Simultaneous current-, force- and work function measurement with atomic resolution

The local work function of a surface determines the spatial decay of the charge density at the Fermi level normal to the surface. Here, we present a method that enables simultaneous measurements of local work function and tip-sample forces. A combined dynamic scanning tunneling microscope and atomic force microscope is used to measure the tunneling current between an oscillating tip and the sample in real time as a function of the cantilever's deflection. Atomically resolved work function measurements on a silicon (111)-($7\times 7$) surface are presented and related to concurrently recorded tunneling current- and force- measurements.Comment: 8 pages, 4 figures, submitted to Applied Physics Letter

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

Direct measurement of molecular stiffness and damping in confined water layers

We present {\em direct} and {\em linear} measurements of the normal stiffness and damping of a confined, few molecule thick water layer. The measurements were obtained by use of a small amplitude (0.36 $\textrm{\AA}$), off-resonance Atomic Force Microscopy (AFM) technique. We measured stiffness and damping oscillations revealing up to 7 layers separated by 2.56 $\pm$ 0.20 $\textrm{\AA}$. Relaxation times could also be calculated and were found to indicate a significant slow-down of the dynamics of the system as the confining separation was reduced. We found that the dynamics of the system is determined not only by the interfacial pressure, but more significantly by solvation effects which depend on the exact separation of tip and surface. Thus ` solidification\rq seems to not be merely a result of pressure and confinement, but depends strongly on how commensurate the confining cavity is with the molecule size. We were able to model the results by starting from the simple assumption that the relaxation time depends linearly on the film stiffness.Comment: 7 pages, 6 figures, will be submitted to PR

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

A daily-updated tree of (sequenced) life as a reference for genome research

We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy information in concert with unbiased sampling of molecular characters from whole genomes of all sequenced organisms. Via quantifying the extent of agreement between taxonomic and molecular data, we observe there are many potential improvements that can be made to the status quo classification, particularly in the Fungi kingdom; we also see that the current state of many animal genomes is rather poor. To augment the use of sTOL in providing evolutionary contexts, we integrate an ontology infrastructure and demonstrate its utility for evolutionary understanding on: nuclear receptors, stem cells and eukaryotic genomes. The sTOL (http://supfam.org/SUPERFAMILY/ sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype

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

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