Theory of Atomic-Force Microscopy(STM Theory)

The mechanism of force detection of Atomic-Force Microscopy (AFM) is theoretically investigated. First, a theoretical simulation of contact AFM images is performed, and a tip apex structure is studied. It is clarified how the AFM images and the force distributions change as the load varies. It is also revealed that the characteristics of the AFM images such as their detailed microscopic pattern, the symmetry, and the corrugation amplitude, depend strongly on the tip apex structure. Secondly, fundamental features of the atomic-scale friction in Frictional-Force Microscopy (FFM) are studied. Simulated FFM images are in good agreement with observed ones. Then we discuss the mechanism of the image pattern of FFM by an analytical method. It is revealed that the part of the boundary of the stable region of the cantilever basal position, appears as the boundary between the bright and the dark area of FFM images. Thus we clarify the physical meaning of the FFM image patterns. Lastly, we studied dynamics of the large amplitude cantilever oscillations in the noncontact AFM (nc-AFM). The oscillation of the cantilever is treated as a forced oscillation periodically interrupted by collisions with the surface. By solving this extremely nonlinear problem numerically, some remarkable features of the cantilever oscillation are revealed. We observed strange behaviors of the cantilever such as a bimodal state of dynamical touching and non-touching motion, as well as a fractional resonance features

Simulated Nanoscale Peeling Process of Monolayer Graphene Sheet - Effect of Edge Structure and Lifting Position

The nanoscale peeling of the graphene sheet on the graphite surface is numerically studied by molecular mechanics simulation. For center-lifting case, the successive partial peelings of the graphene around the lifting center appear as discrete jumps in the force curve, which induce the arched deformation of the graphene sheet. For edge-lifting case, marked atomic-scale friction of the graphene sheet during the nanoscale peeling process is found. During the surface contact, the graphene sheet takes the atomic-scale sliding motion. The period of the peeling force curve during the surface contact decreases to the lattice period of the graphite. During the line contact, the graphene sheet also takes the stick-slip sliding motion. These findings indicate the possibility of not only the direct observation of the atomic-scale friction of the graphene sheet at the tip/surface interface but also the identification of the lattice orientation and the edge structure of the graphene sheet

Atomic scale friction between clean graphite surfaces

We investigate atomic scale friction between clean graphite surfaces by using molecular dynamics. The simulation reproduces atomic scale stick-slip motion and low frictional coefficient, both of which are observed in experiments using frictional force microscope. It is made clear that the microscopic origin of low frictional coefficients of graphite lies on the honeycomb structure in each layer, not only on the weak interlayer interaction as believed so far.Comment: 4 pages, 7 figure

Aphids acquired symbiotic genes via lateral gene transfer

<p>Abstract</p> <p>Background</p> <p>Aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist <it>Buchnera aphidicola </it>(γ-Proteobacteria). <it>Buchnera </it>has lost many of the genes that appear to be essential for bacterial life. From the bacteriocyte of the pea aphid <it>Acyrthosiphon pisum</it>, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. Southern blot analysis demonstrated that they are encoded in the aphid genome. In this study, in order to assess the possibility of lateral gene transfer, we determined the full-length sequences of these transcripts, and performed detailed structural and phylogenetic analyses. We further examined their expression levels in the bacteriocyte using real-time quantitative RT-PCR.</p> <p>Results</p> <p>Sequence similarity searches demonstrated that these fully sequenced transcripts are significantly similar to the bacterial genes <it>ldcA </it>(product, LD-carboxypeptidase) and <it>rlpA </it>(product, rare lipoprotein A), respectively. <it>Buchnera </it>lacks these genes, whereas many other bacteria, including <it>Escherichia coli</it>, a close relative of <it>Buchnera</it>, possess both <it>ldcA </it>and <it>rlpA</it>. Molecular phylogenetic analysis clearly demonstrated that the aphid <it>ldcA </it>was derived from a rickettsial bacterium closely related to the extant <it>Wolbachia </it>spp. (α-Proteobacteria, Rickettsiales), which are intracellular symbionts of various lineages of arthropods. The evolutionary origin of <it>rlpA </it>was not fully resolved, but it was clearly demonstrated that its double-ψ β-barrel domain is of bacterial origin. Real-time quantitative RT-PCR demonstrated that <it>ldcA </it>and <it>rlpA </it>are expressed 11.6 and 154-fold higher in the bacteriocyte than in the whole body, respectively. LdcA is an enzyme required for recycling murein (peptidoglycan), which is a component of the bacterial cell wall. As <it>Buchnera </it>possesses a cell wall composed of murein but lacks <it>ldcA</it>, a high level of expression of the aphid <it>ldcA </it>in the bacteriocyte may be essential to maintain <it>Buchnera</it>. Although the function of RlpA is not well known, conspicuous up-regulation of the aphid <it>rlpA </it>in the bacteriocyte implies that this gene is also essential for <it>Buchnera</it>.</p> <p>Conclusion</p> <p>In this study, we obtained several lines of evidence indicating that aphids acquired genes from bacteria via lateral gene transfer and that these genes are used to maintain the obligately mutualistic bacterium, <it>Buchnera</it>.</p