted in ductile and/or brittle properties as a result of the deformed and strain-hardened lattice structure

Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective

<p>Abstract</p> <p>Background</p> <p>Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the microbial diversity of environmental samples. However, sequence similarities do not always imply functional or evolutionary relatedness due to many factors, including unequal rates of change and convergence. Thus, relying on top BLASTN hits for phylogenetic studies may misrepresent the diversity of these constituents. Furthermore, attempts to circumvent this issue by including a large number of BLASTN hits per sequence in one tree to explore their relatedness presents other problems. For instance, the multiple sequence alignment will be poor and computationally costly if not relying on manual alignment, and it may be difficult to derive meaningful relationships from the resulting tree. Analyzing sequence relationship networks within collective BLASTN results, however, reveal sequences that are closely related despite low rank.</p> <p>Results</p> <p>We have developed a web application, Phylometrics, that relies on networks of collective BLASTN results (rather than single BLASTN hits) to facilitate the process of building phylogenetic trees in an automated, high-throughput fashion while offering novel tools to find sequences that are of significant phylogenetic interest with minimal human involvement. The application, which can be installed locally in a laboratory or hosted remotely, utilizes a simple wizard-style format to guide the user through the pipeline without necessitating a background in programming. Furthermore, Phylometrics implements an independent job queuing system that enables users to continue to use the system while jobs are run with little or no degradation in performance. </p> <p>Conclusions</p> <p>Phylometrics provides a novel data mining method to screen supplied DNA sequences and to identify sequences that are of significant phylogenetic interest using powerful analytical tools. Sequences that are identified as being similar to a number of supplied sequences may provide key insights into their functional or evolutionary relatedness. Users require the same basic computer skills as for navigating most internet applications.</p

Quantum point contact on graphite surface

The conductance through a quantum point contact created by a sharp and hard metal tip on the graphite surface has features which to our knowledge have not been encountered so far in metal contacts or in nanowires. In this paper we first investigate these features which emerge from the strongly directional bonding and electronic structure of graphite, and provide a theoretical understanding for the electronic conduction through quantum point contacts. Our study involves the molecular-dynamics simulations to reveal the variation of interlayer distances and atomic structure at the proximity of the contact that evolves by the tip pressing toward the surface. The effects of the elastic deformation on the electronic structure, state density at the Fermi level, and crystal potential are analyzed by performing self-consistent-field pseudopotential calculations within the local-density approximation. It is found that the metallicity of graphite increases under the uniaxial compressive strain perpendicular to the basal plane. The quantum point contact is modeled by a constriction with a realistic potential. The conductance is calculated by representing the current transporting states in Laue representation, and the variation of conductance with the evolution of contact is explained by taking the characteristic features of graphite into account. It is shown that the sequential puncturing of the layers characterizes the conductance.Comment: LaTeX, 11 pages, 9 figures (included), to be published in Phys. Rev. B, tentatively scheduled for 15 September 1998 (Volume 58, Number 12

Application of isothermal titration calorimetry in evaluation of protein–nanoparticle interactions

Nanoparticles (NPs) offer a number of advantages over small organic molecules for controlling protein behaviour inside the cell. Protein binding to the surface of NPs depends on their surface characteristics, composition and method of preparation (Mandal et al. in J Hazard Mater 248–249:238–245, 2013). It is important to understand the binding affinities, stoichiometries and thermodynamical parameters of NP–protein interactions in order to see which interaction will have toxic and hazardous consequences and thus to prevent it. On the other side, because proteins are on the brink of stability, they may experience interactions with some types of NPs that are strong enough to cause denaturation or significantly change their conformations with concomitant loss of their biological function. Structural changes in the protein may cause exposure of new antigenic sites, “cryptic” peptide epitopes, potentially triggering an immune response which can promote autoimmune disease (Treuel et al. in ACS Nano 8(1):503–513, 2014). Mechanistic details of protein structural changes at NP surface have still remained elusive. Understanding the formation and persistence of the protein corona is critical issue; however, there are no many analytical methods which could provide detailed information about the NP–protein interaction characteristics and about protein structural changes caused by interactions with nanoparticles. The article reviews recent studies in NP–protein interactions research and application of isothermal titration calorimetry (ITC) in this research. The study of protein structural changes upon adsorption on nanoparticle surface and application of ITC in these studies is emphasized. The data illustrate that ITC is a versatile tool for evaluation of interactions between NPs and proteins. When coupled with other analytical methods, it is important analytical tool for monitoring conformational changes in proteins

Expression and Characterization of Drosophila Signal Peptide Peptidase-Like (sppL), a Gene That Encodes an Intramembrane Protease

Intramembrane proteases of the Signal Peptide Peptidase (SPP) family play important roles in developmental, metabolic and signaling pathways. Although vertebrates have one SPP and four SPP-like (SPPL) genes, we found that insect genomes encode one Spp and one SppL. Characterization of the Drosophila sppL gene revealed that the predicted SppL protein is a highly conserved structural homolog of the vertebrate SPPL3 proteases, with a predicted nine-transmembrane topology, an active site containing aspartyl residues within a transmembrane region, and a carboxy-terminal PAL domain. SppL protein localized to both the Golgi and ER. Whereas spp is an essential gene that is required during early larval stages and whereas spp loss-of-function reduced the unfolded protein response (UPR), sppL loss of function had no apparent phenotype. This was unexpected given that genetic knockdown phenotypes in other organisms suggested significant roles for Spp-related proteases

Advances in atomic force microscopy

This article reviews the progress of atomic force microscopy (AFM) in ultra-high vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows to image surfaces of conductors \emph{and} insulators in vacuum with atomic resolution. The mostly used technique for atomic resolution AFM in vacuum is frequency modulation AFM (FM-AFM). This technique, as well as other dynamic AFM methods, are explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened the theoretical understanding of FM-AFM. Consequently, the spatial resolution and ease of use have been increased dramatically. Vacuum AFM opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms.Comment: In press (Reviews of Modern Physics, scheduled for July 2003), 86 pages, 44 figure